Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Publications

For Center Publication 1998 - Present please select one of the following:

For a list of publications prior to 1998 please contact the Center. 

For hard copies of any Center publication please contact the Center at: 

(360)425-6072 or e-mail Lisa Wilson at lisa_wilson@fws.gov.

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Last updated March 2005

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
U.S. Fish and Wildlife Director and Other Volunteers 

Teach Students The Fine Art of Fishing

U.S. Fish and Wildlife Director H. Dale Hall helps 

student bait a hook during the annual Youth Fishing 

event on the National Mall. Credit LaVonda Walton, 

USFWS

As hundreds of D.

C.-area 

schoolchildren 

descended on the 

Constitution 

Gardens Pond on 

the National Mall, 

Service volunteers 

were ready to 

share their angling 

enthusiasm and 

knowledge with the 

kids. From the 

inaugural cast in 

the morning to the 

last cast of the 

event, the bass and 

bluegill showed their appetite and brought smiles to faces of the 

youthful anglers and volunteers alike.

Volunteers from the Fish and Wildlife Service, Park Service, Bureau of 

Land Management, USDA Forest Service and NOAA's fisheries 

program joined in to teach the kids boating safety, fishing techniques 

and spread the message of conservation.

Department of Interior Press Release

Video Highlights

Audio Interviews

Help Conserve Our Nation's Wetlands - 2006 -2007 

Federal and Junior Duck Stamps Now Available 

A

Information 

B

Learn more 

Information 

Center 

$8 Million 

Grants to Tribes to 

Help Conserve Fish 

and Wildlife

News Release

In

Migratory Bird Day 

2006 Highlights the 

Boreal Forest

News Release

Learn More 

Made in Whooping 

Crane Recovery 

News Release 

American Waterfowl 

Management Plan 

Celebrates 20 Years

Learn More

News Release 

Approach to Fish 

Habitat Conservation 

Launched

Learn More

Video Highlights

Birds

Budget 

Coastal

Fishing

Grants

Habitat

Hunting

Kids / Educators

Offices

Partnerships

Permits

Species

Contaminants

Contracts

Duck Stamps

Endangered Species

Federal Assistance 

Fire

Fisheries and Habitat 

Conservation

History

Human Resources

Images

Information Quality

Index

International Affairs

Jobs

Law Enforcement

Legislation

Library

News

PACR

Planning/ABC

Policies

Questions?

Refuges

Science

Training

Video

Volunteers

Wetlands
USFWS Director Dale Hall Purchases the First 

Federal Duck Stamp and Junior Duck Stamp from 

Postmaster Yverne P. Moore. Credit LaVonda 

Walton/USFWS 

The 2006-2007 

editions of the 

Federal Duck 

Stamp and Junior 

Duck Stamp went 

on sale as part of 

a special First 

Day of Sale 

ceremony held 

June 1, 2006 

during 

Washington 2006, 

the world's 

premier 

international 

philatelic show. 

Held at 

Washington, DC's 

new convention 

center, the stamp 

show is held in the United States only once per decade. Purchasing a 

$15.00 Federal Duck Stamp is an excellent investment because 98 

cents of every dollar is dedicated to help conserve America's fragile 

wetlands. Wetlands help protect our coasts from devastating storms, 

are vital habitat for not only waterfowl but also fish, other species of 

wildlife, and plants, and provide countless opportunities for outdoor 

recreation. 

Learn More -- Video Highlights 

Celebrate National Fishing and Boating Week 

Actress Jane Seymour is Honorary Chairperson for 

National Fishing and Boating Week, June 3-11, 

2006. Photo © and courtesy of the Recreational 

Boating and Fishing Foundation 

National wildlife 

refuges around the 

country will 

celebrate National 

Fishing and 

Boating Week 

June 3-11 with 

fishing derbies for 

kids, open houses 

and other special 

events to highlight 

the week. Fishing 

and Boating Week 

is organized by the 

non-profit 

Recreational 

Boating and 

Fishing Foundation 

(RBFF). RBFF promotes the joys of boating and fishing and, like the U.

S. Fish and Wildlife Service’s National Wildlife Refuge System, also 

News Release1

News Release2

Additional Ordering 

Information
stresses the importance of citizen stewardship of the water resources 

on which boating and fishing depend. National Fishing and Boating 

Week is part of the celebration of June as Great Outdoors Month, 

organized by the non-profit American Recreation Coalition to 

recognize the value of recreation to America’s economy and culture. 

This year’s Great Outdoors Month includes events associated with 

National Boating and Fishing Week, National Trails Day and National 

Clean Beaches Week. The Service will host many of these events 

across the country.

Learn more

Landowners Receive $6.9 Million for Endangered 

Species Conservation 

Acting Assistant Secretary for Fish and 

Wildlife and Parks Matt Hogan and John 

Frampton, Director of The South Carolina 

Department of Natural Resourse tour one of 

the partnership projects. Credit USFWS

Acting Assistant 

Secretary for Fish and 

Wildlife and Parks Matt 

Hogan announced today 

grants totaling more than 

$6.9 million are being 

awarded to private 

landowners and groups 

in 35 states through the 

U.S. Fish and Wildlife 

Service's Private 

Stewardship Grants 

program to undertake 

conservation projects on 

their land for 

endangered, threatened 

and other at-risk species.

News Release 

Mission | Privacy | FOIA | Department of the Interior | First Gov | Contact Us | DOI Print Publishing Council | Regulations.gov | 

No Fear Act 
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Publications: Ecological Physiology

Publications 1998 - Present. Staff names are in bold.

Gale, W. L., R. Patiño, and A. G. Maule. 2004. Interaction of xenobiotics with estrogen receptors 

alpha and beta and a putative plasma sex hormone binding globulin from channel catfish 

(Ictalurus punctatus). General and Comparative Endocrinology 136(3): 338-345. 

Gale, W. L., A. G. Maule, A. Postera, and M. H.Peters. In press. Acute exposure to gas 

supersaturated water does not affect reproductive success of female adult chinook salmon late in 

maturation. Regulated Rivers, Research, and Management.

Zydlewski, G. B., A. Haro, K. G. Whalen, and S. D. McCormick. 2001. Performance of stationary 

and portable passive transponder detection systems for monitoring of fish movements. Journal of 

Fish Biology 58:1471-1475.

Zydlewski, G. B., and J. Johnson. 2002. Response of bull trout fry to four types of water 

diversion screens. North American Journal of Fisheries Management 22:1276-1282.

Zydlewski, G. B., J. S. Foott, K. Nichols, S. Hamelberg, J. Zydlewski, and B. T. Björnsson. 2003. 

Enhanced smolt characteristics of steelhead trout exposed to alternative hatchery conditions 

during the final days of rearing. Aquaculture 222:101-117.

Mesa, M. G., L. K. Weiland, G. B. Zydlewski. 2004. Critical swimming speeds of wild bull trout. 

Northwest Science 78(1): 59-65.

For hard copies of any Center publication please contact the Center at: 

(360)425-6072 or e-mail Lisa Wilson at lisa_wilson@fws.gov.

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Privacy Disclaimer & Copyrights | Contact Us| USFWS | 

USFWS Photos 

VISION FOR THE FUTURE

The vision of the Service and its Fisheries Program is working 

with partners to restore and maintain fish and other aquatic 

resources at self-sustaining levels and support Federal mitigation 

programs for the benefit of the American public... 

Our Vision

Fish Passage

National Fish and Habitat 

Initiative

NATIONAL FISHING AND BOATING 

WEEK JUNE 4-12, 2005

Click here to find out about events in your area!

Click here for:

2005 Highlights 

2004 Highlights

2003 Highlights
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Publications: Conservation Genetics

Publications 1998 - Present. Staff names are in bold.

Ardren, W. R. and A.R. Kapuscinski. 2003. Demographic and genetic estimates of effective 

population size (Ne) reveals genetic compensation in steelhead trout. Molecular Ecology 12:35-

49. 

Bartholomew, J. L., M. J. Whipple, and D. Campton. 2001. Inheritance of resistance to 

Ceratomyxa shasta in progeny from crosses between high- and low-susceptibility strains of 

rainbow trout (Oncorhynchus mykiss). Bulletin of the National Research Institute of Aquaculture, 

Supplement 5:71-75. 

Burger, C. V., K. T. Schribner, W. J. Spearman, C. O. Swanton, and D. E. Campton. 2000. 

Genetic contribution of three introduced life history forms of sockeye salmon to colonization of 

Frazer Lake, Alaska. Canadian Journal of Fisheries and Aquatic Sciences 57:2096-2111. 

Campton, D. E. 1998. Pikefish, not pikeminnow. Fisheries 23(11):38. 

Campton, D. E., A. L. Bass, F. A. Chapman, and B. W. Bowen. 2000. Genetic distinction of 

pallid, shovelnose, and Alabama sturgeon: emerging species and the U. S. Endangered Species 

Act. Conservation Genetics 1:17-32. 

Campton, D. E., and D. E. Olson. In press. Conservation role of salmon hatcheries: genetic 

integration versus segregation. Second International Symposium on Stock Enhancement and 

Sea Ranching. Kobe, Japan.

Gomez-Uchida D., E. A. Hoffman, W. R. Ardren, and M. A. Banks. 2003 Microsatellite markers 

for the heavily exploited canary (Sebastes pinniger) and other rockfish species. Molecular 

Ecology Notes 3(3): 387-389. 

Rossi, A. R., M. Capula, D. Crosetti, L. Sola, and D. E. Campton. 1998. Allozyme variation in 

global populations of striped mullet, Mugil cephalus (Pisces: mugilidae). Marine Biology 131:203-

212. 

Rossi, A. R., M. Capula, D. Crosetti, D. E. Campton, and L. Sola. 1998. Genetic divergence and 

phylogenetic inferences in five species of Mugilidae (Pisces: Perciformes). Marine Biology 

131:213-218. 

Tranah, G. J., H. L. Kincaid, C. C. Krueger, D. E. Campton, and B. May. 2001. Reproductive 

isolation in sympatric populations of pallid and shovelnose sturgeon. North American Journal of 

Fisheries Management 21:367-373.

For hard copies of any Center publication please contact the Center at: 

(360)425-6072 or e-mail Lisa Wilson at lisa_wilson@fws.gov.
USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Helping Meet Tomorrow's Fishery Resource Challenges Today!

 Welcome to the Abernathy Fish Technology Center! 

The mission of the Abernathy Fish Technology Center 

(Center) is to provide leadership in the scientifically based 

management of national fishery resources through 

development of new concepts and techniques to solve 

specific problems in aquatic restoration and recovery 

activities. The Center is the Pacific Region Fisheries 

Program's sole applied research facility and one of only 

seven such facilities nationwide. The Applied Research 

Programs conduct cooperative studies developing, 

promoting, and supporting methodologies and technologies 

resulting in healthy populations of fish including Chinook, 

coho, and chum salmon, steelhead/rainbow, cutthroat, and 

bull trout, Pacific lamprey, and white sturgeon. 

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Last updated March 2005

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

Applied Research Programs

Staff in the Center's Applied Research 

Programs partner and share applied research 

and information with other Pacific Region, 

USFWS offices (National Fish Hatcheries, 

NFHs, Fish Health Centers FHCs, Fishery 

Management Offices, FROs and FWOs, 

Ecological Services, National Wildlife Refuges, 

NWRs), federal, state, and Tribal agencies, 

industry, and recreational groups. The 

information provided is critical to the restoration 

and recovery of declining, threatened, and 

endangered fish populations. The Center 

maintains Applied Research Programs in the 

fields of Ecological Physiology, Conservation 

Genetics, Hatchery Reform/Intergrated 

Hatchery Management, Fish Culture, Nutrition, 

and Pathology. Please click on the links to the 

right to learn more about each Program's 

activities. 

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Location and Directions

The Center is located at 1440 Abernathy Creek Rd., Longview, WA, approximately three miles upstream of the 

confluence of Abernathy Creek with the Columbia River at river mile 57, and is approximately 13 miles west of 

Longview, WA.

Driving Directions:

From the South (Portland, OR)

From the North (Olympia, WA)

Directions From the South (Portland, OR):

From the Portland, OR metro area, the Center is about 1 hour 20 minutes to the north. 

● Travel north on Interstate 5 past Woodland and Kalama, WA. 

● Take Exit 36 for Port of Longview, Ocean Beaches-Hwy 4 (exit ramp curves up and over Interstate 5 to 

the west). 

● Proceed 3-4 miles straight ahead towards City Center.

● Be in middle lane by fourth traffic light, 15th Street, per overhead sign guidance for Long Beach-Hwy 4. 

● Proceed straight through fourth light along left side of Lake Sacajawea for ~ 2-3 miles. You will pass 

through a residential area and by R. A. Long High School. 

● After passing light at intersection with Louisiana Street, road forks. 

● Bear left at sign for NW Nichols Blvd. 

● Turn Left at next traffic light onto State Hwy 4. 

● Travel straight through commercial section of Longview towards Cathlamet and Long Beach for another 

11.5 miles. 

● You will eventually pass through the tiny village of Stella on the Columbia River, and ascend and 

descend "Bunker Hill". 

● As you are descending Bunker Hill, a brown sign for “Abernathy Technology Center” will be visible on 

right (~7/10 of a mile past Mile Post 49). 

● Turn right at bottom of steep hill onto Abernathy Creek Road. 

● Proceed about 3 miles straight ahead, past yellow "Dead End" sign. 

● The Center complex will soon be visible on your right.

Directions From the North (Olympia, WA):

From the Olympia, WA metro area, the Center is about 2 hours to the south. 

● Travel south on Interstate 5 past Castle Rock, WA.

● Take Exit 39 for Three Rivers Mall, Ocean Beaches-Hwy 4. 

● Turn right at base of off ramp. 

● Proceed past the Mall and over a bridge over the Cowlitz River. 
● Go ~ 3 traffic lights and take a left hand turn (in the right hand lane) following the signs for Ocean 

Beaches-State Hwy 4. 

● Immediately merge to the right and into a right hand lane which merges onto State Hwy 4. 

● Drive through Longview, ~10 miles, past shopping malls, Lake Sacajawea, residential areas, Safeway 

and Fred Meyer. 

● Continue traveling straight through Longview towards Cathlamet and Long Beach for another 11.5 

miles. 

● You will eventually pass through the tiny village of Stella on the Columbia River, and ascend and 

descend "Bunker Hill". 

● As you are descending Bunker Hill, a brown sign for “Abernathy Technology Center” will be visible on 

right (~7/10 of a mile past Mile Post 49).

● Turn right at bottom of steep hill onto Abernathy Creek Road. 

● Proceed about 3 miles straight ahead, past yellow "Dead End" sign. 

● The Center will soon be visible on your right. 

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Last updated March 2005

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Helping Meet Tomorrow's Fishery Resource Challenges Today!

The Center's address is: 

U.S. Fish & Wildlife Service 

Abernathy Fish Technology Center 

1440 Abernathy Creek Rd. 

Longview, WA, 98632 

All Center staff can be reached 

by calling: (360)425-6072 

or via FAX at (360)636-1855. 

Our hours of operation are 8:30 am to 4:00 pm (Pacific 

Time). 

We look forward to hearing from you soon! 

Judy Gordon, Director 

Patty Crandell, Deputy Director 

Abernathy FTC Staff List 

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Publications: Fish Culture

Publications 1998 - Present. Staff names are in bold.

Banks, J. L., and E. M. LaMotte. 2002. Effects of four density levels on Tule fall Chinook salmon 

during hatchery rearing and after release. North American Journal of Aquaculture 64:24-33.

Holmes, J. A. S. 2001. Report E. Pages 130-139. In D.L. Ward, editor. White sturgeon mitigation 

and restoration in the Columbia and Snake rivers upstream from Bonneville Dam. Annual 

Progress Report to Bonneville Power Administration. Bonneville Power Administration. Portland, 

Oregon. 

Holmes, J. A. S. 2002. Report E. Pages 134-143. In D.L. Ward, editor. White sturgeon mitigation 

and restoration in the Columbia and Snake rivers upstream from Bonneville Dam. Annual 

Progress Report to Bonneville Power Administration. Bonneville Power Administration. Portland, 

Oregon. 

Holmes, J. A. S. In press. Report E. In D.L. Ward, editor. White sturgeon mitigation and 

restoration in the Columbia and Snake rivers upstream from Bonneville Dam. Annual Progress 

Report to Bonneville Power Administration. Bonneville Power Administration. Portland, Oregon.

For hard copies of any Center publication please contact the Center at: 

(360)425-6072 or e-mail Lisa Wilson at lisa_wilson@fws.gov.

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Publications: Nutrition

Publications 1998 – Present. Staff names are in bold.

Gannam, A. L. 1997. Development of open formula diets and new feeding strategies: A progress 

report. Pages 15-27. In R. Z. Smith editor. Proceedings of the 48th Northwest Fish Culture 

Conference, Gleneden Beach, OR, December 2-4, 1997. National Marine Fisheries Service. 

Portland, OR.

Gannam, A. L. In press. Captive broodstock nutrition: what are we forgetting? C. Nash and B. 

Berejikian, editors. Proceedings of the Captive Broodstock Workshop, Gig Harbor, WA, June 25-

26, 2002. NOAA Fisheries. Manchester, WA.

Gannam, A. L., and R. M. Schrock. 1999. Immunostimulants in fish diets. Journal of Applied 

Aquaculture 9(4):53-89.

Gannam, A. L., and R. M. Schrock. 2001 Immunostimulants in fish diets. Pages 235-266. In C. 

Limm and C. D. Webster editors. Nutrition and Fish Health. The Haworth Press. New York, New 

York.

Odeh, M, R. M. Schrock, and A. L. Gannam. 2004. Comparative hydraulics of two fishery 

research circular tanks and recommendations for control of experimental bias. Journal of Applied 

Aquaculture 14(3/4):1-23.

Pirhonen, J., C. B. Schreck, and A. Gannam. 2000. Appetite of chinook (Oncorhynchus 

tshawytscha) naturally infected with bacterial kidney disease. Aquaculture 189: 1-10.

Tipping, J. M., A. L. Gannam, T. D. Hillson, J. B. Poole. 2003. Use of size for early detection of 

juvenile hatchery steelhead destined to be precocious males. North American Journal of 

Aquaculture 65: 318-323.

Webster, C. D., K. R. Thompson, A. M. Morgan, E. J. Grisby, and A. L. Gannam. 2000. Use of 

hempseed meal, poultry by-product meal, and canola meal in practical diets without fish meal for 

sunshine bass (Morone chrysops x M. saxatilis). Aquaculture 188:299-309.

Webster, C. D., L. J. Tiu, A. M. Morgan, and A. L. Gannam. 1999. Effect of partial and total 

replacement of fish meal on growth and body composition of sunshine bass Morone chrysops x 

M. saxatilis fed practical diets. Journal of the World Aquaculture Society 30(4):443-453.

Webster, C. D., L. J. Tiu, A. M. Morgan, and A. L. Gannam. 2000. Differences in growth in blue 

catfish Ictalurus furcatus and I. punctatus fed low-protein diets with and without supplemental 

methionine and/or lysine. Journal of the World Aquaculture Society 31(2):195-205.

Whipple, M. J., A. L. Gannam, and J. L. Bartholomew. 2002. Inability to control Ceratomyxosis in 

rainbow trout and steelhead with oral treatments of glucan immunostimulant or the fumagillin 

analog TNP-470. North American Journal of Aquaculture 64:1-9.
For hard copies of any Center publication please contact the Center at: 

(360)425-6072 or e-mail Lisa Wilson at lisa_wilson@fws.gov.

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
THE NEED

ABOUT THE PROJECT

HSRG

REFORM PRINCIPLES

REGIONAL REVIEWS

IMPLEMENTATION

PUBLICATIONS

CONTACT US

HSRG 

RECOMMENDATIONS 

HATCHERY REFORM PUBLICATIONS

Jump To: 

NEW! HATCHERY REFORM REPORTS TO CONGRESS

HSRG Hatchery Reform Report to Congress, March 2006

HSRG Hatchery Reform Progress Report to Congress, April 2005 

NEW! HATCHERY REFORM: MANAGING FOR SUCCESS CONFERENCE, 

OCTOBER 28, 2005

Click here to view and download conference agenda, presentations, photo 

gallery, and summary report. 

HATCHERY REFORM: PRINCIPLES AND RECOMMENDATIONS OF THE 

HATCHERY SCIENTIFIC REVIEW GROUP

This document includes the principles, tools and recommendations that resulted 

from the HSRG's three-year review of over 200 hatchery programs at over 100 

hatcheries. April 2004. 

HSRG Report, April 2004

Read Selected Coverage of the HSRG Report Release

PROJECT UPDATES

Hatchery Reform Project: May 2005 Update

All-H Hatchery Analyzer (AHA)

Hatchery Reform Coalition

SCIENTIFIC PUBLICATIONS

Hatchery Reform in Washington State: Principles and Emerging Issues. 

Hatchery Scientific Review Group. Fisheries Magazine, American Fisheries 

Society. June 2005, Vol. 30 No. 6 

TECHNICAL DISCUSSION PAPERS

Integrated Hatchery Programs

Segregated Hatchery Programs 

When Do You Start a Conservation Hatchery Program? 

HATCHERY REFORM RESEARCH GRANTS PROGRAM

Click here to view currently funded research programs. 

HATCHERY SCIENTIFIC REVIEW GROUP MEETING SUMMARIES

Hatchery Reform 

Technical Discussions 

Click here to login 

(Having trouble logging in 

with Netscape? Click here.)

Click here to begin 

Desktop Sharing
Click here to access the meeting summaries archive. 

MAY 25, 2004, JUNEAU AND MAY 27, 2004, ANCHORAGE, ALASKA 

MEETINGS

Click here for information about and presentations from these meetings. 

MAY 5, 2003, HATCHERY REFORM OLYMPIA BRIEFING

Recommendations Executive Summary

Briefing Agenda

Project Description

FEBRUARY 19, 2002, HATCHERY REFORM PRESS CONFERENCE

Press Release

Quote Page

Project Description

Frequently Asked Questions

HSRG POLICIES AND PROCEDURES

Click here to download the HSRG Policies and Procedures document. 

* All publications are in .pdf format and open in new windows. You must have 

Adobe Acrobat Reader 5.0 or greater to open them. Adobe Acrobat Reader can 

be downloaded for free at the Adobe corporate website. (Note: If you 

experience an error when clicking on a report link to open a file in your browser 

window, right-click on the link and download the file to your desktop.) 

CONTACT US | 

HOME
Abernathy Fish Technology Center 

California Idaho Nevada Oregon Washington

 Publications: Pathology 

Publications 1998 – Present. Staff names are in bold.

Taylor, P. W. 2003. Multiple microbial resistance in a chronic bacteremia of Koi (Cyprinus carpio

koi). North American Journal of Aquaculture 65:120-125.

Taylor, P. W., and J. R. Winton. 2002. Optimization of nested polymerase chain reaction assays 

for identification of Aeromonas salmonicida, Yersinia ruckeri, and Flavobacterium psychrophilum. 

Journal of Aquatic Animal Health 14(3):216-224.

Taylor, P. W., and S. D. Roberts. 1999. Clove oil: an alternative anaesthetic for aquaculture. 

North American Journal of Aquaculture 61:150-155.

Taylor, P. W. In press. PCR detection of Flavobacterium psychrophilum in eggs and sexual fluids 

of Pacific salmonids: implications for vertical transfer of bacterial cold water disease. Journal of 

Aquatic Animal Health.

For hard copies of any Center publication please contact the Center at: 

(360)425-6072 or e-mail Lisa Wilson at lisa_wilson@fws.gov.

USFWS Home Page / Pacific Region Home Page / Fish Technology Centers Home Page

Please send Comments about this web site to AFTC Web Master

U.S. Fish & Wildlife Service Privacy Disclaimer Statements
Pacific Region

Hawaii and Other Pacific Islands | Idaho| Oregon | Washington

Regional 

Programs 

& Issues

Our Mission

Refuges and Hatcheries Along 

the Lewis & Clark Trail 

Regional Leadership 

Contact Us | Employee & Office Directory | Text Version | Accessibility/Sec 508

Privacy, Disclaimer & Copyrights | FOIA | No Fear Act

Visit the U.S. Fish and Wildlife Service National Home Page 

questions or comments about the Pacific Region Web site, contact the Webmaster

FWS facilities in California, Nevada and the Klamath Basin 

Translation 

Service

Recent News Release

6/5/06 - Governor, 

Commissioner of Public Lands 

Sign Forest Plan HCP Today

6/5/06 - Oregon to Receive 

Over $1.8 Million for Boating 

Grants

6/1/06 - Funding Awarded to 

Private Landowners in Hawaii 

to Conserve Endangered 

Species

More News Releases 

Find a Refuge or Hatchery 
Privacy, Disclaimer, Copyrights and Logo Use

PRIVACY STATEMENT

The U.S. Fish and Wildlife Service is committed to maintaining a web site that protects the 

individual’s right to privacy. We do not require personal information from our visitors, nor do we 

collect any personally identifying information (name, email address, Social Security number, or 

other unique identifier) unless you knowingly provide it. Likewise, we do not give, sell, or 

transfer any personal information to a third party except as might be required by law .

Data Collection for Statistics

To aid in web site management, certain information is collected for statistical purposes. The 

Service uses specialized software to create summary statistics, which are used for such 

purposes as assessing what information is of most and least interest to our customers, 

determining technical design specifications, and identifying system performance or problem 

areas.

We collect only the following information about your visit:

● The name of the domain from which you access the Internet (for example, "princeton.

edu" if you are connecting from Princeton University’s domain, or "aol.com" if you are 

connecting from an America Online account);

● The web site from which you linked directly to our web site, if you have used another web 

site to reach our site;

● The operating system and web browser you use to view pages;

● The date and time you access our web site.

We use the information we collect to measure the number of visitors to the different sections of 

our web site, allowing us to make our web site more useful and accessible to visitors. We do 

not store any personal identifiers. 

Information Collected from E-mails and Forms

You may decide to send us personally identifying information through e-mail messages or 

through on-line forms. Electronic communication allows us to collect information that will 

improve our web site for you, and we encourage it. We use personally-identifying information 
from consumers in various ways to further our customer's protection and to provide better 

service. This may be to correct broken links that you have identified or provide additional 

information that you have requested. 

Visit the Department's Talk to Us page to learn what can happen to the information you provide 

us when you send us e-mail or fill out a questionnaire or guestbook. Any information that we 

collect via a questionnaire or a guestbook may be subject to disclosure, but will be handled in 

accordance with the requirements of the Privacy Act and the Freedom of Information Act to 

ensure the greatest protection of personal privacy in the face of any required disclosure. 

Security Checks 

For web site security purposes and to ensure that this service remains available to all users, we 

employ software programs to monitor network traffic, identify unauthorized attempts to upload 

or change information, or otherwise cause damage. Unauthorized attempts to upload or change 

information on this web site are strictly prohibited and may be punishable under the Computer 

Fraud and Abuse Act of 1986 and the National Information Infrastructure Protection Act.

Cookies 

When you visit some Web sites, their web servers generate pieces of information known as 

cookies. Some cookies collect personal information to recognize your computer in the future. 

This is not the case at www.fws.gov, where we only use non-persistent cookies or "per-session 

cookies." These cookies do not collect personal information on users and they are erased as 

soon as you leave our Web site. 

Per-session cookies serve technical purposes like providing seamless navigation through www.

fws.gov. These cookies do not permanently record data and they are not stored on your 

computer's hard drive. www.fws.gov cookies are stored in memory and are only available 

during an active browser session. Again, once you close your browser, the cookie disappears.

For Kids!

Please don't send us e-mail, Especially if you are under 13. Instead, have an adult send the 

message. Have your parents, teachers and school librarian contact us if you need further 

assistance. 

For more information: See the Department of the Interior's Children's Privacy statement.

STANDARD DISCLAIMER

The Department of the Interior Disclaimer Statement applies to the Service. 

We will link to external sites that help us perform our mission - "working with others to 
conserve, protect, and enhance fish, wildlife, and plants and their habitats for the continuing 

benefit of the American people." 

● Links to external servers do not imply any official U.S. Fish and Wildlife Service 

endorsement of the opinions or ideas expressed therein, or guarantee the validity of the 

information provided. Links to commercial sites are in no way an endorsement of any 

vendor's products or services. 

● Links will be provided to external servers that are managed in a professional manner (i.

e., it is fully operational, is available most of the time, does not serve inaccurate 

information or obscene graphics, etc.). 

● This server will not link to external servers if such a link would appear to provide an 

official endorsement of fundraising efforts or lobbying for a political agenda. 

COPYRIGHT STATEMENT

Please note: 

1. You are welcome to make a link to any of the Web pages the Service has published on 

the Internet. There is no need to request permission.

2. Not all the information on our site is in the public domain. Some images/graphics are 

licensed for use under the copyright law, and the use of the Service logo is restricted

to official publications (see below). 

We will identify material we use from sources outside the Service, and request others do the 

same when using information published by the Service. Credit can be provided by including on 

the page (or via a link to a credits page) a citation such as: 

Credit: U. S. Fish and Wildlife Service

Photo by Robert Shallenberger/U.S. Fish and Wildlife Service or USFWS photo (if the 

photographer is known) 

USFWS/Elkins, WV (if originating office but not the photographer is known)

RESTRICTIONS ON USING THE SERVICE LOGO

The Service logo is our official "trademark." Its use is reserved for official 

publications or other products of the U.S. Fish and Wildlife Service. Use of the 

Service logo without prior written approval is prohibited. Restrictions on use of the 

Service logo were published in the Federal Register on February 13, 1984 (Vol. 

49, No. 30, page 5387), and 18 USC 701 provides for enforcement.
Please use alternative images if you need a graphic. 

There are procedures for obtaining approval for the use of the official Service logo on a joint 

publication with the Service, including electronic publications such as Web sites. Contact Mitch 

Snow in the External Affairs office at (202) 208-5634 for assistance. 

The restrictions described above apply also to the use of the images of the Federal Duck 

Stamps and the Federal Aid in Wildlife Restoration and Federal Aid in Sport Fish Restoration 

symbols, and the "blue goose" image used to identify wildlife refuges. 

Comments? Questions? Please check our answers to Frequently Asked Questions (FAQ's) 

before you contact us . 

U. S. Fish and Wildlife Service Home Page
THE NEED

ABOUT THE PROJECT

HSRG

REFORM PRINCIPLES

REGIONAL REVIEWS

IMPLEMENTATION

PUBLICATIONS

CONTACT US

HSRG 

RECOMMENDATIONS 

HATCHERY REFORM REPORT TO CONGRESS, MARCH 2006

FULL REPORT

Hatchery Reform Report to Congress, March 2006 (483 KB)

INDIVIDUAL SECTIONS

Introduction

The Necessary Ingredients for Hatchery Reform

2005 Accomplishments

Technical Discussions/Tool Development 

Research and Scientific Publications 

Agency Science Teams 

Communications and Outreach

2006 Work In Progress

HSRG Work In Progress 

Co-Managers Work In Progress 

USFWS Work In Progress 

LLTK Work In Progress

Appendices

A: 2005 Expenditures

B: 2005 Communications

C: 2005 Tribal Implementation Projects

D: 2006 Budget

E: Research Priorities for Hatchery Reform

F: Rationale for Integrated/Segregated Broodstock Management

G: HSRG Memorandum to Hatchery Reform Coordinating Committee Regarding Steelhead Management

H: Letter From WDFW to Tribal Chairs on Future Hatchery Management

I: Letter From WDFW to Shared Strategy on Recovery Plan Implementation

J: Letter From WDFW Director to Staff on Hatchery Reform Conference

K: Hatchery Reform in Washington State: Principles and Emerging Issues, (Fisheries Magazine, June 2005) 

276 KB

L: Hatchery Reform Conference Summary

CONTACT US | 

HOME
HATCHERY REFORM 

Report to Congress 

March 2006 

Table of Contents Report to Congress – March 2006 i 

INTRODUCTION ....................................................................................................................1

THE NECESSARY INGREDIENTS FOR HATCHERY REFORM .................................3

2005 ACCOMPLISHMENTS .................................................................................................7

TECHNICAL DISCUSSIONS/TOOL DEVELOPMENT ............................................................................. 7

RESEARCH AND SCIENTIFIC PUBLICATIONS ..................................................................................... 8

AGENCY SCIENCE TEAMS ................................................................................................................. 8

COMMUNICATIONS AND OUTREACH............................................................................................... 12

2006 WORK IN PROGRESS................................................................................................15

HSRG WORK IN PROGRESS ............................................................................................................ 15

CO-MANAGERS WORK IN PROGRESS.............................................................................................. 15

USFWS WORK IN PROGRESS.......................................................................................................... 16

LLTK WORK IN PROGRESS............................................................................................................. 18

APPENDICES.........................................................................................................................21

A: 2005 EXPENDITURES............................................................................................................ 23

B: 2005 COMMUNICATIONS...................................................................................................... 24

C: 2005 TRIBAL IMPLEMENTATION PROJECTS ......................................................................... 27

D: 2006 BUDGET....................................................................................................................... 33

E: RESEARCH PRIORITIES FOR HATCHERY REFORM ................................................................ 34

F: RATIONALE FOR INTEGRATED/SEGREGATED BROODSTOCK MANAGEMENT ...................... 38

G: HSRG MEMORANDUM TO HATCHERY REFORM COORDINATING COMMITTEE 

REGARDING STEELHEAD MANAGEMENT............................................................................. 39

H: LETTER FROM WDFW TO TRIBAL CHAIRS ON FUTURE HATCHERY MANAGEMENT .......... 41

I: LETTER FROM WDFW TO SHARED STRATEGY ON RECOVERY PLAN IMPLEMENTATION ... 44

J: LETTER FROM WDFW DIRECTOR TO STAFF ON HATCHERY REFORM CONFERENCE.......... 48

K: HATCHERY REFORM IN WASHINGTON STATE: PRINCIPLES AND EMERGING ISSUES,

(FISHERIES MAGAZINE, JUNE 2005) .................................................................................... 50

L: HATCHERY REFORM CONFERENCE SUMMARY.................................................................... 51

Introduction Report to Congress – March 2006 1

Introduction 

This document contains the annual report to Congress from the Hatchery Scientific Review Group 

(HSRG) and Long Live the Kings (LLTK) on the Puget Sound and Coastal Washington Hatchery 

Reform Project. The report begins with a chapter from the HSRG entitled Necessary Ingredients for 

Hatchery Reform. This is intended to provide the state, tribal and federal salmon and steelhead 

managers (Washington Department of Fish and Wildlife or WDFW, Northwest Indian Fisheries 

Commission or NWIFC, National Oceanic and Atmospheric Administration/National Marine Fisheries 

Service or NOAA Fisheries, and US Fish and Wildlife Service or USFWS) with a succinct outline of 

criteria for tracking whether key elements of hatchery reform are being implemented. 

Following this are chapters detailing project accomplishments in 2005 and work in progress for 2006. 

The report concludes with a series of appendices providing more detail on expenditures, activities and 

communications in 2005; a project budget for 2006; and background on some of the key scientific 

concepts that underlie the findings of the HSRG and this approach to reforming how hatcheries—and 

salmonids—are managed. 

These key concepts—and early efforts by the state and tribal co-managers to implement them—were 

presented at an October 2005 conference in Seattle entitled Hatchery Reform: Managing for Success 

(see Communications section of 2005 Accomplishments). Much of the detail from that conference is 

captured in the conference summary, attached as a separately bound publication and/or available 

electronically from the project’s web site. 

More information on this report, on the Hatchery Reform Project, and all 

project publications are available at: 

Long Live the Kings 

1326 Fifth Avenue, Suite 450 

Seattle, WA 98101 

(206) 382-9555 

www.hatcheryreform.org 

Necessary Ingredients for Reform Report to Congress – March 2006 3 

The Necessary Ingredients for 

Hatchery Reform 

The HSRG has developed a set of criteria for determining whether key elements of hatchery reform 

are being implemented in the region. The principal requirements for operating hatcheries consistent 

with resource goals are a Scientific Framework and an Information Sharing System. These 

requirements are described in more detail below. During the coming year, the HSRG will ask the comangers to report on progress in these areas. Their responses will be a part of the HSRG’s 2006 

Report to Congress. 

 

1) A transparent and actively maintained Scientific Framework1

 should include: 

a) Explicitly stated, comprehensive, scientifically-defensible biological premises2

 to support 

decision making. 

b) A research plan to address key uncertainties in the Framework. 

c) A formal procedure to periodically update the Framework. 

2) An Information Sharing System3

 that provides real time access4 to reliable information about 

goals, actions and outcomes at the Evolutionarily Significant Unit (ESU), regional and stockspecific levels. Specifically, for each stock, by region and by ESU, the following should be 

provided: 

a) A Comprehensive Strategic Plan that answers the questions: Where are we currently?

Where do we want to be in the future? 

i) What is current status of harvest and conservation? 

(1) What has been the recent management intent5

 for the stock? 

(2) What is the current average number and composition of the natural spawning 

escapement? 

(3) What is the current average number and composition of the hatchery escapement? 

(4) What is the current average contribution to each fishery from the stock (by hatchery 

and natural components)? 

ii) What is the current condition of habitat, harvest, and hatcheries? 

(1) What has been the recent management strategy6

 for the stock? 

(2) What is the estimated capacity and productivity of the habitat available to the stock? 

 

1

 The Scientific Framework developed by the HSRG should serve as the starting point 2

 The biological premises should include detailed assumptions (models) about genetics, ecology, physiology, 

behavior and fish health, as they relate to the effects of hatchery production. 

3

 The Managing for Success system, including the All-H Analyzer (AHA) calculator, is being designed to meet 

this need. 

4

 Different levels of access should be available for different user groups, e.g., regional managers will have access 

to more detailed and provisional information, whereas public users should have access to summary information 

that meets defined quality criteria. 

5

 The management intent describes goals for harvest, conservation and/or education. 6

 The management strategy describes how habitat, harvest and hatchery management will contribute toward 

goals. 
4 Report to Congress – March 2006 Necessary Ingredients for Reform 

(3) What is the average exploitation rate for the stock (by hatchery and natural 

components)? 

(4) If there is a hatchery associated with the stock, what is: its purpose (harvest and/or 

conservation), type (segregated or integrated), size (number of broodstock and number 

of juveniles released), broodstock composition (percent natural-origin recruits or 

NORs), reproductive success (recruits per spawner), and stray rate7

? 

iii) What is the long-term goal for harvest and conservation?

(1) What is the long-term management intent for the stock? 

(2) What is the target number and composition of the natural spawning escapement? 

(3) What is the long-term goal for composition of the hatchery escapement? 

(4) What is the target contribution to each fishery from the stock (by hatchery and natural 

components)? 

iv) What is the target future condition for habitat, harvest, and hatcheries? 

(1) What is the long-term management strategy for the stock? 

(2) What is the estimated capacity and productivity of the habitat available to the stock? 

(3) What is the targeted average exploitation rate for the stock (by hatchery and natural 

components)? 

(4) If there will be a hatchery associated with the stock, what will be: its purpose (harvest 

and/or conservation), type (segregated or integrated), size (number of broodstock, and 

target number of juveniles to be released), broodstock composition (percent NORs), 

reproductive success (recruits per spawner), and expected stray rate? 

b) An Overview of Actions targeting or affecting the stock. What habitat, harvest, and hatchery 

actions are completed, under way or planned to move toward the long-term goals? For 

example, for each hatchery action provide: 

i) A description of how and to what extent the action will affect goals for harvest and/or 

conservation (including action objectives in terms of response variables and measurable 

indicators). 

ii) An action plan (milestones and schedule). 

iii) The cost of each phase of the action. 

iv) The status of each phase of the action and the identity of the individual responsible (for 

management of time, quality and human resources). 

v) The action categories (e.g., cost, “action type,” others). 

vi) An action priority rating relative to goals for harvest and/or conservation (at the stock, 

regional and ESU levels). 

c) A Summary of Outcomes. Collect and display empirical information that shows if actions are 

correctly implemented and effective, and if progress is made toward long-term goals for 

harvest and conservation. This information would be shown in tables and/or simple graphs 

that also show targets and goals. 

i) Is the action plan fully implemented as intended? For example, if the action was to 

integrate natural fish into the hatchery broodstock, was the target number of broodstock 

and broodstock composition (NORs vs. hatchery-origin recruits or HORs) achieved? Was 

the targeted number of juveniles released? 

ii) Is the action effective—are actions resulting in expected changes in effectiveness 

indicators? Specifically, show: 

(1) composition of natural spawners (NORs vs. HORs). 

(2) stray rates. 

 

7

 The term stray rate as used here means the fraction of returning HORs that does not return to the hatchery. 
Necessary Ingredients for Reform Report to Congress – March 2006 5 

(3) distribution of natural spawners (NORs vs. HORs). 

(4) number and size of fish contributing to each fishery. 

(5) biological traits of adult returns (NORs vs. HORs). 

(6) reproductive success in the natural environment (recruits per spawner). 

(7) reproductive success in the hatchery environment (recruits per spawner). 

(8) biological traits of hatchery fish released. 

(9) biological traits of naturally produced juveniles. 

iii) How is the stock responding over time? Specifically, show: 

(1) time trends in estimated natural escapement abundance. 

(2) time trends in composition (NORs vs. HORs) in natural escapement. 

(3) time trends in diversity of the natural stock. 

(4) time trends in productivity (recruits per spawner) in the natural environment. 

(5) time trends in estimates of the productivity and capacity of the natural environment. 

(6) time trends in harvest by fishery of NORs and HORs. 

(7) identify other species and stocks potentially affected by this stock (link to those stocks 

in the database). 
 
Accomplishments Report to Congress – March 2006 7 

2005 Accomplishments 

TECHNICAL DISCUSSIONS/TOOL DEVELOPMENT 

Following up on a series of technical discussions in 2004 that led to the refinement of hatchery reform 

principles and the development of prototype decision-support tools, HSRG and co-manager scientists 

and technical staff participated in bi-monthly technical discussions from April through December 2005 

on key topics relating to implementing hatchery reform. These topics included refinements to the AllH Analyzer (AHA) and Managing for Success (MFS) tools discussed below; developing a hatchery 

research agenda (see Appendix E); considering ecological interactions between hatchery and wild fish; 

and reviewing the products of the co-managers’ Risk Assessment Management Project (RAMP). 

LLTK facilitated, coordinated, provided conference calling and desktop sharing, and maintained a 

technical discussions web site as a repository for background materials and working drafts. This 

facilitated the exchange of information and allowed co-managers from across the Puget Sound and 

coastal Washington region to participate in the technical discussions. 

State, tribal and HSRG scientists developed and tested AHA during technical discussions and regional 

technical workshops in 2004 (the tool is described in more detail in last year’s report to Congress). 

AHA helps managers explore the likely results of alternative habitat, harvest and hatchery actions and 

strategies, putting the three “H’s” on one page. AHA allows users to apply a scientific approach in the 

face of the uncertainty always present in natural resource management. AHA fosters accountability, by 

documenting goals, assumptions, hypotheses, management decisions and the rationale behind these 

decisions. 

AHA is now being used by managers throughout Washington state and on the Columbia River. But 

there is still need for a practical and cost-effective tool that helps managers monitor, evaluate and 

adaptively manage salmon and steelhead programs, to ensure they are successful and accountable for 

results. The HSRG and co-manager scientists worked throughout 2005 to develop such a tool, MFS. 

MFS will: 

• Feature a publicly-accessible, user-friendly web site where decision-makers, technical personnel 

and other stakeholders can access information, make queries, generate reports, analyze trends, 

prioritize projects and determine if goals are being met. 

• Answer key management questions, while simplifying and/or automating routine management 

tasks, so that both decision-makers and technical staff have incentive to maintain the system. In 

this way, it will be both “top down” and “bottom up.” 

• Answer questions like: “Where are we now? Where are we going? How are we doing? Have we 

done what we set out to do? Are we getting the expected responses? What will proposed actions 

cost? What changes do we need to make to reach our goals?” 
8 Report to Congress – March 2006 Accomplishments 

MFS is available online as a prototype (www.mobrand.com/mfs; log in with user name “public” and 

password “public”), including hatchery actions and outcomes datasets for Puget Sound and coastal 

Washington, from the Hatchery Reform Project. When the MFS interface is completed, managers will 

have a complete set of scientific framework, recommendations and tools for implementing hatchery 

reform and the new approach to salmon and steelhead management. 

LLTK, the HSRG, WDFW, the Northwest Power and Conservation Council and others have begun 

demonstrating the tools for various interested parties. USFWS—with facilitation assistance from 

LLTK—is applying AHA, MFS and other Hatchery Reform Project principles and tools in a review of 

hatchery programs it owns or operates on the Columbia (see USFWS Work in Progress section). 

WDFW has committed to using AHA to evaluate all stocks it manages and finalizing, hosting and 

maintaining MFS (see WDFW Work in Progress section). 

RESEARCH AND SCIENTIFIC PUBLICATIONS 

The HSRG continued in 2005 to oversee a competitive grant program to fund research projects that fill 

knowledge gaps about using hatcheries to meet harvest and/or conservation goals. In February, the 

HSRG held its annual research review meeting at the NOAA Sand Point Auditorium in Seattle, 

receiving reports from funded researchers. Following this review, the HSRG decided to continue 

funding for two projects: Hamma Hamma Steelhead and Snow Creek Coho. 

In June, an HSRG essay entitled Hatchery Reform in Washington State: Principles and Emerging 

Issues was published as the feature article in Fisheries, the magazine of the American Fisheries 

Society (see Appendix K). The HSRG is working on manuscripts providing greater detail on several of 

these emerging issues in hatchery reform. Those will also be submitted to peer-reviewed journals (see 

section on HSRG Work in Progress). 

As mentioned above, the HSRG worked with co-manager scientists during 2005 technical discussions 

to develop hatchery research priorities. The HSRG’s resulting technical discussion paper on the topic 

is attached as Appendix E. 

AGENCY SCIENCE TEAMS 

(Information below provided by the Washington State Department of Fish and Wildlife) 

A central 2005 hatchery reform accomplishment for the WDFW hatchery science team was 

participating in the development of the MFS tool (see above). Ensuring compatibility with MFS 

required modifications to existing methods and types of data collected at WDFW hatcheries. WDFW 

began developing a web-based, hatchery data management application that incorporates the 

documentation of hatchery broodstock integration/segregation plans and allows remote WDFW fish 

rearing facilities to organize fish rearing information, and share data with each other and WDFW’s 

Olympia headquarters. The initial emphasis has been on organizing hatchery data, with a secondary 

effort to organize various related data sets presently maintained by headquarters staff. This work is 

expected to continue through 2006–07. 
Accomplishments Report to Congress – March 2006 9 

WDFW science staff also evaluated WDFW Chinook and coho hatchery programs in Puget Sound, the 

coast and the Columbia River regions using the AHA tool, to determine current levels of 

integration/segregation, and outline potential program modifications to move the programs toward 

HSRG guidelines. This review resulted in the development of integration/segregation broodstock 

management plans for six Chinook and one coho program in Puget Sound (Kendall spring Chinook; 

Marblemount spring, summer and fall Chinook; Issaquah fall Chinook; Wallace summer Chinook and 

coho) and three coho programs on the Columbia River (Elochoman, Washougal, Kalama; while these 

Columbia River programs are outside the scope of the HSRG review, WDFW felt that applying HSRG 

recommendations to the Columbia will aid in the use of WDFW hatcheries for recovery of listed 

populations in this region). The Chinook plans are now being discussed with the co-managers for 

implementation in fall 2006. 

To lessen potential impacts to listed fish and comply with HSRG recommendations, some hatchery 

programs were reduced or eliminated. The Elwha Hatchery Chinook program was reduced from 3.85 

million to 2.7 million fish. The Hoodsport Hatchery Chinook program was reduced from three million 

to 2.8 million fingerlings, and from 250,000 to 120,000 yearlings. The Big Beef Chinook program of 

200,000 sub-yearlings was eliminated. Coho programs were reduced at George Adams and Soos 

Creek hatcheries. There were also reductions in steelhead, chum and pink salmon hatchery programs. 

Hatchery equipment needed to integrate hatchery broodstocks and increase efficiency was acquired at 

several hatcheries. These included rearing tanks, broodstock stunning machines, fish pumps, 

dewatering towers, and an automated snout snipper for coded-wire tag recovery. Ongoing major 

hatchery renovations, as per HSRG recommendations, include Skookumchuck Hatchery and Palmer 

Rearing Ponds. 

(Information below provided by the Northwest Indian Fisheries Commission) 

Tribal hatchery reform funding not devoted to implementation projects at tribal facilities (see below) 

has been used to support the tribal hatchery science team within the Enhancement Services Division at 

NWIFC, as well as the tribal representative to the HSRG, based at the Nisqually Tribe. The NWIFC 

hatchery reform-funded science team consisted of a geneticist, a biometrician and a salmon ecologist, 

who are supervised by a senior geneticist. The geneticists provided technical support for commission 

and tribal staff on issues involving genetics and salmon recovery including: appropriate uses of 

hatcheries in salmon recovery programs; planning, implementation and monitoring of hatchery 

research; risk assessment; and mixed stock fishery analysis using genetic data. The salmon ecologist 

provided technical support for tribal programs on issues involving ecology and artificial production 

such as the role of fish behavior, interspecies interactions and freshwater and nearshore habitats in 

designing hatchery programs; planning, implementation and monitoring of research for hatchery 

activities; and risk assessment of hatchery programs. The biometrician provided technical support for 

NWIFC and tribal enhancement staff on experimental design and monitoring, statistical analysis and 

database maintenance. 

FY 2005 tribal science team work activities: 

• NWIFC staff geneticists worked with tribes on genetic issues associated with the development of 

hatchery management and reform plans; helped collect and analyze morphological and DNA data 
10 Report to Congress – March 2006 Accomplishments 

on all Puget Sound Chinook and Lake Ozette sockeye; developed tribal research to evaluate 

genetic changes in hatchery and wild populations; helped the Tulalip Tribe establish its genetics 

laboratory for monitoring its hatchery programs; reviewed proposals for reintroducing salmon to 

areas in the Puget Sound where they had been extirpated; reviewed proposals for new hatchery 

programs in the Nooksack and White rivers; provided technical expertise to the HSRG in the 

continuing development of the AHA tool and in identifying research priorities for hatchery reform; 

coordinated information exchange between the co-managers, the HSRG, other independent 

scientific review groups such as the Recovery Science Review Panel, federal regulatory agencies, 

and the Shared Strategy for Salmon Recovery in Puget Sound; and developed the only 

probabilistic quantitative models available to assess genetic and ecological risks of hatchery 

programs. 

• The NWIFC staff biometrician worked with the tribes to develop statistical techniques for 

assessing the contribution of hatchery and wild fish to natural spawning aggregations; analyzed 

data on returns of hatchery fish, which is useful for evaluating the success of hatchery programs; 

and provided statistical consulting on tribal research and monitoring projects. The biometrician has 

assisted the HSRG in developing monitoring and evaluation criteria that can be used to determine 

the success of a hatchery program in meeting its goals and objectives. These criteria will also 

consider what data is needed for future research on hatcheries. The biometrician worked 

individually with tribes in the different regions to tailor monitoring and evaluation criteria to the 

features and circumstances of their region. 

• The NWIFC salmon ecologist helped tribes develop and implement estuary research for 

investigating co-occurrence between hatchery and wild fish; expanded the acoustic tracking study 

of juvenile salmon migration initiated by the tribes to a multi-agency, Puget Sound effort; 

continued to build upon a literature database on ecological interactions; and is developing a 

database of tribal hatchery reform recommendations and completed hatchery reform projects. The 

ecologist also worked with individual tribes to assist in development and implementation of 

ecological studies funded through the Hatchery Reform effort. 

• New hatchery management software and a database have been developed and distributed, to 

greatly improve the amount of information available to hatchery managers. The software, called 

HatPro, improves monitoring, management and planning capabilities for hatchery managers, as 

well as allowing on-site electronic transfer of key hatchery data directly to state, tribal and federal 

agencies. Four group training workshops, and numerous on-site training sessions, have been 

provided to tribal hatchery managers. 

Implementation Projects

The goal of tribal hatchery management is to protect, restore and enhance the productivity, abundance, 

and diversity of salmon and their ecosystems to sustain ceremonial, subsistence, commercial and 

recreational fisheries, non-consumptive fish benefits and other cultural and ecological values. The 

purpose of these grants is to promote that goal through hatchery reform by providing financial 

resources for: 1) scientific support for integrating ecological and genetic factors affecting hatchery 

success into hatchery management; 2) identifying and developing projects that improve, evaluate, or 

monitor hatchery practices and strategies; or 3) modifying or constructing hatchery facilities to 

improve hatchery operations in tribal hatcheries. 
Accomplishments Report to Congress – March 2006 11 

To this end, the western Washington Treaty tribes have used hatchery reform funding to: 1) compile 

and maintain accurate information on tribal programs in hatchery and genetic management plans 

(HGMPs); 2) employ a team of three scientists at NWIFC to provide scientific support to the tribes for 

hatchery reform initiatives; 3) develop and award funding for hatchery reform projects through a 

rigorous process to solicit, develop and evaluate proposals; and 4) coordinate with NOAA Fisheries 

and the HSRG to ensure that tribal hatcheries programs pose no jeopardy to ESA listed species and are 

consistent with the intended management goals, respectively. 

The HSRG’s independent review and recommendations of hatchery programs have been an important 

source of ideas and criteria for hatchery reform proposals and projects. Improvements in the process 

for developing tribal hatchery reform proposals, including technical review of the proposals by 

NWIFC scientists and others, has helped maintain competitive balance among proposals from 

different tribes and is leading to higher quality projects. 

In Fiscal Year (FY) 2005, the competitive selection and ranking process resulted in seventeen projects 

receiving tribal hatchery reform funding for a total funding amount of $535,610. Twelve of these 

projects focused on improving, evaluating or monitoring hatchery practices (Type I projects), for a 

cumulative funding amount of $428,362. Five tribal hatchery reform projects received funding to 

improve tribal hatchery facilities and operations (Type II projects), for a cumulative cost of $107,248. 

The majority of funded projects focused on Chinook salmon (Oncorhynchus tshawytscha), which is 

listed under ESA. This reflects the high priority given to projects associated with salmon recovery in 

the project ranking process and the importance of this species to the tribes. The largest portion of 

projects funded to improve hatchery practices (Type I) focused on adult abundance and contribution 

monitoring, followed by projects to develop and/or improve baseline genetic data for broodstock 

selection and monitoring. Other projects focused on evaluating rearing and release strategies and 

critical knowledge gaps in understanding juvenile production, habitat use and interactions between 

hatchery and wild fish. Type II projects allowed tribal programs to upgrade facility structures and 

equipment, allowing for improved operational efficiency and management options. 

Appendix C summarizes funded projects by rank order, respective of project type and associated 

project cost, and then provides greater detail on each project. The table below provides the number and 

description of tribal hatchery reform projects funded for FY 2005. 

Project Number of 

 Type Projects Funded Project Description Category 

 I 2 Broodstock choice, juvenile rearing and release strategies 

 I 5 Adult abundance and contribution monitoring 

 I 2 Hatchery / wild juvenile production and habitat use 

 I 3 Genetic monitoring and characterization 

 II 5 Hatchery facility improvements 
12 Report to Congress – March 2006 Accomplishments 

 (Information below provided by the US Fish and Wildlife Service) 

FY 2005 USFWS science team work activities included: 

• Participation of a USFWS fish geneticist as a member of the HSRG, including preparation of 

reports and scientific papers. 

• Implementing HSRG recommendations at Quilcene, Makah and Quinault NFHs. 

• Participation in a USFWS Hatchery Review Working Group that designed a process for applying 

the HSRG’s principles, tools and recommendations to all USFWS facilities on the Columbia (see 

section on USFWS Work in Progress). 

COMMUNICATIONS AND OUTREACH 

Progress Report to Congress

In April, the HSRG and LLTK provided Congress with an annual report on hatchery reform 

implementation. The report includes the HSRG’s synopsis and evaluation of state, tribal and federal 

regional progress updates. While emphasizing the overall good progress made by the co-managers, the 

HSRG reiterated the necessity of both systemic reform and specific improvements in a watershed 

context. 

Regional Salmon Management Processes

Throughout 2005, LLTK and subcontractors Gordon Thomas Honeywell helped the co-managers 

reach consensus on changes to salmon management documents and processes through which they can 

implement hatchery reform. This included serving on the Development Committee of the Shared 

Strategy for Salmon Recovery in Puget Sound and facilitating regional co-manager decision-making 

meetings (most actively in the Stillaguamish/Snohomish, Hood Canal and South Sound regions). 

Included in the appendices are letters from WDFW Director Jeff Koenings to the chairs of the Puget 

Sound and coastal Washington tribal chairs (Appendix H) and to Shared Strategy for Salmon 

Recovery in Puget Sound chair Bill Ruckelshaus (Appendix I) about each of these processes. 

Hatchery Reform Conference

In October, LLTK sponsored and coordinated Hatchery Reform: Managing for Success, a day-long 

conference held in Seattle. The Mountaineers (one of the Northwest’s oldest and largest conservation 

organizations) hosted the conference and provided the meeting facilities. The event highlighted the 

independent scientific recommendations and co-manager implementation actions resulting from the 

Puget Sound and Coastal Washington Hatchery Reform Project. Joint presentations by WDFW, treaty 

Indian tribes, and the HSRG included the role of hatcheries, and hatchery reform in the future of 

salmon recovery and sustainable fisheries. Conference attendees included congressional and other 

federal agency officials and staff; legislative and gubernatorial officials and staff; tribal officials and 

staff; state and tribal agency representatives; and scientific, academic, fishing, and environmental 

representatives. The conference was cablecast by TV-W, the public access channel of Washington 

state government. A summary document is attached separately as Appendix L and/or available from 
Accomplishments Report to Congress – March 2006 13 

the project’s web site. Included in Appendix J is a letter from WDFW Director Jeff Koenings to all 

WDFW staff about the conference. 

Hatchery Reform Coalition

LLTK has convened a coalition of organizations to build a constituency for hatchery reform. The 

Hatchery Reform Coalition includes organizations that are not always on the same side on all issues, 

but all have agreed that the HSRG’s principles and recommendations represent the right way to 

proceed with managing the hatchery system. The Mountaineers, Northwest Sportsfishing Industry 

Association, Puget Sound Anglers, Recreational Fishing Alliance, Trout Unlimited, Wild Steelhead 

Coalition and other recreation, sports fishing and conservation organizations have signed letters of 

support for hatchery reform as recommended by the HSRG. The Coalition now features 20 regional 

and national organizations and advocates, with a combined membership base greater than 300,000. 

LLTK coordinated and facilitated meetings approximately every other month during 2005, where 

Coalition members received presentations from state, tribal and federal managers on topics central to 

hatchery reform. 

Other Communications/Outreach

Throughout 2005, LLTK worked with the HSRG and the co-managers to implement a strategy for 

communicating Hatchery Reform Project background, activities and progress to federal, state, tribal, 

regional and local stakeholders (see Appendix B for more detail). This included providing briefings 

for legislators, agency managers and their staffs; making presentations at a wide range of venues; 

authoring or being interviewed for articles on the project for mainstream and stakeholder media 

publications; keeping project communication materials (such as the project overview sheet, website 

and PowerPoint presentation) updated; and many other activities. Preparing for the Hatchery Reform 

Conference in October 2005 (see above) also required a concerted communications effort. 

Work in Progress Report to Congress – March 2006 15 

2006 Work in Progress 

HSRG WORK IN PROGRESS 

The HSRG has drafted a Scientific Framework, reviewed all hatchery programs in the study area, and 

helped develop some of the tools needed for successful implementation of hatchery reform. In the 

coming year, the HSRG will help guide effective implementation, continue tool development, bring 

hatchery reform concepts to the scientific literature, and review progress by the co-managers. Specific 

objectives for 2006 are: 

1. Tool Development: Identify additional funding for continued development and populating the 

analytical tools—Managing for Success (MFS) and All-H Analyzer (AHA). 

2. Grant Program: Establish a grant program using HSRG funds to help implement hatchery 

reform demonstration projects. 

a. Develop criteria for prioritizing demonstration projects. 

b. Develop process for soliciting demonstration projects. 

c. Select and fund demonstration projects. 

d. Review progress on projects. 

3. Scientific Publications: Prepare three scientific papers for publication. 

4. Long-Term Hatchery Reform Implementation: Support development of long-term hatchery 

reform programs by state, tribal and USFWS managers. 

5. Columbia Basin Program: Identify funding to expand hatchery reform to the Columbia that 

will replicate the Puget Sound and coastal Washington hatchery reform process. 

The HSRG’s budget for 2006 is included in Appendix D. 

CO-MANAGERS WORK IN PROGRESS 

(Information below provided by the Washington State Department of Fish and Wildlife) 

WDFW continues to develop integration/segregation broodstock management plans for remaining 

WDFW Chinook and coho programs in Puget Sound, the Washington coast and the Columbia River. 

These include Green River, Voights Creek, Deschutes, Minter Creek, Garrison, Elwha and Skokomish 

fall Chinook, and Dungeness spring Chinook. For Puget Sound, these plans will be presented to the 

co-managers for discussion, modification and agreement, with anticipated implementation to occur in 
16 Report to Congress – March 2006 Work in Progress 

fall 2006. Draft plans for the remaining eight coho programs in Puget Sound are in development. In 

addition, WDFW will be working with others as the HSRG process is duplicated within the Columbia 

River Basin. 

Recognizing that a staged, prioritized and incremental approach to hatchery reform is necessitated by 

funding, logistical and environmental constraints, WDFW has embarked on a multiyear effort to 

transform hatcheries from an “all-H risk factor” to a productive tool for restoring salmon and 

enhancing fishing opportunities. The expected benefits are substantial—enhanced fishing 

opportunities, improved stock status, economic stimulation of rural communities, and a reduced risk of 

third party litigation. 

Building upon the broad consensus emerging from the independent reviews of hatchery programs 

conducted by the HSRG (Puget Sound and Washington coast) and Artificial Production Review and 

Evaluation or APRE (Columbia Basin), WDFW has developed a strategic initiative entitled Salmon 

and Steelhead for the 21st Century: Salmon Recovery, Hatchery Reform and Sustainable Fisheries. 

This initiative will build the foundation for scientifically defensible programs, implement priority 

actions to improve hatchery programs, and assure continued program modifications through resultsoriented, performance-based management. WDFW has asked LLTK to provide facilitation, 

communications and strategic planning assistance for this initiative (see LLTK Work in Progress 

section). 

(Information below provided by the Northwest Indian Fisheries Commission) 

Because Congress did not provide any funds to the Tribes for continued scientific expertise and 

implementation of hatchery reform in 2006, both the salmon ecologist and biometrician position will 

be eliminated, along with the scientific support for these aspects of hatchery reform. Hatchery reform 

funding has been greatly appreciated by the tribes, but has always been less than the amount needed. 

Inadequate funding remains the single biggest obstacle to hatchery reform. As quality proposals for 

hatchery reform projects continue to increase in response to the review and recommendation process, 

available funding has not been adequate to fully implement the hatchery reform initiative. Ultimately, 

inadequate funding means that sacrifices in the ability to protect and restore productive salmon runs 

will lead to sacrifices in legally mandated benefits of tribal hatcheries. 

USFWS WORK IN PROGRESS 

(Information below provided by US Fish and Wildlife Service) 

In addition to continued participation of a USFWS fish geneticist on the HSRG and implementing 

HSRG recommendations at its three western Washington hatchery facilities, the US Fish and Wildlife 

Service (USFWS) is beginning a three-year review of the 21 Columbia River Basin salmon and 

steelhead hatcheries that USFWS owns or operates. The goal is to ensure that USFWS hatcheries are 

operated on the best scientific principles, and contribute to sustainable fisheries and the recovery of 

naturally-spawning populations of salmon, steelhead and other aquatic species of concern. 

This internal review will, in many ways, resemble the Puget Sound and Coastal Washington Hatchery 

Reform Project, which USFWS believes provides both a solid template and operational tools (e.g. 
Work in Progress Report to Congress – March 2006 17 

software spreadsheets, population dynamic models) for reviewing USFWS hatcheries in the Columbia 

River Basin. USFWS also believes that much of the background information necessary for reviewing 

hatcheries in the Columbia Basin has already been compiled in Hatchery and Genetic Management 

Plans (HGMPs), Comprehensive Hatchery Management Plans (CHMPs) and the APRE database 

developed by the Northwest Power and Conservation Council (NWPCC). 

Based on the recommendations of the USFWS Pacific Regional Office Hatchery Review Working 

Group (Working Group), the Assistant Regional Director for Fisheries (ARD) has assembled a 

Columbia Basin Hatchery Review Team (Review Team). This Review Team, comprised of USFWS 

and other federal agency scientists, has adapted the HSRG’s scientific framework, principles and 

hatchery review tools and is applying them to create reform recommendations for each hatchery 

program. The team provides excellent continuity with the HSRG because two members (including the 

chair) have served on the HSRG, the vice chair has served on the policy-makers’ Hatchery Reform 

Coordinating Committee, and three other members represented USFWS at HSRG regional review 

meetings. USFWS has contracted for project facilitation with LLTK, which has provided facilitation, 

communications and coordination for the Puget Sound/Coastal Washington process. 

The Fisheries ARD has appointed a Hatchery Oversight Team (Oversight Team) to succeed the 

Working Group as USFWS’ primary internal mechanism to oversee the review process, monitor its 

progress, and transmit communications and reports from the Review Team to the ARD and project 

leaders within the USFWS Pacific Region Fisheries Program. The Oversight Team is coordinated by 

the Pacific Region Hatchery/Science Team Leader and includes participation by line supervisors 

within the Fisheries Program. The Oversight Team, along with the ARD, will be the primary contact 

group between USFWS and its partners, to develop policies for implementing or modifying the 

Review Team’s recommendations. 

The process began in October 2005 with a review of the Warm Springs National Fish Hatchery (NFH) 

on the Warm Springs River in the Deschutes River watershed/Columbia Plateau province in Oregon. 

This review is being conducted as a pilot, to help USFWS test and refine the review process. Fishery 

co-managers and stakeholders are involved in the review process and have been asked to comment on 

draft reports and recommendations. The Warm Springs NFH report will be published in spring 2006, 

following co-manager and stakeholder/public review and comment periods. 

Following this pilot review, USFWS will adjust the process as necessary and then review three more 

regions, including three NFHs in the Mid-Columbia region (Leavenworth, Entiat and Winthrop); five 

NFHs in the Lower Columbia region (Eagle Creek, Carson, Little White Salmon, Willard and Spring 

Creek); three NFHs in the Snake River region (Dworshak, Kooskia and Hagerman); and nine 

federally-owned hatcheries that are operated by the states of Washington, Oregon and Idaho as part of 

the Lower Snake River Compensation Plan (Lyons Ferry, Tucannon, Irrigon, Lookingglass, Wallowa, 

Clearwater, McCall, Sawtooth and Magic Valley). USFWS plans to complete reviews of all these 

facilities by 2008. For more information, visit <www.fws.gov/pacific/fisheries/hatcheryreview/>. 
18 Report to Congress – March 2006 Work in Progress 

LLTK WORK IN PROGRESS 

State, tribal and federal managers have started to turn the HSRG’s recommendations into reality. This 

includes making systemic use of tools like AHA and MFS that enable—for the first time—

simultaneous evaluation of the benefits and risks of changes to hatchery, harvest and habitat 

investments, in order to help return the greatest number of healthy, fit adult salmon to fisheries and the 

spawning grounds. 

In Puget Sound and coastal Washington, a large portion of responsibility for implementing this new 

approach falls on WDFW. In addition to hatchery reform recommendations, WDFW is facing several 

other obligations and commitments related to salmon/steelhead recovery and sustainable fisheries that 

need to be addressed simultaneously. 

Recognizing the complex and multiple challenges it faces, WDFW’s director and senior leadership has 

asked LLTK to help them make operational the science-based, ecosystem-focused salmonid 

management needed to meet these obligations. LLTK has accepted this invitation to help create a 

framework for institutionalizing reform, and facilitate the transformation of WDFW into an 

internationally-recognized model for 21st century salmon and steelhead management. LLTK expects 

this 21st Century Salmon and Steelhead Management initiative to include: 

• Short-, medium- and long-term strategic planning. 

• Work plans with measurable benchmarks and methods/assignments for tracking and 

communicating progress. 

• Staff training and technical consultation. 

• An effective communication strategy with stakeholders and the public, to ensure transparent 

decision-making and a broad-based constituency supportive of the dramatic changes ahead. 

LLTK will work with senior WDFW management to: 

• Develop a cross-agency and cross-discipline WDFW Core Management Team. 

• Facilitate the development of internal Departmental plans and processes for ensuring hatchery 

reform implementation. 

• Help WDFW take a leadership role in fostering regional ESA salmon recovery processes that 

bring together habitat, harvest and hatchery management. 

• Help WDFW prepare for participation in watershed-by-watershed co-management meetings with 

the tribes, communications with user groups, and Pacific Salmon Treaty negotiations. 

• Help further develop “all-H” decision-support tools like AHA and a transparent action/outcome 

tracking and evaluation system (MFS), to demonstrate accountability. 

• Communicate hatchery reform and “all-H” integration achievements and plans. 

• Improve communications with the Washington Fish and Wildlife Commission, and between the 

different divisions in charge of science, hatcheries, habitat and harvest. 
Work in Progress Report to Congress – March 2006 19 

• Help identify and secure resources and expertise. 

• Develop a comprehensive monitoring strategy that is consistent statewide and relevant for each 

region. 

• Establish Washington State Government Management Accountability and Performance (GMAP) 

reporting criteria. 

LLTK will also continue in 2006 to build a constituency for new fisheries management and beneficial 

roles for hatcheries, broadening the base of support among sports and commercial fishermen, 

environmental organizations, and state and federal legislators and other elected officials. This is 

critical to ensure reforms get implemented. It is also necessary to ensure that the traditional 

constituencies for WDFW and the tribes understand why the co-managers are making the changes they 

are, some of which will be dramatic. Methods for broadening this support will include: 

• Coordinating and expanding the Hatchery Reform Coalition. 

• Maintaining the <www.hatcheryreform.org> website. 

• Taking advantage of other communications opportunities, such as briefings, conference and 

symposia presentations and newsletters. 

LLTK’s intended expenditures for this initiative are included in Appendix D. LLTK will supplement 

the federal funds provided for this initiative with private and foundation funding. In addition, LLTK 

will continue providing facilitation in 2006 for USFWS’ Columbia Basin Hatchery Review (see 

USFWS Work in Progress section). That work is supported by a separate contract with USFWS. 

Appendices Report to Congress – March 2006 21 

Appendices 

Appendices Report to Congress – March 2006 23 

A: 2005 Expenditures 

Puget Sound and Coastal Washington Hatchery Reform Project Expenditures FY 2005 

Hatchery Scientific Review Group 

HSRG Members, Travel, Meeting Expenses $335,000 

Research Grants $125,269 

SUBTOTAL $460,269 

Washington Department of Fish and Wildlife 

Agency Staffing 

HSRG member; HSRG support staff; hatchery biologist 

$175,000 

Hatchery Database Development and Managing for Success Initiative $100,000 

Hatchery Broodstock Integration/Segregation 

 Plan development and implementation, equipment 

$100,000 

Coded-wire Tagging Chinook and Coho $355,000 

Hatchery New Technology Equipment $50,000 

Hatchery Monitoring and Evaluation 

Fish counting, recovery of tagged experimental fish, spawning surveys; downstream 

enumeration, predator control, electronic tag detection, various experiment follow-ups. 

$31,000 

SUBTOTAL $801,000 

Northwest Indian Fisheries Commission 

HSRG Member $39,031 

NWIFC Support Staff $242,206 

Improve, Monitor and Evaluate Hatchery Practices 

Type I projects at Stillaguamish, Makah, Tulalip, Quileute, Squaxin Island, Skagit River System 

Cooperative, Nooksack, Port Gamble and Lower Elwha 

$428,362 

Improve Hatchery Facilities 

Type II projects at Tulalip, Stillaguamish, Makah, Nisqually and Quinault 

$107,248 

SUBTOTAL $816,847 

US Fish and Wildlife Service 

Science Team $70,550 

Management, Accountability and Demonstration Projects $41,500 

SUBTOTAL $112,050 

NOAA Fisheries 

Science Team $70,550 

Long Live the Kings

Project Coordination, Facilitation, Communications $238,118 

Subcontracts (Gordon Thomas Honeywell) $175,000 

Hatchery Reform Conference (does not reflect full costs; LLTK supplemented from other sources) $31,882 

SUBTOTAL $445,000 

Budget Administration 

Interagency Commission for Outdoor Recreation $34,000 

US Fish and Wildlife Service $34,731 

SUBTOTAL $68,731 

FY 2005 TOTAL $2,774,447 
24 Report to Congress – March 2006 Appendices 

B: 2005 Communications 

OUTREACH 

Recreational Fishing 

Alliance 

January 4, 2005 

LLTK Executive Director Barbara Cairns, Jim Waldo of Gordon 

Thomas Honeywell and LLTK Project Director Michael Kern met with 

Corey Freeman, who at the time represented the Recreational Fishing 

Alliance on the Hatchery Reform Coalition. 

Briefing for Environmental 

Leaders 

January 6, 2005 

Barbara Cairns and Michael Kern hosted a small gathering of key 

environmental leaders, to ensure they had a full understanding of the 

Hatchery Reform Project, update them on recent progress and discuss 

the project’s next steps. 

Steelhead and Cutthroat 

Policy Advisory Group 

January 12 & 21, 2005 

HSRG Vice Chair Lee Blankenship presented to this WDFW advisory 

committee in Olympia on the HSRG’s system-wide recommendations 

for steelhead. HSRG member Paul Seidel and WDFW’s Andy Appleby 

led a follow-up workshop featuring case studies applying the All-H 

Analyzer (AHA) to steelhead stocks. 

Wild Salmon Center 

January 25, 2005

Barbara Cairns and then-LLTK Director of Project Development Betsy 

Daniels met with Elliott Marks, who was directing a project for the Wild 

Salmon Center, to introduce him to the Hatchery Reform Project. 

Shortly thereafter, he was named Natural Resources Advisor to 

Washington Governor Christine Gregoire. 

Shared Salmon Strategy for 

Puget Sound Summit 

January 26, 2005

HSRG Chair Lars Mobrand participated in the hatchery break-out 

session of this conference in Tacoma. LLTK reviewed and edited the 

“platform statement” for that session. 

Hatchery Reform Coalition 

February 17, 2005

LLTK coordinated this meeting held to discuss how hatchery reform 

fits into other salmon recovery processes, the Washington State 

Department of Fish and Wildlife (WDFW) biennial budget submission, 

and hatchery reform beyond 2005. 

Adaptive Management 

Workshop 

February 28 & March 1, 2005

LLTK Fish Program Coordinator Michael Schmidt participated in a 

workshop in Seattle co-hosted by Washington Trout, Seattle Public 

Utilities and Shared Strategy on applying adaptive management to 

salmon recovery in Puget Sound. 

WRIAs 7–10 Technical 

Committees 

March 3, 2005

Michael Kern worked with King County staff to coordinate a workshop 

on AHA for WRIAs 7–10. Paul Seidel and Andy Appleby conducted 

the workshop. 

Hatchery Reform Coalition 

March 21, 2005

LLTK coordinated this meeting held to discuss how hatchery reform 

was reflected in the WDFW biennial budget submission. 

Hatchery Reform Coalition 

April 12, 2005

LLTK coordinated this meeting held to review the purposes of the 

Hatchery Reform Project and the Coalition. 

Cedar River Anadromous 

Fish Committee Presentation

April 25, 2005

Michael Kern provided an overview and update on the Hatchery 

Reform Project to this committee chartered as part of the City of 

Seattle’s Habitat Conservation Plan for the Cedar River. 

Steelhead Summit Alliance 

May 14, 2005

Michael Kern provided an update on the Hatchery Reform Project in 

Bellevue at the spring meeting of this informal network of west coast 

steelhead groups. 

Department of Fisheries and 

Oceans-Canada (DFO) 

June 22, 2005

HSRG Vice Chair John Barr and member Trevor Evelyn presented the 

HSRG’s principles and recommendations to a team of DFO personnel 

who were applying those principles and recommendations to DFO’s 

hatchery programs. 
Appendices Report to Congress – March 2006 25 

Seattle Foundation 

Community Conversation 

June 29, 2005

Michael Kern participated in this forum in Seattle, sponsored by the 

Seattle Foundation, to ensure a hatchery reform perspective was 

included in the Foundation’s new giving priorities for environmental 

issues. 

NOAA Fisheries 

July 6, 2005

Barbara Cairns and Michael Kern met with NOAA Fisheries policy 

advisors Todd Ungerecht and Karl Anderson to update them on the 

Hatchery Reform Project, including the AHA and Managing for 

Success (MFS) tools. 

Hatchery Reform Coalition 

August 4, 2005

LLTK coordinated this meeting held to receive an update on Hatchery 

Reform Project activities and a presentation on the US Fish and 

Wildlife Service’s (USFWS) upcoming review of all USFWS-affiliated 

hatchery programs on the Columbia River. 

Northwest Marine Trade 

Association (NMTA) 

August 8 & September 12, 

2005

Barbara Cairns and Michael Kern met with NMTA’s president, vice 

president and director of fishing affairs in August to introduce the 

Hatchery Reform Project. This led to an invitation to present to the 

NMTA Fish Committee in September. 

Hatchery Reform Coalition 

October 19, 2005

LLTK coordinated this meeting held to receive a briefing on the 

Mitchell Act Coalition and an update on WDFW hatchery reform 

implementation activities. 

Hatchery Reform Conference 

October 28, 2005

LLTK sponsored and coordinated a conference at the Mountaineers 

Building in Seattle REI highlighting the independent scientific 

recommendations and co-manager implementation case studies 

resulting from the Hatchery Reform Project. The HSRG presented its 

scientific findings. 

Northwest Fish Culture 

Conference 

December 6-8, 2005

Hatchery Reform Coordinating Committee member and USFWS 

Hatchery Review Team Vice Chair Doug DeHart provided an update 

on the Hatchery Reform Project at this gathering in Boise, ID of 

Northwest hatchery personnel. 

PUBLICATIONS 

All-H Analyzer (AHA) 

Overview 

January, 2005

The HSRG and LLTK developed a one-page overview of AHA and 

sent it to a list of over 300 decision-makers, managers, scientists and 

stakeholders. It became the basis for an HSRG/Co-Manager technical 

discussion paper (see below). 

Conservation Hatcheries 

Technical Discussion Paper 

March 11, 2005

The HSRG publish a technical discussion paper on when to start a 

conservation hatchery program. It is available from the web site. 

Report to Congress 

April 28, 2005

LLTK sent the 2005 Hatchery Reform Project Report to Congress to 

20 members of Congress, Congressional staffers, and others involved 

in the appropriations process. It included the HSRG’s synopsis and 

evaluation of state, tribal and federal regional progress updates, 

alongside co-manager and USFWS reports on accomplishments and 

work in progress. 

Shared Salmon Strategy for 

Puget Sound Recovery Plan 

June, 2005

LLTK provided edits to the Regional Hatchery Strategy, H-Integration, 

and Adaptive Management sections of this plan, to encourage 

consistency with the HSRG’s principles and recommendations. 

Shared Salmon Strategy for 

Puget Sound E-Bulletin 

October 19, 2005

This email bulletin included the Hatchery Reform Conference 

announcement. 

Fisheries Magazine Essay 

June 2005 

The HSRG authored Hatchery Reform in Washington State: Principles 

and Emerging Issues, as the feature article in the American Fisheries 

Society’s peer-reviewed journal. It is available from the web site. 
26 Report to Congress – March 2006 Appendices 

AHA Technical Discussion 

Paper 

August, 2005

The HSRG and co-manager scientists published a technical 

discussion paper on AHA. It is available from the web site. 

Managing for Success (MFS) 

Overview 

October, 2005

The HSRG developed a one-page overview of MFS, for inclusion in 

the Hatchery Reform Conference meeting materials. 

Hatchery Reform Project 

Update Sheet 

LLTK revised a four-page update on the Hatchery Reform Project in 

January and May, for use throughout the year and on the web site.

Hatchery Reform PowerPoint Throughout the year, LLTK kept the project’s PowerPoint presentation 

up to date and tailored it for the various audiences to whom HSRG 

members and LLTK staff made presentations.

LLTK and Hatchery Reform 

Project Web Sites 

(www.lltk.org, 

www.hatcheryreform.org) 

Throughout the year, LLTK kept this site up to date, providing 

electronic access to information about the projects and publications 

including reports, meeting summaries and background information. 

LLTK added and maintained a background/draft documents page for 

the HSRG/Co-Manager Hatchery Reform Technical Discussion Group.

Hatchery Reform Coalition 

Overview/Membership List 

Throughout the year, LLTK kept up to date a one-pager overview of 

the Hatchery Reform Coalition and its membership. It is available from 

the web site. 
Appendices Report to Congress – March 2006 27 

C: 2005 Tribal Implementation Projects 

(Type I projects evaluate, improve or monitor hatchery practices; Type II projects retrofit, modify or 

build facilities) 

Type Sponsor Project Title Cost 

Cumulative 

Cost 

I Stillaguamish Stillaguamish Chinook Smolt Production EstimationCharacteristics of Hatchery & Wild Contributions $32,601 $32,601

I Makah Umbrella Creek Sockeye Adult Escapement Monitoring and 

Brood Stock Capture 

$46,394 $78,995

I Tulalip Assessment of the Contribution of Tulalip Hatchery 

Chinook to Terminal Fisheries & Local Spawning 

Populations Using Otoliths 

$29,088 $108,083

I Makah Lake Ozette Calcein Marking and Monitoring $28,420 $136,503

I Quileute Coded-wire Tag Study of Sol Duc Native Summer Chinook $13,574 $150,077

I Squaxin 

Island 

Acoustic Tagging & Tracking of Squaxin Island Coho, 

Hammersley Inlet Wild Salmon and Percival Cove Chinook

$34,554 $184,631

I Skagit River 

System 

Coop 

Evaluation of the Need to Continue Both the Fall and 

Summer Chinook Hatchery CWT Releases in the Skagit 

River 

$57,623 $242,254

I Nooksack South Fork Nooksack River Smolt Outmigration & Tissue 

Sampling Project 

$40,775 $283,029

I Port Gamble North Hood Canal Coho Straying Study $51,658 $334,687

I Quileute DNA Fingerprinting Used to Evaluate the Degree of 

Introgression Between Native Summer Chinook and 

Introduced Spring Chinook Stocks in the Sol Duc River 

$24,478 $359,165

I Makah & 

Lower Elwha 

DNA Comparison of Chinook from Pysht, Hoko, & Seiku 

Rivers 

$21,678 $380,843

I Skagit River 

System 

Coop 

Identifying Relationships and Exploring Possible 

Mechanisms That Influence Nearshore Survival Between 

Hatchery & Wild Chinook in the Skagit River 

$47,519 $428,362

 Type I Total 428,362

II Makah Emergency Oxygen Backup System for Makah Remote 

Sockeye Rearing Sites 

$16,154 $16,154

II Nisqually Predator Net System for Kalama Creek Hatchery $23,540 $39,694

II Stillaguamish Emergency Oxygen Backup System for Circular Rearing 

Tanks at Harvey Creek 

$20,439 $60,133

II Tulalip Install Bird Net Support Structure in Upper Tulalip Creek 

Pond (Augment FY 2004 Project Due to Unforeseen Costs) 

$28,065 $88,198

II Quinault Fish Loading and Transfer Pump $19,050 $107,248

Type II Total $107,248

GRAND TOTAL $535,610
28 Report to Congress – March 2006 Appendices 

Type I Projects - projects to improve, evaluate or monitor hatchery practices 

Tribe: Makah 

Name of Project: Umbrella Creek sockeye adult escapement monitoring and broodstock 

 capture 

Stock and Status: Lake Ozette sockeye, ESA threatened 

Hatchery: Makah National Fish Hatchery, Umbrella Creek Hatchery 

Project Benefit: Essential for recovery of ESA listed stock

Project Description: The primary goal of the Umbrella Creek sockeye hatchery program is to 

establish viable naturally spawning populations in the habitats deemed suitable for sockeye in the Lake 

Ozette watershed. To determine optimum fish size at time of release in conjunction with different 

rearing and release strategies, all program fish are differentially thermal marked for subsequent 

identification using fish otolith recoveries with a subset of fish releases marked with external adipose 

fin clips. The marking strategy provides a mechanism to evaluate unfed fry, fed fry, and fingerling 

release strategies and to differentiate hatchery origin adult returns from naturally spawned adult 

returns. The data collected through this project will allow accurate estimation of hatchery and natural 

origin contribution rates for the Umbrella Creek sockeye escapement and will provide a basis to 

systematically collect broodstock that are representative of the entire population. 

Tribe: Makah 

Name of Project: Lake Ozette sockeye calcein marking and monitoring trial 

Stock and Status: Lake Ozette sockeye, ESA threatened 

Hatchery: Umbrella Creek Hatchery, Makah National Fish Hatchery, Stony Creek 

 and Elk Lake remote site incubators 

Project Benefit: Essential for recovery of ESA listed stock

Project Description: The primary goal of the Umbrella Creek sockeye hatchery program is to 

establish viable naturally spawning populations in the habitats deemed suitable for sockeye in the Lake 

Ozette watershed. This pilot-study is to evaluate the effectiveness of calcein as a mass-mark for 

hatchery reared Lake Ozette sockeye, especially as a non-lethal method to differentiate natural and 

hatchery origin smolts during outmigration. See above project for further background context. 

Tribe: Makah and Lower Elwha 

Name of Project: DNA comparison of fall Chinook from the Hoko, Seiku and Pysht rivers. 

Stock and Status: Fall Chinook, SASSI depressed 

Hatchery: Hoko River Hatchery 

Project Benefit: Reintroduction and recovery of historical Chinook populations

Project Description: The goal of this project is to determine the degree of genetic relatedness 

between Chinook salmon populations in the Hoko, Pysht and Seiku watersheds. Results from this 

study will facilitate evaluation of the Hoko population as an appropriate source to reestablish fall 

Chinook in the Pysht and Seiku watersheds, which are historical Chinook habitats. 

Tribe: Nooksack 

Name of Project: South Fork Nooksack smolt outmigration and tissue sampling 

Stock and Status: Native spring Chinook, ESA threatened 

 Nooksack coho, SASSI unknown 

Project Benefit: Essential for preserving critical ESA listed stock 
Appendices Report to Congress – March 2006 29 

Project Description: The goal of this project is to operate a smolt outmigrant trap to 1) estimate 

juvenile salmonid abundances, and 2) collect representative Chinook and wild coho salmon tissue 

samples to genetically determine relative stock compositions while improving basin DNA baselines. 

This information is critical towards the development of an integrated hatchery recovery program for 

South Fork early Chinook, in accordance with recovery actions submitted to the Shared Strategy 

process. 

Tribe: Port Gamble S'Klallam 

Name of Project: North Hood Canal hatchery coho straying study 

Stock and Status: Northeast Hood Canal coho, SASSI depressed 

Hatchery: Port Gamble Bay net pens 

Project Benefit: Protect genetic resources while allowing for treaty harvest rights 

Project Description: The underlying issue with regard to several Hood Canal HSRG 

recommendations and Co-manger responses to these recommendations is straying of hatchery coho in 

general and of net pen reared fish in particular. This proposal is to begin a three-year study to evaluate 

straying of hatchery coho into north Hood Canal streams by intensively sampling coho adults in the 

fall and juveniles in the spring. The study will be done in collaboration with the USFWS in its 

investigation of the genetic makeup of regional coho populations. 

Tribe: Quileute 

Name of Project: Coded-wire tagging to determine contribution of wild and hatchery fish 

 for broodstock management of native summer Chinook 

Stock and Status: Sol Duc native summer Chinook, status unknown 

 Introduced spring Chinook, SASSI healthy 

Hatchery: Lonesome Creek 

Project Benefit: Preserve genetic integrity of the natural fish population while allowing for 

 treaty harvest rights 

Project Description: Proper hatchery management of an integrated program requires accurate 

identification of returning adult salmon of hatchery versus natural origin for broodstock purposes. This 

project will allow for proper management of an integrated hatchery program by coded-wire tagging 

juvenile summer Chinook. Additionally, project funding will be used to execute sampling for adult tag 

recoveries in the fisheries and on the spawning grounds. This information is necessary for estimation 

of adult harvest and survival rates and ultimately, evaluation of program success. 

Tribe: Quileute 

Name of Project: DNA fingerprinting of native summer Chinook and introduced spring 

 Chinook stocks on the Sol Duc River. 

Stock and Status: Sol Duc native summer Chinook, status unknown 

 Introduced spring Chinook, SASSI healthy 

Hatchery: Lonesome Creek 

Project Benefit: Preserve genetic integrity of the natural fish population while allowing for 

 treaty harvest rights 

Project Description: Historically, summer and spring Chinook in the Sol Duc River have coincided 

in the hatchery and on the spawning grounds despite management goals to segregate these two stocks. 

Both the Co-managers and the HSRG agree that a better understanding of the current genetic 

composition of the two Chinook stocks and the degree of genetic mixing that may have occurred is 

necessary in evaluating management success and developing future management strategies. 
30 Report to Congress – March 2006 Appendices 

Tribe: Skagit River System Cooperative (Swinomish and Sauk-Suiattle tribes) 

Name of Project: Evaluation of the need to continue both the fall and summer Chinook 

 salmon coded-wire tag hatchery releases in the Skagit River 

Stock and Status: Skagit lower river fall Chinook, ESA threatened 

 Skagit upper river summer Chinook, ESA threatened 

Hatchery: Marblemount (WDFW) 

Project Benefit: Critical for recovery monitoring of ESA threatened stocks 

Project Description: The Skagit River System Cooperative currently conducts two hatchery 

indicator stock programs. In the interest of improving hatchery efficiency and per HSRG 

recommendations, this project will evaluate whether the two programs provide duplicative information 

on pre-terminal exploitation rates and catch distributions, and if so, which stock is most suitable for 

indicator stock purposes. Based upon results from this study, if there are significant differences 

between the two stocks, then both programs will be retained to compile component-specific estimates 

of trends in marine survival rates, exploitation rates and catch distributions. 

Tribe: Skagit River System Cooperative (Swinomish and Sauk-Suiattle tribes) 

Name of Project: Identifying relationships and exploring possible mechanisms that 

 influence nearshore survival between hatchery and wild Chinook in the 

 Skagit River 

Stock and Status: Skagit lower river fall Chinook, ESA threatened 

 Skagit upper river summer Chinook, ESA threatened 

Project Benefit: Critical for recovery of ESA threatened stocks 

Project Description: The goal of this project is to help quantify survival estimates and investigate 

the degree to which biotic variables are influencing survival of juvenile Chinook salmon in the 

estuarine delta and marine nearshore environments. 

Tribe: Squaxin Island 

Name of Project: Acoustic tagging and tracking Squaxin Island coho, Hammersley Inlet 

 wild coho and Percival Cove Chinook 

Stock and Status: Wallace River coho, SaSI Healthy 

Hatchery: Squaxin Island South Sound net pens / Wallace River (WDFW) 

 Tumwater Falls (WDFW) 

Project Benefit: Collaborative cutting-edge research with significant cost-sharing between 

 agencies and groups to investigate fish interactions 

Project Description: Coho salmon stocks in south Puget Sound continue to exhibit exceptionally 

low survival. There is speculation that the region is acting as a bottleneck on juvenile survival, in part 

due to carrying capacity effects. The objective of this project is determine fish behavior, duration of 

residency, rates of outmigration and survival of both hatchery and wild juvenile coho salmon in south 

Puget Sound. This work is in collaboration with several agencies and groups conducting similar 

research and involving numerous fish species. 

Tribe: Stillaguamish 

Name of Project: Stillaguamish Chinook smolt production estimation - characteristics of 

 hatchery and wild contributions 

Stock and Status: North Fork Stillaguamish summer Chinook, ESA threatened 

 South Fork Stillaguamish fall Chinook, ESA threatened 
Appendices Report to Congress – March 2006 31 

Hatchery: Harvey Creek 

Project Benefit: Critical for recovery of ESA threatened stocks 

Project Description: This hatchery program is a critical component of the overall recovery strategy 

for Chinook populations in the Stillaguamish watershed. To direct recovery efforts, it is critical to 

monitor fish life-history attributes and trends in productivity and survival. More so, it is imperative to 

operate the hatchery program in a manner that minimizes risks to limited existing genetic resources. 

This project will provide information necessary to evaluate and adapt hatchery management strategies 

towards recovery of listed Chinook populations. 

Tribe: Tulalip 

Name of Project: Assessment of the contributions of Tulalip hatchery Chinook to fisheries 

 escapement using thermal mass-marking of otoliths 

Stock and Status: Snoqualmie and Skykomish Chinook, ESA threatened 

Hatchery: Bernie Kai-Kai Gobin 

Project Benefit: Provides treaty harvest rights while protecting ESA listed populations 

Project Description: The Snohomish system is managed for natural production of all species of 

salmon. The Tulalip Tribe wishes to maintain this management objective while providing treaty 

harvest opportunity on Chinook salmon during the period of natural stock rebuilding through 

segregated harvest and hatchery management. This project provides program accountability by 

demonstrating that 1) harvest targeting hatchery production has minimal impact on local wild stocks, 

and 2) that the stray rates of hatchery fish to natural spawning areas is within appropriate guidelines. 

Type II Projects - construction projects to retrofit, modify, or build facilities; and/or purchase of 

equipment to improve hatchery practices. 

Tribe: Makah 

Name of Project: Emergency oxygen backup system for remote sockeye rearing sites 

Stock and Status: Lake Ozette sockeye, ESA threatened 

Hatchery: Umbrella Creek, remote site incubators 

Project Benefit: Minimize risk of catastrophic loss of ESA listed sockeye while in the 

 hatchery 

Project Description: The primary goal of the Umbrella Creek sockeye hatchery program is to 

establish viable naturally spawning populations in the habitats deemed suitable for sockeye in the Lake 

Ozette watershed. This project will enable the Lake Ozette sockeye reintroduction program to increase 

the abundance of threatened sockeye salmon by protecting the progeny of natural origin adults from 

catastrophic loss while residing in the hatchery environment. 

Tribe: Nisqually 

Name of Project: Predator net system for Kalama Creek Hatchery 

Stock and Status: Fall Chinook, ESA threatened 

 Coho, SASSI healthy 

Hatchery: Kalama Creek 

Project Benefit: Improve program efficiency in providing treaty harvest opportunity 

Project Description: Inventory estimates have indicated losses of up to 12% of total hatchery 

production prior to release of juvenile fish due to predation. This project will minimize in-hatchery 

losses due to predation and improve operation efficiency towards providing treaty harvest opportunity. 
32 Report to Congress – March 2006 Appendices 

Tribe: Quinault 

Name of Project: Fish loading and transfer pump 

Stock and Status: Quinault steelhead 

Hatchery: Lake Quinault net pens and Salmon River Fish Culture Facility 

Project Benefit: Optimize fish survival and improve program efficiency 

Project Description: This project will provide needed equipment for reliable and efficient means to 

load and handle steelhead smolts for transport from their rearing location in Lake Quinault to point of 

hatchery releases in the lower mainstem Quinault River. Off-station releases below Quinault Lake are 

favored to minimize risks to natural populations within the lake due to hatchery -wild fish interactions, 

including direct predation by hatchery steelhead smolts. Purchased equipment facilitates this 

management strategy while minimizing injury and stress to both program fish and hatchery personnel. 

Tribe: Stillaguamish 

Name of Project: Emergency oxygen backup system for circular rearing tanks 

Stock and Status: North Fork Stillaguamish summer Chinook, ESA threatened 

 Stillaguamish Coho, SaSI healthy 

 Stillaguamish chum, SaSI healthy 

Hatchery: Harvey Creek 

Project Benefit: Minimize risk of catastrophic loss of ESA listed Chinook while in the 

 hatchery 

Project Description: The objective of this project is for design, construction and operation of a 

backup emergency oxygen delivery system. This hatchery modification will reduce the risk of loss of 

listed summer Chinook in the event of a reduction or loss of gravity fed water into circular tanks 

holding both adult broodstock and juveniles. 

Tribe: Tulalip 

Name of Project: Install bird net support structures in upper Tulalip Creek pond 

Stock and Status: Skykomish River coho, SaSI healthy 

Hatchery: Bernie Kai-Kai Gobin 

Project Benefit: Improve program efficiency by reducing in-hatchery loss of program fish 

 due to predation 

Project Description: Hatchery inventory methods have indicated significant in-hatchery loss of 

program fish, primarily due to bird predation. This project will provide funding for purchase and 

installation of bird netting at the upper Tulalip Creek rearing and release pond. Expected project 

benefit is reduced loss of program fish due to bird predation, improved program efficiency and 

increases in returns and tribal harvest of adult salmon. 
Appendices Report to Congress – March 2006 33 

D: 2006 Budget 

Puget Sound and Coastal Washington Hatchery Reform Project Budget FY 2006

Hatchery Scientific Review Group

HSRG Members, Travel, Meeting Costs $50,000

Tribal Hatchery Reform Demonstration Projects $200,000

SUBTOTAL $250,000

Long Live the Kings

21st Century Salmon and Steelhead Management Initiative (Project 

Management, Facilitation and Communications) 

$250,000

TOTAL $500,000
34 Report to Congress – March 2006 Appendices 

E: Research Priorities for Hatchery Reform 

Hatchery Scientific Review Group Technical Discussion Paper 

November 2005 

Introduction 

 

Application of sound genetic and ecological principles is central to the management of salmon and 

steelhead hatcheries. Research to promote and evaluate actions stemming from these principles is a 

necessary priority in support of hatchery reform. Without the refinement and application of these 

principles, the sustainability of salmon and steelhead populations in Pacific Northwest watersheds will 

be compromised, and the goals of hatchery reform will not be achieved. 

 

However, determining the correct focus for hatchery reform research is not an easy task. Various 

groups have undertaken to produce hatchery operational guidelines and research plans in the past 

(RASP 1992; SRT 1998; APR 1999; ISAB 2003: APRE 2003; NWFSC 2001, 2004). A common 

approach in these documents is the description of a vast number of operational parameters and 

research topics that are deemed relevant to understanding the risks and benefits associated with 

hatchery operations, and using hatcheries to supplement natural populations. 

 

In these research guidance documents, statements about necessary reforms in hatchery technology 

often imply that research must encompass problems encountered in all life history stages of salmon, 

and that reform of current practices should be approached by applying several scientific disciplines 

including genetics, physiology, behavior, nutrition, and microbiology. Direction and guidance is often 

provided in diverse areas of fish genetics, culture, health and nutrition; hatchery release strategies; 

ecological interactions (competition, predation); nutrient enhancement; habitat improvements in 

estuary, migration corridor, and in tributary spawning and rearing habitats; carrying capacity 

dynamics; etc. However, most of these past plans have provided little or no prioritization among these 

extensive areas of possible research, to focus on the actions most necessary to achieve hatchery goals. 

 

We are reaching a point in the Pacific Northwest where the number of possible questions is expanding, 

while the funding available to study all aspects of salmon recovery is diminishing. A number of 

metrics and evaluators need to be used in determining how to prioritize actions necessary to resolve 

the key questions pertaining to where supplementation efforts will add to—rather than reduce—the 

total natural production of salmon and steelhead. As a result of our recent technical discussions, this 

group suggests that the following criteria should be the primary metrics used to prioritize hatchery 

research. In the present funding climate, it would seem most appropriate to focus available resources 

on research topics that fit these four parameters: 

 

1) The context for the research and the importance of the question to be resolved. 

2) The degree of uncertainty associated with the question. 

3) The tractability of defining an answer to the question. 

4) How generally applicable the results of the research will be. 

 

In applying these parameters to our discussion of hatchery research priorities, we found two areas that 

are foundational to hatchery reform: 1) application of genetically integrated and segregated hatchery 
Appendices Report to Congress – March 2006 35 

operational principles to the management of hatcheries; and 2) application of physiological and 

ecological principles to produce hatchery fish following a wild fish template, which we hypothesize is 

the appropriate approach to promote ecological integrity. The genetic goal for hatchery reform is to 

ensure that hatchery operations do not affect the genetic constitution of natural stocks resident in these 

watersheds. Instead, hatchery operations should be designed so that the natural environment is the 

driving force in determining the genetic make-up of natural stocks within these watersheds. Secondly, 

hatchery operations should be consistent with ecological principles that meet the ecological objectives 

of the program. It is essential, therefore, that hatchery fish be reared on life history trajectories that 

mimic natural trajectories and releases sized so that they do not: 1) exceed the carrying capacity of the 

available riverine, estuarine and marine habitat; 2) displace natural stocks that also depend on that 

habitat; 3) overwhelm the food base present in that habitat, and 4) diminish the productivity of natural 

stocks through predation. Areas of focus for these genetic and ecological research topics are described 

below. 

 

Background and Recommended Research Relating to Stock Genetics 

 

Adaptation to watersheds by the salmonid populations resident in them is critical to the sustainability 

of these populations. It is also important that the diversity of populations in any given watershed be 

respected and preserved. Hence, populations should be afforded the opportunity to adapt to the 

conditions in the watersheds and extended environments they inhabit. 

 

Hatchery practices that inhibit adaptation are inconsistent with long-term goals for both naturallyspawning and hatchery stocks. The frequent past practice of transferring hatchery broodstock among 

watersheds should be phased out. Instead, hatchery broodstock should be collected from returnees to 

the watershed where the offspring will be released. Further, all phases of hatchery operations should 

be consistent with and/or supportive of the continuous process of local adaptation. 

 

Hatchery programs should be operated as either genetically integrated or segregated. Both of these 

strategies are designed to promote local adaptation and minimize fitness loss of both naturallyspawning and hatchery populations. A critical question is whether segregated and integrated hatchery 

programs will prove effective, over the long term, in accomplishing this important goal of promoting 

local adaptation. It is important, therefore, that key natural- and hatchery-origin stocks be monitored 

over the long-term for evidence of fitness loss or gain attributable to hatchery/natural population 

interactions. The development of practical methods to quantify fitness loss or gain in salmonid 

populations should be a high research priority. 

 

In river systems where the infrastructure will permit it, well-controlled experiments to measure rates of 

adaptation in integrated or segregated populations should be undertaken. These experiments might, for 

instance, be modeled after genetic monitoring protocols employed in the breeding of other animals. 

For example, the fitness or breeding values of fish from a founder population that has been allowed to 

adapt to local conditions for a number of generations might be compared with that of portions of the 

same population (derived by using cryo-preserved gametes) that have not had the chance to adapt to 

local conditions for as many generations. Alternatively, fitness changes might rely on identification 

and monitoring of quantitative trait loci in thoroughly mapped genomes of salmon and steelhead trout 

populations. Such experiments should be able to identify phenotypic traits that will prove useful as 

indexes of domestication and adaptation, if the experiments encompass the diversity of ecosystems 

and the variety of species and life history patterns found in the region. 
36 Report to Congress – March 2006 Appendices 

 

Background and Recommended Research Relating to Ecological Principles 

 

In planning hatchery programs, the co-managers of the salmonid resource are often confronted with 

questions relating to the nature (e.g., the type and purpose of the programs, and the strategies used for 

releasing fish in order to maintain life history patterns of the reared species) and size (in terms of 

numbers of juvenile fish released) that their hatchery programs should assume. These questions arise 

because of uncertainties about the amount of suitable habitat available, the size and nature of the 

natural salmonid populations and other species dependent on the habitat, the capacity of the habitat to 

provide adequate feed for both natural- and hatchery-origin fish, and behavioral, physiological, and 

morphological differences between natural and hatchery raised fish. 

 

In conducting research to resolve these questions, the research priority should be the development of 

qualitative and quantitative models that describe ecological processes and outcomes that could be 

tested and used as tools for making informed decisions on hatchery release sizes and strategies. These 

models should be based on general biological principles (i.e., the needs and behavior of salmonids and 

of the species with which they interact), so that it can take into account site-specific circumstances and 

be applied to all hatchery programs. In developing these models, monitoring will be needed to provide 

input data that may be lacking. Monitoring to check the performance of the models will also be 

required, so that appropriate adjustments can be made to improve the accuracy of the outcomes 

predicted by the models, with respect to hatchery/wild fish interactions. 

 

Another area of ecological research that is of high importance, but did not seem as tractable, has to do 

with the role of hatchery fish in freshwater and marine food webs. Salmon are important determinants 

of aquatic and marine community structure, both as sources of abundant prey and as keystone 

predators. In some cases, hatchery fish may compensate for natural salmon population decline and 

help maintain community structure. In other cases, hatchery salmon may disrupt an existing balance. 

A better understanding of the role that hatchery salmon play in food webs is very important in 

determining the overall effect of hatchery programs. Further discussion with ecologists and other 

experts may help us develop tractable approaches to this research in the future. 

 

References 

 

Artificial Production Review (APR). 1999. Artificial Production Review in the Columbia River Basin. 

Report 9-15, Northwest Power Planning Council, Portland, OR. (www.nwcouncil.org/library/1999/99-

15.htm) 

 

Artificial Production Review and Evaluation (APRE). 2003. Artificial Production Review in the 

Columbia River Basin, Basin Level Report. Report 2003-17, Northwest Power Planning Council, 

Portland, OR. (www.nwcouncil.org/library/2003/2003-17.htm) 

 

Independent Science Advisory Board (ISAB). 2003. A review of salmon and steelhead 

supplementation. ISAB Report 2003-3, Northwest Power Planning Council, Portland, OR. 

(www.nwcouncil.org/library/isab/isab2003-3.htm) 

 

NWFSC. 2001. Northwest Fisheries Science Center, Salmon Research Plan, Volumes I & II, Seattle, 

WA. (www.nwfsc.noaa.gov/publications/researchplans/index.cfm) 
Appendices Report to Congress – March 2006 37 

 

NWFSC. 2004. Northwest Fisheries Science Center, Salmon Hatchery Strategic Research Plan 2004. 

Seattle, WA. (www.nwfsc.noaa.gov/publications/researchplans/index.cfm) 

 

Regional Assessment of Supplement Project (RASP). 1992. Supplementation in the Columbia Basin. 

RASP Summary Report Series. Proj. 85-62. Bonneville Power Administration, Portland, OR, 321 p. 

Available at: (www.efw.bpa.gov/integrated_Fish_and_Wildlife_Program/technicalreports.aspx) 

 

Science Review Team (SRT). 1998. Review of salmonid artificial production in the Columbia River 

Basin. Report 98-33, Northwest Power Planning Council, Portland, OR, 77 p. 

(www.nwcouncil.org/library/1998/98-33/98-33.htm) 
38 Report to Congress – March 2006 Appendices 

F: Rationale for Integrated/Segregated 

Broodstock Management 

The HSRG developed the following text in May 2005, to help clarify what the HSRG meant when it 

recommended that managers identify each hatchery program as either having an integrated or 

segregated broodstock management strategy. 

• We know from theory and observation that interactions between hatchery- and natural-origin fish 

will diminish the fitness of naturally-spawning populations, even though this fitness loss is 

difficult to measure. 

• The only way to completely eliminate this fitness loss is to eliminate hatchery programs. 

• However, hatcheries can provide harvest benefits. 

• Hatcheries have also, in some cases, increased the abundance of populations at risk of extinction. 

• Where managers choose to use a hatchery program as part of a strategy to meet harvest and/or 

conservation goals, there are two ways to manage hatchery broodstocks to address the associated 

fitness loss. 

1. Segregated Hatchery Programs—In these programs, the intent is to manage for two separate 

gene pools (one adapted to the hatchery, the other to the natural environment) and that 

hatchery-origin fish do not spawn in the wild. 

2. Integrated Hatchery Programs—In these programs, the intent is for the genetic make-up of 

hatchery-origin fish to be the same as that of the underlying natural population, and that 

natural selection in the wild drives the fitness of both components of the population. This 

requires that natural-origin fish be included in the hatchery broodstock and that natural 

spawning of hatchery-origin fish be minimized. 

• In practice, it is in most cases not possible to perfectly achieve either of these strategies. 

• It is a reasonable hypothesis that the increased population abundance derived from well-managed 

integrated or segregated hatchery programs can outweigh the associated fitness losses. Where this 

hypothesis cannot be supported, a hatchery program may not be appropriate. 

• Both integrated and segregated programs can potentially provide fish for conservation purposes, 

where natural spawning by hatchery-origin fish may be desired. 

• When hatchery-origin fish spawn and reproduce successfully in the natural environment, genetic 

risks of properly-integrated hatchery programs are expected to be less than those from segregated 

programs for the same level of gene flow from a hatchery program to a natural population. 

• Watershed-specific goals and circumstances determine whether a segregated or integrated 

hatchery program is most appropriate. 

• Hatcheries should be used as part of an integrated strategy (alongside harvest management, and 

habitat protection and restoration) to meet conservation and harvest goals on a sustainable basis. 
Appendices Report to Congress – March 2006 39 

G: HSRG Memorandum to Hatchery Reform 

Coordinating Committee Regarding 

Steelhead Management 

MEMORANDUM 

May 17, 2005 

To: Hatchery Reform Coordinating Committee 

From: HSRG Chair Lars Mobrand 

Re: HSRG Steelhead Recommendations 

The HSRG understands that the co-managers are presently developing a new statewide 

steelhead management plan, beginning with a white paper. Recent conversations with comanager personnel and stakeholders indicate that there is some confusion about the HSRG’s 

recommendations relating to Puget Sound and coastal Washington hatchery steelhead 

programs. The following bullets are presented to help clear up this confusion. We hope they 

will also be useful in the drafting of the white paper. The HSRG remains interested in 

providing technical and scientific assistance to the co-managers in the development of the 

white paper and management plan. 

• During the regional review process, the co-managers identified most naturallyspawning steelhead stocks in Puget Sound and coastal Washington as being of high 

biological significance and low abundance/productivity. 

• Most hatchery programs were identified as segregated harvest and released/outplanted 

non-native stocks of Chambers or Skamania origin. This approach was ubiquitous 

across the system. 

• Also ubiquitous in these programs was inadequate provision for the recapture of 

unharvested returning hatchery adults. 

• Currently, few steelhead programs in Puget Sound are providing significant harvest. 

• While it is difficult to monitor escapement and survival of steelhead, it has been 

shown that significant genetic and ecological8, 9 interactions occur between hatcheryand natural-origin steelhead. For example, there is a spawning overlap between the 

 

8

 Mackey, G., J.E. McLean, and T.P. Quinn. 2001. Comparisons of run timing, spatial distribution, and length of 

wild and newly established hatchery populations of steelhead in Forks Creek, Washington. North American 

Journal of Fisheries Management 21:717-724. 

9

 Kostow, K.E., A.R. Marshall, and S.R. Phelps. 2003. Naturally spawning hatchery steelhead contribute to 

smolt production but experience low reproductive success. Transactions by the American Fisheries Society 

132:780-790. 
40 Report to Congress – March 2006 Appendices 

hatchery (Chambers Creek origin), early-timed, winter run stock and the native, latetimed winter run stock at Forks Creek. 

• Even small contributions from segregated hatchery populations to small natural 

populations can lead to a significant loss of fitness. 

• Any segregated harvest program conducted under these circumstances will pose a high 

risk to naturally-spawning steelhead stocks. This creates a conflict between the comanagers’ steelhead harvest goals and their conservation goals for natural steelhead 

populations. 

• Because of low abundance and productivity, wild steelhead populations in Puget 

Sound cannot provide the natural-origin broodstock needed to support integrated 

harvest programs. Therefore, integrated harvest programs are not currently a viable 

alternative in most places. 

• The steelhead recommendations that resulted from the HSRG’s regional reviews were 

designed to resolve the conflict identified above between the co-managers’ harvest and 

conservation goals. These recommendations include the following elements: 

o Select a balance of large and small streams and habitat types in each region that 

are not planted with hatchery fish and are instead managed for native stocks. This 

would reduce the risk of naturally spawning fish interbreeding with hatchery fish, 

and provide native stocks for future fisheries programs. 

o Fishing for steelhead in these streams would not be incompatible with this 

approach, but no hatchery-produced steelhead should be introduced. 

o To meet harvest goals, hatchery releases should be in those streams selected for 

hatchery production. Use locally-adapted broodstock for those streams. 

o Decrease reliance on out-of-basin transfers to backfill shortages in locally adapting 

hatchery stock. Actions such as harvest restrictions should be implemented to 

achieve 100% local broodstock. 

o Manage the hatchery stock to maintain its early spawn timing and reduce the 

likelihood of interaction with naturally-spawning steelhead. 

o Include adult collection capability wherever steelhead are released, to capture as 

many adults from the returning segregated population as possible. Discontinue 

releases where adults cannot be collected at return. Investigate feasible sites with 

adult collection capability, so that returning adults can be collected and removed 

from natural spawning population. 

o Size the hatchery program in a manner that achieves harvest goals with minimal 

impact on wild populations. 

o Release hatchery yearling steelhead smolts between April 15 and May 15 at target 

size of six fish to the pound, and a condition factor of less than 1.0. 

o Implement monitoring and evaluation as a basic component. 

o Investigate the reasons for the recent decline in adult winter steelhead returns, 

formulate a working hypothesis for the decline and take appropriate actions. 
Appendices Report to Congress – March 2006 41 

H: Letter from WDFW to Tribal Chairs on 

Future Hatchery Management 

State of Washington 

DEPARTMENT OF FISH AND WILDLIFE 

Mailing Address: 600 Capitol Way N • Olympia, WA 98501-1091 • (360) 902-2200, TDD (360) 902-2207 

Main Office Location: Natural Resources Building • 1111 Washington Street SE • Olympia, WA

August 2, 2005

Chair 

Tribe 

Address 

RE: Future Hatchery Management 

Dear Chair, 

We share a unique and important government-to-government relationship as co-managers of 

the salmonid resources in the State of Washington. It is this relationship that carries us 

through the challenges associated with management of a valuable natural resource that is in 

part dependent upon an unpredictable environment. We hold in common a commitment to the 

protection, enhancement and recovery of the salmonid resources and their habitat to ensure 

conservation of the species and perpetuation of harvest opportunity into the future. In 

addition, we have a strong interest in ensuring the co-managers drive the decisions relating to 

operation of the hatchery system into the future. 

During the past six years of hatchery reform activities, which have had a principally scientific 

emphasis to date, a number of tools were developed that afford us as co-managers the 

opportunity to move our hatchery programs forward through a more informed decisionmaking process. It also provides the co-managers a means to determine if our hatchery 

system is meeting our shared goals and objectives. The purpose of this communication is to 

indicate our interest to work with tribal co-managers on a watershed specific basis to review 

our stock goals, hatchery program goals, and identify appropriate actions. 

Several recent events have prompted our interest in initiating these discussions. The most 

recent rule by National Oceanic and Atmospheric Administration (NOAA Fisheries) to 
42 Report to Congress – March 2006 Appendices 

include several of our hatchery Chinook populations within the threatened listing status for 

the Puget Sound Evolutionarily Significant Unit (ESU); the hatchery Environmental Impact 

Statement (EIS) currently in preparation; the recovery plan development through the Shared 

Strategy process; and the recommendations coming out of the Hatchery Scientific Review 

Group. We believe it is important and the timing unparalleled for the co-managers to take the 

lead on how we expect our hatchery system to operate into the future, not only because of 

these recent events, but also because if we are to be successful at improving our hatchery 

system (from facility modifications to natural production management) so that our shared 

goals and objectives are met, then we need significant financial support at both the state and 

federal levels. If the co-managers lead the decision-making process and show a commitment 

through action, then we believe the financial support will come. 

WDFW believes the tools developed by the co-managers and the Hatchery Scientific Review 

Group through the hatchery reform process are value neutral. That is, the tools inform 

decision-making, but don’t make the decision. We liken the tools to a vehicle provided to the 

co-managers to drive. The details of what the vehicle looks like, how fast it moves, and in 

what direction will be determined by the co-managers. For example, the application of the 

integrated/segregated concept of a hatchery program is a policy decision. WDFW believes 

the concept represents a dial the co-managers turn to set a direction. However, timing and 

speed will influence progress of the direction. 

The WDFW welcomes the co-manager decision to have a regional focus. We propose 

holding annual progress meetings between co-managers at the regional level to ensure the 

actions/activities that influence the direction we take meet our shared objectives. Building 

from the annual management meeting concept, is the recognition that an in-depth review and 

coordination at a higher policy level would be appropriate periodically as well. The timeline 

for a higher-level policy discussion may occur at intervals more consistent with evaluating 

major actions that have been taken or are proposed to be taken in a your region. In addition 

the more in-depth reviews could be timed based on brood cycles to allow for thorough 

technical support efforts. Sound technical information and adaptive management should 

inform decision-making at these policy level meetings. 

It’s important to reiterate the hatchery reform process has had a principally scientific 

emphasis to date in order to increase our understanding of the hatchery production programs. 

Tools were developed to facilitate this knowledge, and these tools have subsequently 

simplified some of the complexity that surrounds our management. We recognize comanagement decisions are complex and multi-faceted, however, the foundation from which 

we make decisions has become more informed through the use of these tools. The WDFW 

values the tools developed, because we believe they represent an important means to assist in 

our decision-making. Therefore, we intend to use the tools and welcome joint discussion, 

input, review, and decision-making with our co-managers. 
Appendices Report to Congress – March 2006 43 

The annual co-manager meeting on August 10, 2005 will provide an opportunity to 

communicate more thoroughly the context for use of the tools, as well as WDFW’s interest in 

meeting with tribal co-managers at the watershed level to determine the direction of 

respective hatchery programs into the future. We look forward to our meeting and your 

response. 

Sincerely, 

Jeff Koenings, Ph.D. 

Director
44 Report to Congress – March 2006 Appendices 

 I: Letter from WDFW to Shared Strategy on 

Recovery Plan Implementation 

State of Washington 

DEPARTMENT OF FISH AND WILDLIFE 

Mailing Address: 600 Capitol Way N • Olympia, WA 98501-1091 • (360) 902-2200, TDD (360) 902-2207 

Main Office Location: Natural Resources Building • 1111 Washington Street SE • Olympia, WA

February 15, 2006 

Mr. Bill Ruckelshaus, Chair 

Puget Sound Shared Strategy 

1411 - 4th Avenue, Suite 1015 

Seattle, WA 98101 

Dear Bill, 

Congratulations on the completion of the Regional Salmon Recovery Plan for Puget Sound. It 

is an outstanding document, and provides a valuable roadmap for salmon recovery in Puget 

Sound. More importantly it represents a consensus of federal, state, local and tribal 

governments, is based on sound scientific principles and was developed in partnership with 

local citizens and watershed groups. I am particularly proud of the role that Lead Entities 

played in the development of the plan. 

Implementation of the Puget Sound Salmon Recovery Plan will take coordinated, dedicated 

efforts of all organizations with a stake in salmon recovery. It will also take leadership and 

commitment. Broadening the Development Committee to include leadership from each of the 

watersheds and other organizations that have a clear role in implementation is an excellent 

step and I look forward to joining you on February 15th to meet the new group. I gladly accept 

your request for the continued participation of Washington Department of Fish and Wildlife 

(WDFW) on this new regional leadership group. 

I also want to assure you that WDFW is committed to implementing the components of 

salmon recovery that fall under our jurisdiction. As you know there are many areas where 

WDFW will play a key role in salmon recovery. I am committed to ensure WDFW continues 

to address the important building blocks of recovery summarized below. 
Appendices Report to Congress – March 2006 45 

3⁄4 All-H Integration: One of our greatest priorities for 2006 is to move ahead quickly on AllH Integration. WDFW will work with tribes, Shared Strategy and watersheds to advance 

this important aspect of successful salmon recovery. We are starting this process with an 

All-H Integration work group on February 17th. The group includes members of Puget 

Sound’s Technical Review Team, NOAA, Shared Strategy workgroup, Hatchery 

Scientific Review Group, Tribes and WDFW. It is my goal, that by the end of the year, 

we have advanced all-H integration so that each watershed can produce a chapter similar 

to the “Integration” chapter in the Snohomish River Basin Salmon Conservation plan. 

3⁄4 Harvest Management: The co-manager’s Puget Sound Chinook Comprehensive Harvest 

Management plan serves as the scientific foundation for the development of annual 

protection strategies that are consistent with the conservation and recovery of naturally 

spawning fish. The implementation of this plan is having positive results with proven 

increases in the numbers of listed salmon on the spawning grounds. The plan has long 

recognized the importance of adaptive management, and that evolution in harvest 

management will occur in response to improved understanding of the status and 

productivity of populations. To that end, in conjunction with the upcoming H-Integration 

process, WDFW intends to review assessment data and ensure that the incidental harvest 

of Chinook is consistent with estimates of productivity and recovery of the Puget Sound 

ESU. In short, we must be progressive in where and how to focus harvest opportunities to 

assure both healthy populations and healthy fisheries. 

3⁄4 Hatchery Reform: The Hatchery Scientific Review provided valuable guidelines and 

principles to reform hatchery programs. While over 700 of the 1,100 actions are 

underway, significant work remains to be done. Watershed by watershed, WDFW’s 

hatchery objectives will be reviewed as part of the H-Integration process. This review 

may lead to changes in hatchery goals and objectives or operations or both. When changes 

are identified by the co-managers, a hatchery program will be re-evaluated using the 

scientific tools provided through the hatchery reform process to ensure that the hatchery 

program is the appropriate size and type for helping to achieve harvest and conservation 

goals for the watershed. 

3⁄4 Habitat: The Department is supporting implementation of salmon recovery plans through 

five major efforts: 

o Puget Sound Nearshore Partnership (PSNP): The WDFW is the lead nonfederal partner in the Puget Sound Nearshore Ecosystem Restoration Project. 

The Army Corps of Engineers project is working to complete a science-based 

feasibility study for a large-scale ecosystem restoration project in Puget Sound. 

We are also working in conjunction with Puget Sound Action Team to provide 

support and coordination with the Governor’s Puget Sound Initiative and the 

Puget Sound Partnership. PSNP will continue to provide technical support to 

priority large-scale restoration activities. In addition, the Department is 
46 Report to Congress – March 2006 Appendices 

working with Lead Entities to identify regional priority salmon recovery 

projects for funding through the “Estuary and Salmon Recovery” budget 

request. 

o Salmon Recovery Funding Board: The department will continue to actively 

participate in the Salmon Recovery Funding Board and by supporting the 

“2496” process. Watershed Stewards will assure that local implementing 

organizations have access to agency technical tools, data and expertise. In 

addition, we will expand our efforts to help Lead Entities improve their local 

prioritization processes. The Department is initiating a project to provide 

watershed groups with habitat project management tools through development 

of Habitat Work Schedules. These schedules will help potential project 

funders find local and regional priority projects. And finally, the Department 

will continue to support local sponsors, such as Regional Fish Enhancement 

Groups to identify priority salmon recovery projects to bring forward. 

o Habitat Protection: WDFW is beginning implementation of a project to assure 

that the HPA program and agency land management are being executed in 

compliance with the federal Endangered Species Act through a variety of 

potential tools and programs, including HCP’s. The Department’s Mitigation 

Optimization project is developing collaborative processes that will bring 

local, state and federal permitting agencies together to improve the 

effectiveness of mitigation by linking mitigation decisions to priority 

watershed restoration and protection needs. Through the Puget Sound 

Nearshore Ecosystem Restoration Project, WDFW is developing science 

“white papers” detailing the habitat needs of various species, including 

juvenile salmon, in the estuaries and shorelines of Puget Sound. The 

Department will work with local governments to incorporate this science into 

local land and water management processes. The Department will continue to 

pursue acquisition and conservations easements for the long-term protection of 

priority salmon habitat through a variety of local, state, and federal programs, 

such as the WWRP as outlined in it’s recently published “Lands 2020” 

document. And finally, the Department is committed to improving the 

effectiveness and efficiency of the HPA permitting process. 

o Monitoring and Adaptive Management: WDFW will continue to co-chair and 

provide staff support to the Governor’s Monitoring Forum. WDFW will also 

continue to participate in the Shared Strategy AAM workgroup and upcoming 

workshops. Scheduling these workshops to avoid major fish management 

forums, like North of Falcon, will help us get the appropriate staff at these 

important workshops. A recent letter from the Association of Washington 

Cities and the Washington State Association of Counties to Jay Manning, 

(Director of the Department of Ecology) suggested that Ecology, WDFW, 
Appendices Report to Congress – March 2006 47 

Shared Strategy, Northwest Indian Fish commission and local jurisdictions get 

together to discuss common monitoring principles. It is important for all of us 

to work with them on this request. The Department will continue to expand 

and improve on its ability to monitor “fish in” and “fish out” for core 

populations critical to salmon recovery in the Puget Sound basin. 

o Finally, all of these activities require adequate funding. The Department will 

continue to work closely with you, Bill, and to serve as lead for a multi-agency 

effort to advocate for state and federal funding for the Pacific Coastal Salmon 

Recovery Fund, the Puget Sound Nearshore Ecosystem Restoration Project, 

and other projects, programs and activities critical to the implementation of the 

Puget Sound recovery plan. 

Sara LaBorde, WDFW Salmon Recovery Coordinator, will work with Shared Strategy to 

detail the timeline of these actions, as well as develop a reporting system to ensure that 

WDFW fulfills these commitments as we move forward. 

Bill, thank you for your outstanding leadership and for absolute commitment to a citizen-led, 

“bottom-up” approach to salmon recovery. I look forward to the opportunity to advance 

implementation of the Puget Sound Salmon Recovery plan and being an integral part in 

developing health, sustainable salmon populations in Washington. 

Sincerely, 

Jeffrey P. Koenings, Ph.D. 

Director
48 Report to Congress – March 2006 Appendices 

 J: Letter from WDFW Director to Staff on 

Hatchery Reform Conference 

State of Washington 

DEPARTMENT OF FISH AND WILDLIFE 

Mailing Address: 600 Capitol Way N • Olympia, WA 98501-1091 • (360) 902-2200, TDD (360) 902-2207 

Main Office Location: Natural Resources Building • 1111 Washington Street SE • Olympia, WA

December 9, 2005 

Name 

Division 

Dear Name, 

On October 28th, the Long Live the Kings and the Mountaineers hosted the “Hatchery 

Reform: Managing for Success” workshop. This event marked an important step in hatchery 

reform as it represented the transition from the science-based review and identification of 

necessary actions to implementation. It also affirmed the commitment by the co-managers to 

state/tribal implement hatchery reform at a watershed level to achieve our shared goals and 

objectives. 

The Hatchery Scientific Review Group’s (HSRG) process that each of you contributed to was 

a monumental effort. In reviewing over 200 Puget Sound and Coastal Washington programs, 

you have participated in a process unparallel anywhere in the country. Placing your programs 

and your efforts under the magnifying glass takes courage as well as an extraordinary amount 

of time and effort. I am glad you were up to this challenge. 

Often times such program reviews fail either under their own weight or from a lack of interest 

on the “reviewee’s” part. I want to thank each of you for your dedication and effort in helping 

the HSRG make this review process successful. The results of this process – the 

recommendations and tools like the “All H Analyzer” and “Managing for Success” are 

excellent contributions to Washington’s hatchery and fishery management programs. 
Appendices Report to Congress – March 2006 49 

An important next step in implementation is making sure there is co-manager agreement on 

goals and actions. At the annual co-manager meeting in August, there was agreement by the 

co-managers to collaborate at the watershed level for implementation of hatchery reform, and 

optimally to integrate our hatchery and harvest actions. WDFW is developing a schedule in 

cooperation with the Tribes to begin these watershed level specific discussions. Watershed 

level discussions by the co-managers will focus on stock goals, hatchery program goals, and 

identification of appropriate actions to achieve our shared goals. Clearly, this watershed 

specific collaboration will involve significant effort and commitment by all of us, but it is an 

important step in implementation of hatchery reform. 

To make sure we continue making progress, I am asking Heather Bartlett, Paul Seidel, Pat 

Frazier, and Ron Warren to provide me with a current status and then regular updates on the 

following: 

⎯ Hatchery Reform Actions 

o Actions completed 

o In progress 

o Funded 

o Remaining to be done, their priority and implementation plans 

⎯ Goals of hatchery and harvest programs 

o Stock, escapement and program goals 

o Status of joint discussion, input, review, and agreement with our co-managers 

⎯ Managing for Success tool 

o Steps to completion for hatchery, harvest and habitat sections 

o Capability to use to report WDFW salmon recovery actions 

o Viewable by staff and citizens 

⎯ Communication 

o Method WDFW employees involved in hatchery reform will be kept updated 

on progress 

o Method this will be included and salmon recovery reporting 

It is important that the great work and momentum for hatchery reform continue. Thank you 

for your continued efforts. 

Sincerely, 

Jeffrey P. Koenings, Ph.D. 

Director
50 Report to Congress – March 2006 Appendices 

 K: Hatchery Reform in Washington State: 

Principles and Emerging Issues, 

(Fisheries Magazine, June 2005) 

(Available at www.fisheries.org/html/fisheries/F3006/F3006p11-23Seeb.pdf) 
feature

fisheriess management

Introduction

An extensive hatchery system for Pacific salmon (Oncorhynchus spp.) and

steelhead (O. mykiss) has developed over the past 100 years in the Pacific

Northwest to mitigate for the effects of overfishing, logging, agriculture,

hydropower, urbanization, and associated losses of freshwater salmon habitats

(Lichatowich 1999). The Washington Department of Fish and Wildlife

(WDFW), several Native American tribes, and the U.S. Fish and Wildlife

Service operate more than 100 hatchery facilities within Puget Sound and the

Pacific coast of Washington state. These hatcheries release more than 100 million juvenile salmon and steelhead each year and contribute approximately 70%

of all salmon harvested in Puget Sound (WDFW 1997). The state of

Washington and the treaty tribes of western Washington jointly manage fishery

resources in western Washington and are collectively referred to as “co-managers.”

A large number of naturally-spawning populations of Pacific salmon and steelhead are currently listed as threatened or endangered under the U.S. Endangered

Species Act (www.nwr.noaa.gov/1salmon/salmesa/fractlist.htm). Genetic and

ecological interactions with hatchery-origin fish are often cited as one cause of

the decline of naturally spawning populations (Waples 1991; Hilborn 1992; Levin

et al. 2001). However, the biological effects of hatcheries on natural populations

are the subject of much scientific uncertainty and controversy (Busack and

Currens 1995; Campton 1995; Brannon et al. 2004). The potential use of

hatcheries to help recover natural populations also presents many scientific

uncertainties (Hedrick et al. 2000; ISAB 2002; Flagg et al. 2004). 

To resolve conflicts between hatcheries and the need for both sustained fisheries and conservation of Pacific salmon and steelhead in Washington state, the

U. S. Congress funded the Western Washington Hatchery Reform Project beginning in FY2000 (www.hatcheryreform.org). This project was motivated by recent

ESA listings and the important economic and cultural roles of salmon and steelhead fisheries in Puget Sound and coastal Washington. The goal of the project is

to determine how hatcheries can best support sustainable fisheries while, at the

same time, assist with the conservation and recovery of naturally spawning populations. The project represents a systematic review of all hatchery programs in

western Washington, excluding the Columbia River. Congress provided funding

to: (a) establish and support an independent panel of scientists to review all

hatchery programs and guide the reform process, (b) support a competitive

research grants program to address scientific uncertainties associated with

hatcheries, (c) support state and tribal efforts to implement hatchery reforms, and

(d) facilitate project management by a non-government organization. The independent science panel was established in early 2000 under the name Hatchery

Scientific Review Group (HSRG). 

June 2005 | www.fisheries.org | Fisheries 11 ABSTRACT

Hatchery Scientific 

Review Group:

Lars E. Mobrand, Chair

John Barr

Lee Blankenship

Donald E. Campton

Trevor T. P. Evelyn

Tom A. Flagg

Conrad V. W. Mahnken

Lisa W. Seeb

Paul R. Seidel

William W. Smoker

Mobrand is chair of the Hatchery Scientific Review

Group and is a biometrician with Mobrand-Jones

and Stokes, Inc., Vashon, WA. Barr is a fish

biologist, Nisqually Indian Tribe Natural Resources

Department, Olympia, WA. Blankenship is director

of Biological Services, Northwest Marine

Technology, Tumwater, WA. Campton is senior

scientist/geneticist, U.S. Fish and Wildlife Service

Abernathy Fish Technology Center, Longview, WA.

Evelyn is scientist emeritus, Department of Fisheries

and Oceans, Pacific Biological Station, Nanaimo,

BC, Canada. Flagg is supervisory fisheries biologist

and Mahnken is a retired fisheries biologist, NOAA

Fisheries Northwest Fisheries Science Center, Port

Orchard, WA. Corresponding author Seeb is

principal geneticist, Alaska Department of Fish and

Game Division of Commercial Fisheries,

Anchorage, and can be contacted at

lisa_seeb@fishgame.state.ak.us. Seidel is Hatchery

Evaluation and Assessment unit leader,

Washington Department of Fish and Wildlife,

Olympia. Smoker is professor, University of Alaska

Fairbanks, School of Fisheries and Ocean Sciences,

Juneau. 

Hatchery Reform in Washington State:

Principles and Emerging Issues

Hatcheries support nearly all major fisheries for Pacific salmon (Oncorhynchusspp.) and steelhead (anadromous O. mykiss) in the Pacific Northwest. However, hatcheries have been a

major source of controversy for over 30 years. The Hatchery Scientific Review Group (HSRG)

was tasked by Congress to identify solutions to well-known problems so hatcheries could

better meet their goals of supporting sustainable fisheries and assisting with the conservation of natural populations. We reviewed over 100 facilities and 200 programs and identified

three principles of hatchery reform: (1) goals for each program must be explicitly stated in

terms of desired benefits and purposes; (2) programs must be scientifically defensible; and

(3) hatchery programs must respond adaptively to new information. We also identified several emerging issues critical to the success of hatcheries. We concluded that hatcheries must

operate in new modes with increased scientific oversight and that they cannot meet their

goals without healthy habitats and self-sustaining, naturally-spawning populations.
fisheries management

feature

12 Fisheries | www.fisheries.org | vol 30 no 6

Here, we summarize major conclusions resulting

from our reviews of hatchery programs during the

past four years. Details of the review process have

been described elsewhere (Blankenship and Daniels

2004; Blankenship and Kern 2004) but are briefly

summarized below (see also www.hatchery.org).

The Hatchery Review Process

We visited over 100 facilities and evaluated over

200 hatchery programs encompassing 10 major

regions in western Washington (Figure 1). Early in

the project, we concluded that hatchery programs

must be evaluated separately within each region, particularly in the context of the specific ecosystems and

watersheds in which they operate; that is, hatcheries

must be considered part of the ecosystem in terms of

biomass inputs, biomass outputs, predation and competition effects of released fish, effluents, etc.

Moreover, each region has unique attributes (e.g.,

Seattle versus Olympic National Park) that precluded a single, generalized review.

We evaluated the benefits and risks of each hatchery program within each region relative to: (1) the

purpose and goals of the hatchery program where

goals focused primarily on harvest and conservation

but included other goals such as research, education

and outreach, and social/cultural needs of the western

Washington tribes; (2) the biological significance of

every hatchery and natural stock within the region

relative to other conspecific stocks (see Box 1); (3)

the population viability of every hatchery and natural stock (see Box 2); and (4) the current and

predicted future status of the habitats on which each

stock depends. In addition, salmon biologists and

fishery managers, representing state and federal agencies and many tribes, provided us with their

short-term (15 years) and long-term (50 years) goals

(or predictions) for the biological significance and

viability of each stock and the habitats on which

those stocks depend. Hence, our evaluations did not

simply consider current conditions but predicted,

future conditions as well. 

Our reviews produced over 1,000 program-specific

recommendations and 18 system-wide recommendations for Puget Sound and coastal Washington (Table

1). We are now entering an implementation phase.

For example, our reviews led to an $8 million appropriation by the state legislature in FY2005 to initiate

implementation of our recommendations.

Additional funds will be needed in future years, and

ultimately some level of prioritization will be necessary. To assist with prioritizing and implementing our

recommendations, we have established three principles of hatchery reform as guidelines.

Three Principles of Hatchery

Reform

Principle 1: Every hatchery program must have

well-defined goals in terms of desired benefits and

purpose. 

Well-defined goals provide both targets and

measures for success. During our reviews, the goals

for many hatchery programs were often not stated

clearly or understood by the biologists and managers responsible for the program. For example, the

number of juvenile fish released annually was often

cited as the goal of a hatchery program. In contrast,

we believe the goals for each hatchery program

must reflect its intended purpose and desired benefits. The two primary benefits of hatcheries are

harvest and conservation, but benefits can include

research and education. Wherever possible, goals

should be quantified. 

Hatcheries should operate as part of an integrated

strategy that includes short-term and long-term goals

for habitat and harvest. Goals should be related to

measures of success, including: (a) the desired number of hatchery-origin fish to be harvested each year

so that constraints on the size of the hatchery program can be established, (b) the number of fish

returning to a hatchery or spawning naturally in a

Figure 1. Ten regions in Puget Sound and coastal Washington are shown with locations

of state Washington Department of Fish and Wildlife, federal U.S. Fish and Wildlife,

and Tribal hatcheries. 
June 2005 | www.fisheries.org | Fisheries 13

Each population or stock was assigned a total score ranging from 3 to 14 according to the following scoring system. 

Note that either question 3 or 4 would be answered for a natural or hatchery population, respectively.

4) What is the estimated genetic effective size (Ne) of the population or stock? (possible scores = 1-5)

a) Ne > 5,000. Score = 5.

b) 2,500 < Ne < 5,000. Score = 4.

c) 500 < Ne < 2,500. Score = 3.

d) 100 < Ne < 500. Score = 2.

e) Ne < 100. Score = 1.

5) What is the mean number of recruits per spawner R/S over the preceding 10 years? (possible scores = 1-5)

a) R/S > 5. Score = 5.

b) 3 < R/S < 5. Score = 4.

c) 2 < R/S < 3. Score = 3.

d) 1 < R/S < 2. Score = 2.

e) R/S < 1. Score = 1.

6) For natural populations only, what proportion of natural spawners is composed of hatchery-origin adults?

a) < 1%. Score = 4.

b) 1–5%. Score = 3.

c) 5–30%.Score = 2.

d) >30%. Score = 1.

7) For hatchery populations only, what proportion of eggs, fry, juveniles, or adults are derived from another hatchery, watershed, or 

natural-origin fish?

a) < 1%. Score = 4.

b) 1–5%. Score = 3.

c) 5–30%.Score = 2.

d) >30%. Score = 1.

Sum of scores and ratings to assess the viability of a population or stock:

11–14: Population viability = High.

7–10: Population viability = Medium.

3–6: Population viability = Low.

Each population or stock was assigned a total score ranging from 5 to 17 according to the following scoring system.

1) What is the genetic origin of the population or stock? (possible scores = 1–5)

a) Native population. Score = 5.

b) Genetically admixed population between native and introduced populations.

i) > 50% native genes? Score = 4.

ii) < 50% native genes? Score = 3.

c) Reintroduced population: species occurred historically in watershed, was extirpated, but stock transfers re-established species in watershed. 

Score = 2.

d) Introduced population: species was historically absent from watershed. Score = 1.

2) How unique are the biological characters (e.g., life history, physiology, morphology, behavior, disease resistance, etc.) of the stock 

and to what extent are they considered irreplaceable attributes? (possible scores = 1–5)

a) Population has unique, irreplaceable biological attributes that are not shared with other stocks/populations within the same Genetic Diversity.

Unit (GDU)1 or with other GDUs within western Washington. Score = 5.

b) Population has no unique biological attributes, but shares some unique attributes with other stocks/populations within the GDU not shared 

with other GDUs. Score = 3.

c) Population has no unique biological attributes that are not shared with other stocks/populations in other GDUs. Score = 1.

3) To what extent is the population or stock part of a larger subdivided population structure or metapopulation? (possible scores = 3–7)

a) Number of distinct spawning aggregations (e.g. tributaries) within the stock or population under consideration

i) Number of spawning aggregations < 5. Score =2.

ii) Number of spawning aggregations > 5. Score = 1.

b) Total number of populations or stocks within the GDU.

i) Number of populations/stocks within GDU < 3. Score = 2.

ii) Number of populations/stocks within GDU > 3. Score =1.

c) What is the viability of other populations or stocks within the same GDU (see Box 2)?

i) Mean viability = "high.".= Score = 1.

ii) Mean viability = "medium." Score = 2.

iii) Mean viability = "low." Score = 3.

Sum of scores and ratings to assess the biological significance of a population or stock:

14-17: Biological significance = High.

9-13: Biological significance = Medium.

5-8: Biological significance = Low.

1 The Washington Department of Fish and Wildlife defines a GDU as follows: A genetic diversity unit (GDU) is a group of genetically similar stocks that is genetically distinct from other groups. The 

Stocks typically exhibit similar life histories and occupy ecologically, geographically, and geologically similar habitats. A GDU may consist of a single stock ( Busack and Shaklee 1995).

Box 2. Criteria for assessing the viability of a natural or hatchery population (or stock) within the Puget Sound and coastal regions of Washington state.

Box 1. Criteria for assessing the biological significance of a natural or hatchery population (or stock) within the Puget Sound and coastal regions of

Washington state.
Table 1. Principles for

hatchery management

and system-wide

recommendations

developed by the

Hatchery Scientific Review

Group. fisheries management

feature

14 Fisheries | www.fisheries.org | vol 30 no 6

watershed (i.e., escapement), (c) the expected results

of scientific research, and (d) the educational benefits to be derived from outreach. 

Principle 2: Hatchery programs must be scientifically defensible. 

Hatchery programs and operations must be consistent with stated goals, and they must be defensible

scientifically. Hatchery programs are often not consistent with goals or the best available scientific

information (e.g., Campton 2004). Once the goals

for a program are established, the scientific rationale

for the design and operation of the program must be

explicitly stated and understood by all personnel.

These requirements may necessitate a written, comprehensive management plan for every hatchery

program. Scientific oversight and peer review should

be integral components of every hatchery program.

Every hatchery program provides research

opportunities. Indeed, one of the recognized benefits of salmon hatcheries is the opportunity to

advance scientific knowledge. For example, every

hatchery program creates research opportunities

related to the effects of culture on the biology of the

propagated species and the effects of the released

species on aquatic ecosystems. Partnerships

between hatchery staffs and scientists should be

encouraged. These research opportunities should

be exploited wherever possible.

Every hatchery program needs to have operational

guidelines and standard operating procedures (e.g.,

selection of adults for broodstock, spawning protocols, feeding protocols, etc.) that are scientifically

defensible. These guidelines should include decisionmaking pathways for dealing with unexpected

contingencies.

Principle 3: Hatchery programs must respond

adaptively to new information.

Measuring Success and Accountability.

Scientific monitoring and evaluation (M&E) of

hatchery programs needs to be expanded to determine whether hatcheries are achieving their goals. If

conservation is the goal, a major effort should be

made to obtain a census of marked hatchery fish

spawning with their natural counterparts and to estimate the impact of hatchery fish on the fitness of the

natural component. If harvest is a goal, the focus

should be on the contribution of hatchery-origin fish

to fisheries and the potential impacts of hatchery fish

on natural spawners. M&E should assess smolt-toadult survival, return rates of adults, contribution of

adults to harvest and natural spawning, the proportion of naturally-spawning fish composed of

hatchery-origin adults, stray rates of adults to nontarget watersheds, and life history traits related to

fitness. Where possible, M&E should include assessments of genetic and ecological interactions (e.g.,

interbreeding, competition, predation, and reproductive success) between hatchery- and natural-origin

fish. Biologists should also monitor life history, morphological, and other traits related to fitness because

of the potential domestication effects of hatcheries.

Most importantly, centralized and standardized

databases need to be developed for collating, storing,

and retrieving data. Results need to be evaluated

annually to allow programmatic adjustments.

In most cases, the existing hatchery staff may not

necessarily have the expertise to also serve as M&E

biologists. Hence, a hatchery evaluation team,

including perhaps the manager of each facility, may

need to be developed for a particular region. Indeed,

biologists responsible for collecting and analyzing

1) Well-defined goals: 

• Set goals for all stocks and manage hatchery programs on a regional scale

• Measure success in terms of contribution to harvest, conservation, and other goals

• Have clear goals for educational programs

2) Scientific Defensibility: 

• Operate hatchery programs within the context of their ecosystems

• Operate hatchery programs as either genetically integrated or segregated relative to 

naturally-spawning populations

• Size hatchery programs consistent with stock goals

• Consider both freshwater and marine carrying capacity in sizing hatchery programs

• Ensure productive habitat for hatchery programs

• Emphasize quality, not quantity, in fish releases

• Use in-basin rearing and locally-adapted broodstocks

• Select adults randomly throughout the natural period of adult return

• Use genetically-benign spawning protocols that maximize effective population size and minimize 

potential artificial or domestication selection under hatchery conditions.

• Reduce risks associated with outplanting and net pen releases

• Develop a system of wild steelhead management zones (a special case)

• Use hatchery salmon carcasses for nutrification of freshwater ecosystems, while reducing associated fish 

health risks

3) Informed Decision Making: 

• Adaptively manage hatchery programs

• Incorporate flexibility into hatchery design and operation

• Evaluate hatchery programs regularly to ensure accountability for success
data, including the generation of annual reports and

publications, should be considered an integral component of every hatchery, equal in importance to

fish health specialists who monitor pathogenic loads

and help reduce the risk of disease outbreaks.

However, it should be recognized that the statistical

power to detect undesirable effects, particularly on

fitness-related traits, may be very low, so the absence

of a detectable effect should not be used as a justification to violate a scientifically-defensible guideline

(e.g., as described by Campton 2004). In this context, policies and operational guidelines need to be

established and followed accordingly. Moreover,

those policies and guidelines need to be subject to

change in response to new information generated

from M&E activities.

Adaptive Management. Hatcheries need to be

flexible and managed adaptively. Many scientific

uncertainties are associated with salmon

hatcheries. Hatchery programs and facilities must

respond to new goals, new scientific information,

and changes in the status of natural stocks and

habitat. A structured adaptive management program is necessary for the success of hatcheries.

Institutional resistance to programmatic flexibility

and change needs to be overcome.

We should also note that the three basic principles of hatchery reform are equally applicable to all

hatchery programs regardless of whether the purpose

of the program is to provide fish for harvest, to assist

with conservation of natural populations and their

indigenous genetic resources (e.g. Flagg et al. 2004),

or both (e.g., Olson et al. 2004). The

details of an individual program will be

case-specific for both harvest-oriented

and conservation-oriented programs,

but the underlying principles and operational guidelines will be similar.

However, conservation hatchery programs designed to prevent extirpation

of an imperiled population do present

some special challenges, and those

challenges and special considerations

are described in detail elsewhere (Flagg

et al. 2004).

Emerging Issues 

and Concepts

A number of key issues emerged

during our review process. Here, we

summarize our conclusions and recommendations for some of those key

issues. More detailed analyses and

descriptions are available at

www.hatcheryreform.org. 

Genetic Integration vs. Segregation

of Hatchery Broodstocks Relative to

Natural Populations.

Adult spawners for broodstock are

usually obtained from returnees back to

a hatchery or from trapped adults diverted by a barrier weir. Whether such adults are of natural- or

hatchery-origin was usually unknown. In short,

hatcheries have historically had no formal genetic

management plan or strategy for their component

broodstocks.

Consequently, the first step towards “hatchery

reform” is to develop a detailed genetic management

plan or strategy for every hatchery broodstock.

Managers have two options: (1) manage a hatchery

broodstock as a reproductively distinct population

that is genetically segregated from naturally spawning

populations, or (2) manage a hatchery broodstock as

a genetically integrated component of an existing

natural population (Figures 2,3). Each of these

broodstock strategies leads directly to a different set

of operational guidelines. Genetically segregated

broodstocks are generally derived strictly from hatchery-origin adults returning to the hatchery each year.

Conversely, genetically integrated broodstocks systematically include a prescribed proportion of

natural-origin fish in the broodstock each year to

maintain genetic integration with a natural population. One goal of integrated hatchery programs is to

minimize the genetic effects of domestication by

allowing selection pressures in the natural environment to drive the genetic constitution of

hatchery-origin fish and the mean fitness of the population as a whole. In contrast, segregated hatchery

programs create a genetically distinct, hatcheryadapted population. 

Figure 3. Schematic diagram of a

genetically segregated program. The

segregated approach treats hatchery fish as

a distinct population or isolated gene pool.

Natural spawning by hatchery-origin fish (ps

> 0) from a genetically-segregated program

can pose a high risk to natural populations if

those hatchery-origin fish are able to

reproduce successfully.

featurefisheriess management

June 2005 | www.fisheries.org | Fisheries 15

Figure 2. Schematic diagram of a

genetically integrated hatchery program.

The integrated approach treats hatchery and

natural-origin fish as two components of a

common gene pool, where pb is the

proportion of the hatchery broodstock

composed of natural-origin fish, and ps is

the proportion of natural spawners in the

watershed composed of hatchery-origin fish.

Natural spawning by hatchery-origin fish

from a properly integrated program (pb >

ps) presents a lower genetic risk than

segregated programs (pb = 0) for the same

value of ps

. For many hatcheries and

geographic locations, the value of ps cannot

be directly controlled, and the mean value

of ps may thus be a deciding factor for

determining whether a segregated or

integrated program is most appropriate for

a particular facility and geographic location

where fish are released. Regardless of

program type, ps should be minimized.
fisheries management

feature

16 Fisheries | www.fisheries.org | vol 30 no 6

The goals of genetic integration can be achieved

only if the rate of gene flow from the natural environment to the hatchery environment exceeds the

reverse rate of gene flow (e.g., Ford 2002). These

gene flow parameters are difficult to estimate

directly but can be approximated by the proportion

of the hatchery broodstock composed of natural-origin fish (pb) and by the proportion of natural

spawners in the watershed composed of hatcheryorigin fish (ps

), with the goal pb > ps (Figure 2). The

mean fitness (f) of an integrated population in the

natural environment, relative to a natural population by itself, will largely be determined by the

relationship f = pb /(pb + ps

) (Lynch and O’Hely

2001; Ford 2002). The parameter f also equals the

proportion of time that genes are transmitted from

parents to offspring in the natural environment versus the hatchery environment. At a minimum, we

recommend pb > 0.1 for integrated programs to help

overcome the effects of genetic drift and unknown

amounts of domestication selection in the hatchery

environment, even when ps may be near zero (see

Ford 2002). In most cases, ps will not equal zero

because of logistic difficulties controlling the natural spawning of hatchery-origin adults.

Consequently, one major motivation

for an integrated hatchery program is

to substantially reduce the genetic

risks of hatchery-fish spawning naturally relative to genetic and ecological

risks imposed by hatchery-origin fish

from a genetically segregated broodstock. We are currently developing

mathematical models to address these

concepts further.

An integrated hatchery program

requires, as a long-term goal, a self-sustaining, naturally-spawning population

capable of providing adult fish for

broodstock each year. Integration thus

requires suitable natural habitat capable of sustaining a natural population.

Under this strategy, an integrated

hatchery does not replace habitat but

adds to existing habitat. An implicit

goal of an integrated program is to

demographically increase the abundance of a natural population while

minimizing the genetic effects of artificial propagation. This demographic

increase in abundance could simply be

for the purpose of supporting harvest

while minimizing genetic risks to natural populations or it could reflect a

conservation component of the program itself. Thus, integrated programs

can have both harvest and conservation goals (e.g., Olson et al. 2004).

However, the size of an integrated

hatchery program will necessarily be

limited by the habitat available to the natural populations with which it is integrated and by the ability

of the hatchery program to restrain natural spawning

by hatchery-origin adults. 

Segregated hatchery populations will diverge

genetically from naturally spawning populations

over time because of founder effects, genetic drift,

and domestication selection in the hatchery environment. Such changes may be intentional (e.g., via

selective breeding) to maximize benefits or the

operational efficiency of a hatchery program.

However, natural spawning by hatchery-origin fish

can have a significant genetic influence on natural

populations after several generations when ps

approaches 10% (Ford 2002); consequently, we recommend that hatchery-origin spawners from

genetically segregated programs represent < 5% of

the natural spawners as an upper-limit guideline

(Figure 3). Segregated programs are, thus, most

appropriate when harvest is the principal purpose of

the program and the probability of hatchery-origin

adults spawning naturally and reproducing successfully is very low. On the other hand, hatchery-origin

fish from a segregated broodstock could support a

conservation goal if fish were “outplanted” into

areas where a natural population was extirpated.

Hence, both integrated and segregated programs

can have both harvest and conservation goals

depending on the specific situation.

The development and management of genetically

integrated or segregated hatchery broodstocks clearly

requires a mechanism to distinguish natural and

hatchery-origin adult fish via intrinsic and extrinsic

marks and tags (e.g., otolith marks, DNA profiles,

coded-wire tags, fin marks, etc.). Such a distinction is

required during the selection of adults for broodstock

and for monitoring the potential genetic contribution of hatchery-origin fish to natural reproduction.

Moreover, this distinction is required also for monitoring harvest impacts on both hatchery-propagated

and natural populations. Hatchery reform cannot

occur independently of “harvest reform” and habitat

improvements. All three components must be managed together to achieve long-term and sustainable

conservation and harvest goals for Pacific salmon and

steelhead resources. 

During our HSRG reviews, the co-managers identified the intent of every hatchery program as either

integrated or segregated. The breakdown between

integrated and segregated programs identified by the

co-managers was 54% versus 46% respectively. They

also needed to identify the purpose of the program as

either harvest, conservation, research, and/or education. We then provided recommendations for

achieving those collective goals. In some cases, we

recommended that they change the intent of their

program from an integrated program to a segregated

program, or vice versa, if their intended strategy was

inconsistent with the capability of the habitat, stray

rates from the hatchery, or other factors beyond their

Hoodsport Hatchery is located within the

Hood Canal region of western

Washington. Hoodsport Hatchery

annually releases 15 million chum

salmon fry. The HSRG recommended

reducing the program size to avoid large

surpluses of unharvestable fish and to

minimize potential risks to natural-origin

chum salmon juveniles.

Issaquah Hatchery is located in the Lake

Washington drainage of western

Washington. The hatchery includes

extensive educational programs and

public access facilities serving the greater

Seattle area. 
feature

fisheriess management

immediate control. Simply establishing these hatchery broodstock strategies for each hatchery program

was a major step towards satisfying Principle 2 of

hatchery reform.

Marine Carrying Capacity

Trends in the carrying capacity of the marine environments must be considered for determining the

number of fish released from a hatchery. Until

recently, marine ecosystems were believed to be stable, internally regulated, and largely deterministic.

The current view is that these systems are dynamic

with much environmental stochasticity and ecological uncertainty (Mahnken et al. 1998; Francis 2002).

Based on earlier assumptions that marine carrying

capacity was unlimited or had not yet been reached,

the goal of increasing fisheries was pursued by building more hatcheries and releasing more fish. As a

result, the number of juvenile salmon released from

Pacific Northwest hatcheries increased substantially

after the early 1960s (Mahnken et al. 1998). Equally

large increases occurred in Japan and Alaska

(NPAFC 2003; Smoker and Heard in press).

However, during the same period, the mean length

and weight of returning adults decreased and their

mean age at maturity increased for most stocks of

Pacific salmon (Kaeriyama and Urawa 1992; Rogers

and Ruggerone 1993; Bigler et al. 1996). In general,

between the mid 1970s and the late 1990s, the

marine survival rates of the great majority of

Northeast Pacific salmon stocks north of 54o

40' N

increased rapidly while southern hatchery stocks

exhibited decreasing marine survival (Hilborn and

Eggers 2000; Wertheimer et al. 2001; Wertheimer et

al. 2004). Decreasing smolt-to-adult survivals of

southern North American hatchery stocks during the

late 1970s and late 1980s only motivated co-managers to release more hatchery fish to compensate for

reduced fisheries catch.

The ocean ecosystem in which Pacific salmon

reside is dynamic, changing seasonally and on longer

decadal scales. El Niños and the Pacific Decadal

Oscillation (PDO) are examples of short- and longterm oscillations in the ocean environment that can

affect Pacific salmon survival and abundance. At present, it will be difficult to manage Pacific salmon

hatcheries on time scales as short as the El Niño

owing to the unpredictability of onset of the event.

However, for decadal time scales on the order of the

PDO, it may be possible to modulate hatchery production to accommodate gradually changing ocean

productivity. Agencies need to engage in dialogue to

address managing hatchery production during these

longer, more predictable periods of natural oscillations in Pacific ecosystem productivity.

Smolt Quality 

The quality of hatchery-origin smolts has often

been described in terms of mean size, numbers, or

condition index of fish produced, and whether they

met a pre-determined time window for smoltification

and release. Fish size at release was used almost invariably as a surrogate for fish quality. Although the

scientific literature provides physiological, morphological, and behavioral definitions of a quality smolt,

those definitions were rarely used by hatchery personnel. Moreover, the biological relationship between

those measures and parameters associated with

returning adults (e.g., age class structure, mean size at

maturity, etc.) was rarely investigated. With the

advent of coded-wire tags, most studies to identify

relationships between smolt quality and adult returns

were aimed at manipulating the mean size and release

time of juveniles with the goal of maximizing smoltto-adult survivals. In addition, some researchers

investigated the role of nutrition (proximate composition, constituent quality, etc.) for maximizing adult

returns.

We now recognize that smolt quality includes

morphological, physiological, and behavioral characters that embody the rate and

completeness of the parr-smolt transformation. A quality smolt is defined as

a metamorphosed, anadromous

salmonid that exhibits rapid downstream migration, increased

hypo-osmoregulatory capability, sustained growth in the ocean, and high

survival to adulthood. Smolt quality is

not an absolute concept; it has to be

evaluated in the context of program

goals. If the primary goal is conservation, then an analysis of smolt quality

needs to consider how hatchery smolts

compare in life history traits to wild

fish. Mimicking the growth pattern,

size, and out-migration timing of natural fish has been shown to have the

potential to produce a higher quality

hatchery smolt with greater smolt-toadult survivals (Larsen et al. 2001;

Maynard et al. 2004).

As an operational guideline, we recommend

expanding the definition of smolt quality to include

additional physiological, morphological, and behavioral measurements taken throughout the culture

cycle. Examples include gill Na–K ATPase enzyme

activity, blood concentrations of thyroid hormones,

growth hormone, insulin, insulin-like growth factor,

and body lipid levels. Such an approach will require

increased physiological monitoring of juveniles prior

to release. One simple measure of physiological smolt

development is the rate of change in growth rate

June 2005 | www.fisheries.org | Fisheries 17

Research, funded by the

HSRG, is being conducted

at the Lilliwaup Hatchery

to evaluate release

strategies for steelhead

recovery in Hood Canal in

western Washington. 
fisheries management

feature

18 Fisheries | www.fisheries.org | vol 30 no 6

immediately preceding and during the parr-smolt

transformation (Beckman et al. 1996). Increasing the

accuracy of smolt quality indices may allow the number of smolts released to be reduced while achieving

the same number of returning adults.

Outplanting and Remote Releases. 

The vast majority of salmon hatcheries in the

Pacific Northwest operate largely as adult spawning

and juvenile rearing facilities. The standard method

of propagation is to release smolts into stream areas

where returning adults can be recaptured for broodstock. In practice, though, smolts are often released

from sites where adult collection facilities do not

exist, primarily to support fisheries in off-site areas. In

many situations, smolts are transported by hatchery

truck into other watersheds, sometimes over relatively large distances (e.g., >100 km) prior to release.

Adults generally return to areas where they were

released as smolts, not where they were reared. 

Releasing smolts into streams geographically

removed from a hatchery or adult collection facility,

primarily for the purpose of supporting fisheries in

specific streams or areas, is commonly called “outplanting.” Steelhead programs in Washington State

outplant smolts into a large number of small streams

to support recreational fisheries where no hatchery

facilities exist. Salmon smolts are also released

remotely from floating net pens in marine areas

where a targeted fishery on returning adults is

desired. Outplanting, as defined above, should not

be confused with supplementation which, in the

Pacific Northwest, refers specifically to the deliberate release of fish in areas where managers explicitly

desire returning adult fish to spawn and naturally

reproduce as a mechanism to increase the abundance

of natural-origin adults one generation later. In general, natural spawning of hatchery-origin fish is not a

goal of “outplanting.”

A common feature of outplanting and net pen

programs is the absence of facilities to trap returning

adults that escape target fisheries. Non-harvested

adults can then spawn in streams far-removed from

the source hatchery or geographic location where

their parents were trapped for broodstock (e.g.,

Pascual and Quinn 1994). Moreover, stray rates of

fish released off-station are generally greater than

those of fish released directly from hatcheries

(Quinn 1993). Indeed, tagging and genetic studies

have shown that outplanting and net pen programs

promote stray rates that far exceed natural levels

(Candy and Beacham 2000; Mackey et al. 2001).

Many studies have further indicated a genetic component to homing such that non-native fish and

their progeny stray at higher rates than identicallyreared native fish (Bams 1976; McIsaac and Quinn

1988; Pascual et al. 1995; but see Smoker and

Thrower 1995; Gilk et al. 2004). We concluded that

outplanting and net pen releases pose significant,

and potentially unacceptable, genetic risks to natural

populations and recommended several measures to

reduce risks associated with outplanting (HSRG

2004). These recommendations include reductions

in the number of fish released from saltwater net

pens, removal of all or nearly all hatchery returnees

in concentrated fisheries, the construction of juvenile acclimation and adult recapture facilities, and

the potential establishment of wild salmon and steelhead management zones. 

Predation on Natural-Origin

Salmonids. 

Concern is often expressed about the potential for

hatchery-reared salmon and steelhead to prey on natural-origin juvenile Pacific salmonids, particularly

regarding the impact of predation on threatened or

endangered populations (Lichatowich 1999; Levin et

al. 2001; see also Sholes and Hallock 1979;

Beauchamp 1990; Hawkins and Tipping 1999 for the

potential of predation). Predation on natural-origin

fish is most likely in the freshwater environment,

where potential salmonid predators are concentrated

and exposed to large numbers of prey in a relatively

small area. There is little evidence that natural-origin

salmonids are preyed on by hatchery-reared

salmonids in estuarine, nearshore, or offshore marine

environments. However, estimation of the overall

predation risk to natural-origin salmonids from

hatchery-reared salmonids is complicated because

such risks depend on the pisciverous nature of an

individual stock and on a number of stochastic factors

including migration rates, stream conditions, and

spatial and temporal overlap between hatchery- and

natural- origin fish.

There is evidence that salmonids are able to prey

on fish up to approximately 50% of their body length

(e.g., Damsgard 1995; Pearsons and Fritts 1999;

Finstad et al. 2001). However, Keeley and Grant

(2001) estimated that the mean prey size for 100–200

mm salmonids feeding on fish in streams is normally

13–15% of predator body size. The relative sizes of

downstream-migrating smolts or fry of different

species of salmonids in Washington suggest that several possible predator/prey combinations are likely to

occur (Figure 4). Natural-origin pink (O. gorbuscha)

and chum salmon (O. keta) and ocean-type (i.e., that

smolt as subyearling) Chinook salmon (O.

tshawytscha) are most likely to be preyed upon by

hatchery-reared salmonids in Washington. Hatcheryreared chum, pink, sockeye (O. nerka), and

ocean-type Chinook salmon are unlikely to prey on

wild salmonids due to their relatively small size at

release and/or their non-piscivorous feeding habits.

Yearling coho (O. kisutch), stream-type (i.e., that

smolt as yearlings) Chinook salmon, and steelhead

smolts have the greatest likelihood of preying on wild

salmonid fry due to their large relative size at release.

Smolts that remain (residualize) in rivers for months

or years after release may represent an important predation risk to wild salmon populations.
Hatchery managers have numerous production

tools that can minimize predation risk of migratory

hatchery fish with their natural-origin counterparts.

For example, design of rearing and release protocols

allow the hatchery manager the option of producing

fully-developed, highly-migratory smolts that rapidly

migrate to the marine environment. The relative vulnerability of wild juvenile salmonids to predation in

freshwater may depend on the release location of

hatchery fish. Hatchery managers will need to conduct case-by-case determinations of predation risk

that may require specific research on spatial and temporal overlap of hatchery-reared and wild fish,

estimation of specific predation rates, and modeling

to determine the potential population effects on wild

salmonid populations.

Stream Nutrification and Fish Health

Returning adult salmon transfer marine nutrients

into terrestrial and freshwater ecosystems, contributing significantly to primary production, riparian

vegetation, and even old-growth forests (Kline et al.

1990; Bilby et al. 1996). Those nutrients also contribute significantly to the food sources of juvenile

salmonids. For example, in one study, up to 60% of

the fixed nitrogen in benthic insects was derived from

salmon carcasses (Johnston et al. 1997). Those latter

investigators also found that juvenile salmon have

higher growth rates in streams where adult salmon

spawn than in streams without spawning adults.

Hatchery-origin salmon carcasses also increased the

density of age 0+ coho salmon and age 0+ and 1+

steelhead in small streams in southwestern

Washington (Bilby et al. 1998). Distributing spawned

out salmon carcasses from hatcheries into watersheds

can thus confer a positive ecological benefit to stream

nutrification and naturally spawning populations. 

However, spawned-out salmon carcasses from

hatcheries can pose a fish health risk to natural populations if the carcasses are not properly treated or

inspected prior to distribution. Pathogenic organisms

present in salmon carcasses can be transmitted to other

salmonids either through

release of those organisms into water or

through their direct consumption. It is well

established, for example,

that bacterial and viral

pathogens of salmonids

can be transmitted via

water or the oral route,

and, in the laboratory,

challenges by both

routes have been used in

various studies for establishing infections with a

number of microbial fish

pathogens (see, for

example, Evelyn 1996

for various bacterial fish diseases and Helmick et al.

1995 for infectious hematopoietic necrosis virus infections). In addition, the shedding of bacteria and

viruses responsible for these diseases from infected fish

has been well documented (see, for example, Mulcahy

et al. 1983 and Zhang and Congleton 1994 for infectious hematopoietic necrosis; McKibben and Pascho

1999 for bacterial kidney disease; Rose et al. 1989 and

Perez et al. 1996 for furunculosis; Madetoja et al. 2002

for bacterial coldwater disease). Such horizontal transmission is enhanced in hatcheries. Adult salmon

trapped for hatchery broodstock are typically held in

crowded ponds or raceways for days or weeks prior to

spawning, potentially exacerbating the prevalence

and transmission of pathogenic organisms among

hatchery-spawned adults. In many of those fish, the

infectious load can be expected to approach the loads

found in fish dying of various infections. In such fish,

the infectious load of bacterial cells or virus particles

can reach titers of 103 to 109 infectious units per gram

of tissue, depending on the tissue (see Evelyn 2001).

Consequently, every effort should be made to ensure

that hatchery-origin carcasses intended for use in

stream nutrification projects undergo some form of

post-spawning treatment to minimize the disease risks

to natural populations (e.g., deep freezing of the carcasses at –20O C, which kills certain fish pathogens or

preferably processing of the carcasses into pellets, such

as those studied by Wipfli et al. (2004) would almost

certainly be pathogen-free). Failing that, pathogen-free

certification of the carcasses prior to distribution for

stream nutrification projects would be strongly recommended.

Conclusions

Salmon hatcheries have been a major source of

controversy in the Pacific Northwest for over 30

years (Lichatowich 1999; Brannon et al. 2004).

Several panels of scientists have been assembled in

the past to identify and evaluate the biological risks

posed by hatcheries on anadromous salmonid

resources (e.g., IHOT 1994; NRC 1996; Brannon et

June 2005 | www.fisheries.org | Fisheries 19

Figure 4. Relative sizes of

hatchery-reared salmonid

predators (at release) and

their potential migratory

salmonid prey in

Washington, assuming

that predators may

consume fish up to 50%

of their body size. feature

fisheriess management
20 Fisheries | www.fisheries.org | vol 30 no 6

al. 1999; ISAB 2002). Virtually all of those previous assessments

have focused on the problems and risks posed by hatcheries.

However, few of those assessments were tasked with developing

scientifically-defensible solutions to the problems they identified.

The HSRG was mandated by Congress to identify potential

solutions to widely-recognized problems to ensure that hatcheries

contribute to supporting sustainable fisheries while supporting conservation, restoration, and recovery of natural populations. A

significant portion of the Puget Sound area is urbanized, and

hatcheries provide an essential component to the commercial,

tribal, and recreational fisheries of the region. In addition, major

habitat restoration programs are in place, or are planned, thus providing significantly improved opportunities for naturally spawning

populations in the future.

We focused our review efforts during the past four years on identifying scientific uncertainties and proposing solutions based on

the best available science. The need to develop broodstock genetic

management plans for every hatchery program with the goal of

managing each broodstock as either a genetically-segregated

“hatchery population” or as a genetically-integrated component of

an existing “natural population” became a fundamental foundation for our recommendations. Both strategies require the ability

to distinguish hatchery- and natural-origin adults, both in the

hatchery when adults are spawned for broodstock and on the natural spawning grounds, to assess the genetic risks and gene flow

rates of hatchery-origin fish to natural populations.

Commensurate with these reforms is the need for increased monitoring and evaluation, scientific oversight, and accountability of

hatchery operations. In many cases, these reforms will require

additional funding by the management agencies, but this investment should be considered a cost of operating hatcheries to ensure

benefits are achieved and risks controlled. Ultimately, the success

or failure of a hatchery program may be measured by the relative

benefits and risks it confers. Although it is beyond the scope of

this article to deal with benefit-risk analyses of hatchery operations, readers should consult other essays on this topic as a

complement to our presentation here (Busack and Currens 1995;

Currens and Busack 2004; Waples and Drake 2004). 

Unless all habitat has been irrevocably lost to a dam or other

impassible barrier, hatcheries should not be regarded as surrogates or

substitutes for lost habitat. Hatcheries need to operate in scientifically-defensible modes with well-defined goals and substantially

increased data collection and evaluation. Hatcheries also need to be

flexible and adaptable; that is, they need to operate and be evaluated in the context of both the ecosystem (watersheds) in which

the hatcheries occur and other ecosystems and ecological processes

on which hatchery-origin fish depend.

Scientific uncertainties associated with hatchery operations are

numerous. The science to manage these risks is still inadequate, and

some of the risks are still poorly understood (e.g., Currens and

Busack 2004). However, one point is clear. Maintaining healthy

habitat is critical not only for viable, self-sustaining natural populations, but also to adequately control risks of hatchery programs and

realize the benefits of hatcheries to recover populations and sustain

healthy harvests in increasingly populated environments.

Moreover, the principles and emerging issues we describe here are

not only applicable to hatcheries for Pacific salmon and steelhead

in western Washington state, they also have direct application to

other regions of the Pacific Northwest and to artificial propagation

programs for other species worldwide. 

Acknowledgements

Funding for this project was provided by the Western

Washington Hatchery Reform Project, administered by the U.S.

Fish and Wildlife Service through the Washington State

Interagency Commission for Outdoor Recreation. We are

indebted to the numerous fishery biologists and managers

throughout Puget Sound and western Washington from the

Washington Department of Fish and Wildlife, numerous Native

American tribes, Northwest Indian Fisheries Commission, U.S.

Fish and Wildlife Service, and NOAA Fisheries, who unselfishly

shared their knowledge and expertise with us and contributed to

our thinking on hatchery issues. The foundation for Boxes 1 and

2 was based on a manuscript entitled “Benefit-Risk Assessment

Framework for Washington Department of Fish and Wildlife

Artificial Propagation Programs” written by the Washington

Department of Fish and Wildlife. We thank Bob Piper, retired

member of the HSRG for his assistance and technical insights,

and Robin Waples, NOAA Fisheries; Tom Quinn, University of

Washington; and five anonymous reviewers for their thoughtful

comments on the manuscript. We are indebted to the excellent

facilitation provided by Long Live the Kings and Gordon,

Thomas, Honeywell, particularly the contributions of Michael

Kern, Kathy Hopper, Betsy Daniels, Barbara Cairns, Michael

Schmidt, “B. J.” Mirk, and Jim Waldo. We also thank the

Hatchery Reform Coordinating Committee, representing the

needs of the co-managers and Tribes, for their perspectives and

policy insights. This manuscript is dedicated to the memory of

Steve Phelps who helped shape the vision of hatchery reform in

Western Washington.
References

Bams, R. A. 1976. Survival and propensity for homing as affected by

presence or absence of locally adapted paternal genes in two

transplanted populations of pink salmon (Oncorhynchus gorbuscha).

Journal of Fisheries Research Board of Canada 33:2716-2725.

Beauchamp, D. A. 1990. Seasonal and diel food habitats of rainbow

trout stocked as juveniles in Lake Washington. Transactions of the

American Fisheries Society 119:475-482.

Beckman, B. R., D. A. Larsen, B. Lee-Pawlak, and W. W. Dickhoff.

1996. Physiological assessment and behavior interaction of wild and

hatchery juvenile salmonids: the relationship of fish size and growth

to smoltification in spring Chinook salmon. Bonneville Power

Administration Report, Portland, OR, October 1996.

Bigler, S. B., D. W. Welch, and J. H. Helle. 1996. A review of size

trends among north Pacific salmon (Oncorhynchus spp.). Canadian

Journal of Fisheries and Aquatic Sciences 53:455-465.

Bilby, R. E., B. R. Fransen, and P. A. Bisson. 1996. Incorporation of

nitrogen and carbon from spawning coho salmon into the trophic

system of small streams: evidence from stable isotopes. Canadian

Journal of Fisheries and Aquatic Sciences 53:164-173.

Bilby, R. E., B. R. Fransen, P. A. Bisson, and J. K. Walter. 1998.

Response of juvenile coho salmon (Oncorhynchus kisutch) and

steelhead (Oncorhynchus mykiss) to the addition of salmon carcasses

to two streams in southwestern Washington, U.S.A. Canadian

Journal of Fisheries and Aquatic Sciences 55: 1909-1918.

Blankenship, H. L., and E. Daniels. 2004. A scientific and systematic

redesign of Washington state salmonid hatcheries. Pages 561-572 in

M. Nickum, P. Mazik, J. Nickum, and D. MacKinlay, eds.

Propagated fish in resource management. American Fisheries

Society Symposium 44, Bethesda, Maryland.

Blankenship, H. L., and M. A. Kern. 2004. An independent scientific

evaluation of Washington State salmonid hatcheries. Pages 133-141

in K. M. Leber, S. Kitada,T. Svasand, H. L. Blankenship, and T.

Svasand, eds. Stock enhancement and sea ranching 2. Blackwell

Science Ltd, Oxford, UK.

Brannon, E. L., D. F. Amend, M. A Cronin, J. E. Lannan, S.

LaPatra, W. J. McNeil, R. E. Noble, C. E. Smith, A. J. Talbot, G.

A. Wedemeyer, and H. Westers. 2004. The controversy about

salmon hatcheries. Fisheries 29(9):12-31.

Brannon, E. L., K. P. Currens, D. Goodman, J. A. Lichatowich, B.

E. Riddell, and R. N. Williams; W. E. McConnaha, chair. 1999.

Review of artificial anadromous and resident fish in the Columbia

River basin. Part I: A scientific basis for Columbia River production

programs. Northwest Power Planning Council Document 99-4.

Scientific Review Team, Independent Scientific Advisory Board,

Bonneville Power Administration, Portland, OR.

Busack, C. A., and K. P. Currens. 1995. Genetic risks and hazards in

hatchery operations: fundamental concepts and issues. American

Fisheries Society Symposium 15:71-80.

Busack, C. A., and J. B. Shaklee, editors. 1995. Genetic diversity

units and major ancestral lineages of salmonid fishes in Washington.

Fish Management Program, Resource Assessment Division,

Washington State Department of Fish and Wildlife, Technical

Report Number RAD 95-02, Olympia.

Campton, D. E. 1995. Genetic effects of hatchery fish on wild

populations of Pacific salmon and steelhead: what do we really

know? American Fisheries Society Symposium 15:337-353.

________. 2004. Sperm competition in salmon hatcheries: the need to

institutionalize genetically benign spawning protocols. Transactions

of the American Fisheries Society 133:1277-1289.

Candy, J. R., and T. D. Beacham. 2000. Patterns of homing and

straying in southern British Columbia coded-wire tagged Chinook

salmon (Oncorhynchus tshawytscha) populations. Fisheries Research

47:41-56.

Currens, K. P., and C. A. Busack. 2004. Practical approaches for

assessing risks of hatchery programs. Pages 277-290 in M. Nickum,

P. Mazik, J. Nickum, and D. MacKinlay, eds. Propagated fish in

June 2005 | www.fisheries.org | Fisheries 21
22 Fisheries | www.fisheries.org | vol 30 no 6

resource management. American Fisheries Society Symposium 44,

Bethesda, Maryland.

Damsgard, B. 1995. Arctic charr, Salvelinus alpinus (L.), as prey for

piscivorous fish—a model to predict prey vulnerabilities and prey

size refuges. Nordic Journal Freshwater Research 71:190-196.

Evelyn, T. P. T. 2001. The effect of chilling, freezing and cold-smoking

on the infectious titre of certain microbial fish pathogens that may

occasionally be present in marketed salmonid flesh. Pages 215-229

in C.J. Rogers, ed. Risk analysis in aquatic animal health.

Proceedings of an international conference held in Paris, France, 8-

10 February 2000. World Organisation for Animal Health (Office

International des Epizooties), Paris, France.

_____. 1996. Infection and disease. Pages 339-366 in G. Iwama and T.

Nakanishi, eds. The fish immune system—organism, pathogen, and

environment. Academic Press, San Diego.

Finstad, A.G., P. A. Jansen, and A. Langeland. 2001. Production and

predation rates in a cannibalistic Arctic char (Salvelinus alpinus L.)

population. Ecology of Freshwater Fish 10:220-226.

Flagg, T. A., C. V. W. Mahnken, and R. N. Iwamoto. 2004.

Conservation hatchery protocols for Pacific Salmon. Pages 603-619

in M. Nickum, P. Mazik, J. Nickum, and D. MacKinlay, eds.

Propagated fish in resource management. American Fisheries

Society Symposium 44, Bethesda, Maryland.

Ford, M. J. 2002. Selection in captivity during supportive breeding may

reduce fitness in the wild. Conservation Biology 16:815-825.

Francis, R. C. 2002. Some thoughts on sustainability and marine

conservation. Fisheries 27(1):18-22.

Gilk, S. E., I. A.Wang, C. L. Hoover, W. W. Smoker, S. G. Taylor,

A. K. Gray, and A. J. Gharrett. 2004. Outbreeding depression in

hybrids between spatially separated pink salmon, Oncorhynchus

gorbuscha, populations: marine survival, homing ability, and

variability in family size. Environmental Biology of Fishes

69:287-297.

Hawkins, R. S., and J. M. Tipping. 1999. Predation by juvenile

hatchery salmonids on wild fall Chinook salmon fry in the Lewis

River, Washington. California Fish and Game 85(3):124-129.

Hedrick, P. W., D. Hedgecock, S. Hamelberg, and S. J. Croci. 2000.

The impact of supplementation in winter-run Chinook salmon on

effective population size. Journal of Heredity 91:112-116. 

Helmick, C. M., J. F. Bailey, S. LaPatra, and S. Risto. 1995. The

esophagus/cardiac stomach region: site of attachment and

internalization of infectious hematopoietic necrosis virus in

challenged juvenile rainbow trout Onchorynchus mykiss and coho

salmon O. kisutch. Diseases of Aquatic Organisms 23:189-199.

Hilborn, R. 1992. Hatcheries and the future of salmon in the

Northwest. Fisheries 17(1):5-8.

Hilborn, R., and D. Eggers. 2000. A review of the hatchery programs

for pink salmon in Prince William Sound and Kodiak Island,

Alaska. Transactions of the American Fisheries Society

129:333-350.

HSRG (Hatchery Scientific Review Group: L. Mobrand, J. Barr, L.

Blankenship, D. Campton, T. Evelyn, T. Flagg, C. Mahnken, R.

Piper, P. Seidel, L. Seeb, and B. Smoker). 2004. Hatchery reform:

principles and recommendations of the HSRG. Long Live the

Kings, WA. Retrieved from www.hatcheryreform.org, November

2004.

IHOT (Integrated Hatchery Operations Team). 1994. Policies and

procedures for Columbia Basin anadromous salmonid hatcheries.

Bonneville Power Administration DOE/BP-2432. Portland,

Oregon.

ISAB (Independent Scientific Advisory Board). 2002. Hatchery

surpluses in the Pacific Northwest. Fisheries 27(12):16-27. 

Johnston, N. T., J. S. Macdonald, K. J. Hall, and P. J. Tschaplinski.

1997. A preliminary study of the role of sockeye salmon

(Oncorhynchus nerka) carcasses as carbon and nitrogen sources for

benthic insects and fishes in the ‘Early Stuart’ stock spawning

streams, 1050 km from the ocean. Fisheries Project Report RD55,

Fisheries Branch, Ministry of Environment, Lands, and Parks,

British Columbia, Canada.

Kaeriyama, M., and S. Urawa. 1992. Future research by the Hokkaido

Salmon Hatchery for the proper maintenance of Japanese salmon

stocks. Pages 57-62 in Y. Ishida, K. Nagasawa, D. Welch, K. Meyers,

and A. Shershnev, eds. Future salmon research in the North Pacific

Ocean, Special Publication National Research Institute Far Seas

Fisheries 20, Shimiu, Japan.

Keeley, E. R., and J. W. A. Grant. 2001. Prey size of salmonids fishes

in streams, lakes, and oceans. Canadian Journal of Fisheries and

Aquatic Sciences 58:1122-1132.

Kline, T. C. Jr., J. J. Goering, O. A. Mathisen, P. H. Poe, and P. L.

Parker. 1990. Recycling of elements transported upstream by runs

of Pacific salmon. 15N and 13C evidence in Sashin Creek,

southeastern Alaska. Canadian Journal of Fisheries and Aquatic

Sciences 47:136-144.

Larsen, D. A., B. R. Beckman, and W. A. Dickhoff. 2001. The effect

of low temperature and fasting during the winter on growth and

smoltification of coho salmon. North American Journal of

Aquaculture 63:1-10. 

Levin, P. S., R. W. Zabel, and J. G. Williams. 2001. The road to

extinction is paved with good intentions: negative associations of

fish hatcheries with threatened salmon. Proceedings Royal Society

London B 268:1-6.

Lichatowich, J. 1999. Salmon without rivers. Island Press, Covelo,

California.

Lynch, M., and M. O’Hely. 2001. Supplementation and the genetic

fitness of natural populations. Conservation Genetics 2:363-378.

Mackey, G., J. E. McLean, and T. P. Quinn. 2001. Comparisons of run

timing, spatial distribution, and length of wild and newly established

hatchery populations of steelhead in Forks Creek, Washington.

North American Journal Fisheries Management 21:717-724.

Madetoja, J., I. Dalsga and T. Wikland. 2002. Occurrence of

Flavobacterium psychrophylum in fish-farming environments.

Diseases of Aquatic Organisms 52:109-118. 

Mahnken, C., G. Ruggerone, W. Waknitz, and T. Flagg. 1998. A

historical perspective on salmonid production from Pacific Rim

hatcheries. North Pacific Anadromous Fish Commission Bulletin

1:38-53.

Maynard, D. J., T. A. Flagg, R. N. Iwamoto, and C. V. W. Mahnken.

2004. A review of recent studies investigating seminatural rearing

strategies as a tool for increasing Pacific salmon postrelease survival.

Pages 573-584 in M. Nickum, P. Mazik, J. Nickum, and D.

MacKinlay, editors. Propagated fish in resource management.

American Fisheries Society Symposium 44, Bethesda, Maryland.

McIsaac, D. O., and T. P. Quinn. 1988. Evidence for a hereditary

component in homing behavior of Chinook salmon (Oncorhynchus

tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences

45: 2201-2205.

McKibben, C. L. and R. J. Pascho. 1999. Shedding of Renibacterium

salmoninarum by infected Chinook salmon Oncorhynchus

tshawytscha. Diseases of Aquatic Organsims 38:75-79.

Mulcahy, D. R. J. Pascho, and C. K. Jenes. 1983. Detection of

infectious haematopietic necrosis virus in river water and

demonstration of water-borne transmission. Journal of Fish Diseases

6:321-330.

NPAFC (North Pacific Anadromous Fish Commission). 2003.

NPAFC Statistical Yearbook 1999. NPAFC, Vancouver, British

Columbia, Canada.

NRC (National Research Council). 1996. Upstream: salmon and

society in the Pacific Northwest. National Academy Press,

Washington, DC.

Olson, D. E., B. Spateholts, M. Paiya, and D. E. Campton. 2004.

Salmon hatcheries for the 21st century: a model at Warm Springs

National Hatchery. Pages 585-602 in M. Nickum, P. Mazik, J.

Nickum, and D. MacKinlay, eds. Propagated fish in resource

management. American Fisheries Society Symposium 44, Bethesda,

Maryland.

Pascual, M.A., and T. P. Quinn. 1994. Geographical patterns of

straying of fall Chinook salmon, Oncorhynchus tshawytscha
(Walbaum), from Columbia River (USA) hatcheries. Aquaculture

and Fisheries Management 25:17-30.

Pascual, M. A., T. P. Quinn, and H. Fuss. 1995. Factors affecting the

homing of fall Chinook salmon from Columbia River hatcheries.

Transactions of the American Fisheries Society 124:308-320. 

Pearsons, T. N., and A. L. Fritts. 1999. Maximum size of Chinook

salmon consumed by juvenile coho salmon. North American Journal

of Fisheries Management 19:165-170.

Perez, M. J., A. I. G. Fernandez, L. A. Rodriguez, and T. P. Nieto.

1996. Differential susceptibility to furunculosis of turbot and rainbow

trout and release of the furunculosis agent from furunculosis-affected

fish. Diseases of Aquatic Organisms 26:133-137.

Quinn, T. P. 1993. A review of homing and straying of wild and

hatchery-produced salmon. Fisheries Research 18:29-44.

Rogers, D. E., and G. T Ruggerone. 1993. Factors affecting marine

growth of Bristol Bay sockeye salmon. Fisheries Research 18:89-103.

Rose, A. S., A. E. Ellis, and A. L. S. Munro. 1989. The infectivity by

different routes of exposure and shedding rates of Aeromonas

salmonicida subsp. salmonicida in Atlantic salmon, Salmo salar L., held

in sea water. Journal of Fish Diseases 12:573-578. 

Sholes, W. H., and R. J. Hallock. 1979. An evaluation of rearing

fall-run Chinook salmon, Oncorhyncus tshawytscha, to yearlings at

Feather River Hatchery with a comparison of returns from hatchery

and downstream releases. California Fish and Game 65:239-255.

Smoker, W. W., and W. R. Heard. In press. Productivity of Alaska’s

salmon hatchery ocean ranching program and management of

biological risks to wild Pacific salmon. Chapter 18 in T.M. Bert, ed.

Ecological and genetic implications of aquaculture activities. Kluwer

Academic Publishers, Dordrecht. 

Smoker, W. W., and F. P. Thrower. 1995. Homing propensity in

transplanted and native chum salmon. American Fisheries Society

Symposium 15:575-576.

Waples, R. S. 1991. Genetic interactions between hatchery and wild

salmonids—lessons from the Pacific Northwest. Canadian Journal of

Fisheries and Aquatic Sciences 48:124-133.

Waples, R. S., and J. Drake. 2004. Risk-benefit considerations for

marine stock enhancement: a Pacific salmon perspective. Pages 260-

306 in K. M. Leber, S. Kitada, T. Svasand, and H. L. Blankenship,

eds. Stock enhancement and sea ranching, second edition. Blackwell

Science Ltd, Oxford, UK.

Wertheimer, A. C., W. W. Smoker, T. L. Joyce, and W. R. Heard.

2001. Comment: a review of the hatchery programs for pink salmon

in Prince William Sound and Kodiak Island, Alaska. Transactions of

the American Fisheries Society 130:712-720.

Wertheimer, A. C., W. W. Smoker, and W. R. Heard. 2004. Effects of

hatchery releases and environmental variation on wild-stock

productivity: consequences for sea ranching of pink salmon in Prince

William Sound, Alaska. Pages 307-326 in K. M. Leber, S. Kitada, T.

Svasand, and H. L. Blankenship, eds. Stock enhancement and sea

ranching, second edition. Blackwell Science Ltd, Oxford.

WDFW (Washington Department of Fish and Wildlife). 1997. Final

environmental impact statement for the wild salmonid policy.

Washington Department of Fish and Wildlife, Olympia. 

Wipfli, M. S., J. P. Hudson, and J. P. Caouette. 2004. Restoring

productivity of salmon-based food webs: contrasting effects of salmon

carcass analog additions on stream-resident salmonids. Transactions

of the American Fisheries Society 133:1440-1454.

Zhang, Y. and J. L. Congleton. 1994. Detection of infectious

hematopoietic necrosis (IHN) virus in rearing units for steelhead

before and during IHN epizootics. Journal of Aquatic Animal Health

6:281-287.

June 2005 | www.fisheries.org | Fisheries 23
Appendices Report to Congress – March 2006 51 

L: Hatchery Reform Conference Summary 

(Attached as a separately bound publication and/or available electronically from the Publications 

page of www.hatcheryreform.org) 
THE NEED

ABOUT THE PROJECT

HSRG

REFORM PRINCIPLES

REGIONAL REVIEWS

IMPLEMENTATION

PUBLICATIONS

CONTACT US

HSRG 

RECOMMENDATIONS 

HSRG HATCHERY REFORM PROGRESS REPORT TO CONGRESS, APRIL 2005 

FULL REPORT

Hatchery Reform Progress Report to Congress, April 2005 (684 KB) 

INDIVIDUAL SECTIONS

Introduction

Applying Science to Hatchery Management

HSRG Approach to Hatchery Reform 

2004 Project Accomplishments 

Regional Implementation Progress Reports

Eastern Strait of Juan de Fuca

South Puget Sound

Stillaguamish/Snohomish Rivers

Skagit River

Nooksack/Samish Rivers

Central Puget Sound

Hood Canal

Willapa Bay

North Coast

Grays Harbor

Project Coordination

Initial Investments Made/Needed at State, Tribal and Federal Facilities

Work in Progress

Looking Ahead

Appendices

2004 Project Expenditures

2004 Project Communications

2004 Tribal Hatchery Reform Projects

2005 Project Budget

2005 HSRG Work Plan

Technical Discussions Papers on Integrated and Segregated Hatchery Programs

Example Application of the All-H Analyzer (AHA) Management Tool

Hatchery Reform Coalition Members

CONTACT US | 

HOME
HATCHERY REFORM 

Progress Report to Congress 

April 2005 
Please cite as: 

Hatchery Scientific Review Group (HSRG) – Lars Mobrand (chair), John Barr, H. Lee 

Blankenship, Donald Campton, Trevor Evelyn, Tom Flagg, Conrad Mahnken, Paul 

Seidel, Lisa Seeb and Bill Smoker. April 2005. Puget Sound and Coastal Washington 

Hatchery Reform Project: Progress Report to Congress. Long Live the Kings, 1326 Fifth 

Avenue, Suite 450, Seattle, WA 98101 (available from www.hatcheryreform.org). Cite in 

text as HSRG 2005.

All Hatchery Reform Project publications are available from the project’s web site 

(www.hatcheryreform.org) or by contacting Long Live the Kings at (206) 382-9555 ext. 25. 
Table of Contents Progress Report to Congress – April 2005 i 

INTRODUCTION ....................................................................................................................3

APPLYING SCIENCE TO HATCHERY MANAGEMENT ..............................................7

HSRG APPROACH TO HATCHERY REFORM...................................................................................... 7

2004 PROJECT ACCOMPLISHMENTS.................................................................................................. 8

REGIONAL IMPLEMENTATION PROGRESS REPORTS...........................................15

EASTERN STRAIT OF JUAN DE FUCA ............................................................................................... 17

SOUTH PUGET SOUND..................................................................................................................... 22

STILLAGUAMISH/SNOHOMISH RIVERS............................................................................................ 25

SKAGIT RIVER................................................................................................................................. 29

NOOKSACK/SAMISH RIVERS........................................................................................................... 32

CENTRAL PUGET SOUND................................................................................................................. 36

HOOD CANAL.................................................................................................................................. 41

WILLAPA BAY................................................................................................................................. 46

NORTH COAST................................................................................................................................. 50

GRAYS HARBOR.............................................................................................................................. 54

PROJECT COORDINATION..............................................................................................59

INITIAL INVESTMENTS MADE/NEEDED AT STATE, TRIBAL AND FEDERAL 

FACILITIES...........................................................................................................................61

WORK IN PROGRESS.........................................................................................................65

LOOKING AHEAD ...............................................................................................................69

APPENDICES.........................................................................................................................71

A: 2004 PROJECT EXPENDITURES............................................................................................. 73

B: 2004 PROJECT COMMUNICATIONS....................................................................................... 75

C: 2004 TRIBAL HATCHERY REFORM PROJECTS...................................................................... 79

D: 2005 PROJECT BUDGET........................................................................................................ 81

E: 2005 HSRG WORK PLAN..................................................................................................... 83

F: TECHNICAL DISCUSSIONS PAPERS ON INTEGRATED AND SEGREGATED HATCHERY 

PROGRAMS........................................................................................................................... 87

G: EXAMPLE APPLICATION OF THE ALL-H ANALYZER (AHA) MANAGEMENT TOOL........... 103

H HATCHERY REFORM COALITION MEMBERS ...................................................................... 105

Introduction Progress Report to Congress – April 2005 3 

Introduction 

This report provides the Hatchery Scientific Review Group’s (HSRG) synopsis and evaluation of state, 

tribal and (in two regions) federal implementation progress reports for each of the ten hatchery reform 

regions contained within Puget Sound and coastal Washington. Also included are an overview of 

Hatchery Reform Project 2004 accomplishments; information about project coordination, facilitation 

and communications; an update on investments made and needed at hatchery facilities; work in 

progress to continue implementation in 2005 and beyond; and a series of appendices. 

In general, the HSRG is encouraged by the progress the co-managers are making in instituting 

hatchery reform throughout the Puget Sound and coastal Washington hatchery system. For example, 

the co-managers were explicit in their regional implementation progress reports in stating stock goals; 

defining management premises for biological significance, population viability, habitat and harvest; 

and employing new tools for better defining hatchery type (integrated or segregated). In some, but not 

all, regions the co-managers outlined current and future actions taken toward meeting stock goals for 

proper genetic integration or segregation, and described a process for incorporating natural-origin fish 

into the hatchery- and naturally-spawning broodstock. 

The following comments are areas of concern that apply to some, but not all, regions and are meant as 

constructive criticism. The HSRG wishes to emphasize the overall good progress on the part of the comanagers in instituting hatchery reform in the ten regions. 

GOAL SETTING 

For the Stillaguamish/Snohomish, Hood Canal and Eastern Straits regions, it was clear that the comanagers reviewed and confirmed common stock goals. In some other regions, it was apparent that 

the co-managers had not established a unified process for regional reform. For example, it was not 

clear to the HSRG whether the stock goals provided by the co-managers for the regional review 

process in these regions had been revisited and confirmed. Having clear stock goals is essential to 

effectively evaluating benefits and risks from hatchery programs. 

MANAGING FOR SUCCESS 

Successful hatchery management is an ongoing, active process that focuses on long-term goals and 

adapts to changing circumstances, societal values, stock status and scientific information. It requires 

managers to make informed, scientifically defensible decisions based on available information. Future 

adaptive management of the system will require gathering new information (particularly bio-sampling 

surveys in the habitat, at hatcheries and in the fishery) and a systematic decision-making process that 

takes this information into account. An applied research agenda to address critical uncertainties and 

make better informed management decisions in the future is also necessary. Without such an approach, 

the system becomes static and unresponsive. Priority funding is urgently needed to make this system 

effective. For example, funds are needed to provide regular, timely gathering and analysis of data 
4 Progress Report to Congress – April 2005 Introduction 

about stock composition on the spawning grounds, in order to ensure scientifically-sound broodstock 

management strategies. 

Managing for success and accountability (monitoring and evaluation, adaptive management) is the 

weakest element of hatchery reform at the present time, even in regions where good progress has been 

made in all other respects. No formal process for tracking progress and adaptively managing the 

system yet exists in any region. Even in the Stillaguamish/Snohomish region, where it appears that this 

topic has been given a fair amount of attention, a comprehensive adaptive management process is not 

yet in place. This is the top priority for the HSRG’s work with the co-managers in 2005. 

FUNDING 

New funding is a necessity for implementing hatchery reform. Hatchery reform and adaptive 

management will require a significant investment of stable, new funding to annually evaluate 

escapement, stock identification, broodstock composition, natural/hatchery fish interactions, and other 

dynamic processes not previously required. In addition, the hatchery system desperately needs 

upgrading of its physical infrastructure, as significant improvements have not been made in several 

decades. In the near-term, capital funding should be prioritized to alleviate the negative interactions 

from hatcheries and hatchery fish with their ecosystems (for example, facilities for proper integrated 

and segregated programs, meeting federal and state laws for water withdrawal, and eliminating natural 

upstream and downstream migration delays). Future funding needs to be tied to explicit and 

quantitative goals for all hatchery- and naturally-spawning stocks in a given region. The flow of 

information must be sufficiently quantitative to properly size programs to meet those goals. 

In the near-term, the greatest value is likely to be produced from investment in those regions where the 

co-managers are most prepared to implement hatchery reform. The co-managers in those regions—

most notably the Stillaguamish/Snohomish, but also the Hood Canal, Eastern Straits and North Coast 

regions—have demonstrated a firm understanding of the process of hatchery reform and have made 

the decisions to implement change. The HSRG recommends that these regions receive priority funding 

from the state and federal governments. 

Hatchery reform also means reprioritizing and reallocating existing resources. Many changes can be 

instituted without additional funding, and a lack of funding should not be used as an excuse for 

continuing activities inconsistent with stock goals. For example, genetic management of broodstocks 

should be a priority—on par with fish health and quality, water requirements, cost effectiveness, etc. 

The co-managers need to prioritize and develop alternate regional strategies if preferred strategies 

cannot be implemented. At a minimum, where funding is not currently available to implement 

preferred reforms, interim solutions consistent with goals for affected stocks should be identified and 

implemented. 

GENETIC INTEGRATION AND SEGREGATION 

Implementing genetically integrated or segregated broodstock management strategies is the key 

component to hatchery reform as described by the HSRG. It should be clearly noted that HSRG does 

not advocate the use of one strategy over the other. Each has its own set of benefits and risks. What is 
Introduction Progress Report to Congress – April 2005 5 

critical is that the selected strategy is properly implemented and adaptively managed. There is 

encouraging evidence in several regions that this approach is becoming accepted by hatchery 

operators. The Stillaguamish/Snohomish region, in particular, is implementing this concept. Plans for 

integration/segregation are well advanced or planned in the Hood Canal, Eastern Straits and North 

Coast regions. Plans to implement this concept are also being developed in the Nisqually Basin (South 

Sound), on the Green River (Central Sound), and in the Nooksack/Samish region. However, integrated 

or segregated genetic broodstock management has not progressed to the point of implementation in 

most of these and other regions. 

SIZING HATCHERY PROGRAMS 

To assure that harvest and conservation goals are met, hatchery programs must be sized (in terms of 

the number of fish released) appropriately. Unfortunately, in most regions those goals are not 

sufficiently quantified to determine the appropriate size of a hatchery program. Quantifying these 

goals is the next key step to assure successful fisheries management. In many regions, it does not 

appear likely that natural stocks will be productive enough in the short-term to support properly 

integrated hatchery programs at current program sizes, due to the need to remove excessive numbers 

of natural spawners for hatchery broodstock.. Correct sizing is also important to segregated programs. 

Even low levels of straying from a large segregated hatchery population can result in significant loss 

of fitness for a small natural population. If habitat improvements that increase the size and 

productivity of natural populations do not occur, either type of program may pose significant risk to 

natural populations. Therefore, co-managers need to either develop new strategies for stock integration 

or segregation (such as reductions in program size), or reconsider their stock goals, in those situations. 

STEELHEAD WHITE PAPER AND MANAGEMENT 

PLAN 

Throughout the regional reviews, the HSRG expressed concern about the current ubiquitous, systemwide approach to steelhead management, which uses segregated hatchery programs without adequate 

measures to monitor and manage genetic1

 and ecological2 risks. In the HSRG’s opinion, the current 

system of steelhead hatchery management in Puget Sound and coastal Washington is in greater need 

of change than most other programs, based on the principles of hatchery reform. The HSRG proposed 

a comprehensive change to this system consistent with reform principles and the co-managers’ stock 

goals. This included taking steps to ensure segregated programs were operated correctly, and the 

establishment of hatchery-free management zones, where natural steelhead would be free from the 

influence of hatcheries. 

 

1

 Mackey, G., J.E. McLean, and T.P. Quinn. 2001. Comparisons of run timing, spatial distribution, and length of 

wild and newly established hatchery populations of steelhead in Forks Creek, Washington. North American 

Journal of Fisheries Management 21:717-724. 2

 Kostow, K.E., A.R. Marshall, and S.R. Phelps. 2003. Naturally spawning hatchery steelhead contribute to 

smolt production but experience low reproductive success. Transactions of the American Fisheries Society

132:780-790. 
6 Progress Report to Congress – April 2005 Introduction 

The co-managers responded by proposing to develop a comprehensive, new approach to steelhead 

management, beginning with a white paper that would be the foundation for a new, genetically-based, 

statewide steelhead management plan. The HSRG was asked by the Washington State Department of 

Fish and Wildlife (WDFW) to work with the Department on developing this new steelhead approach, 

and has been prepared to assist in this effort. However, the HSRG is concerned that the release of the 

white paper and management plan has been delayed. This has prevented the HSRG from contributing 

to the plan, or commenting on progress made in implementing hatchery reform for steelhead 

programs. In the absence of a new approach that incorporates the elements of hatchery reform, the 

HSRG stands firmly by its previous recommendations, calling for significant changes in the 

management of steelhead hatchery programs. 
Applying Science Progress Report to Congress – April 2005 7 

Applying Science to Hatchery 

Management 

HSRG APPROACH TO HATCHERY REFORM 

In 2000, when the US Congress tasked the HSRG with reviewing the Puget Sound and coastal 

Washington salmon and steelhead hatchery system, the general discussion about hatcheries debated 

whether hatcheries were “good” or “bad.” The HSRG chose a more scientifically sound approach—

applying science to assess the benefits and risks from hatchery programs, and using this science to 

make recommendations that increase the likelihood of improving benefits and reducing risks, on a 

program-specific basis. 

The HSRG determined that management decisions about hatchery programs must be made in the 

context of the particular circumstances in a given watershed. This approach requires an understanding 

of the current and expected future goals for all natural and hatchery stocks in an ecosystem—along 

with the habitat on which they depend—as well as harvest and conservation goals. Only within this 

context can it be determined if a hatchery program is an appropriate tool for helping to reach harvest 

and conservation goals for a given stock and, if so, what size and type of program is appropriate. 

This sophisticated, methodical application of science was the foundation upon which the HSRG 

conducted its review of over 200 hatchery programs in 10 regions of Puget Sound and the coast—

resulting in over 1,000 recommendations for change at individual hatcheries, along with 18 

recommendations to be applied across the entire system. The HSRG called for management based on 

clear goals, scientifically defensible programs and informed decision-making. This process has moved 

the debate from problem identification to problem solving. 

As a foundation for reform, the HSRG recommended that hatchery managers change their measure of 

success from the number of juvenile fish released, to the number of adult fish returning to sustain the 

stock and provide fishing opportunities. This means focusing on quality over quantity, understanding 

the carrying capacity of the freshwater and marine environments into which fish are released, and 

other scientifically sound hatchery practices. 

Central to the HSRG’s work is the concept that hatchery fish must be managed either as part of a wild 

population (genetically integrated) or as a wholly separate population (genetically segregated). 

Segregated programs are for use primarily where the goal is to provide fishing opportunities, and 

where interactions between these fish and wild populations can be limited. Integrated programs are 

most appropriate where conservation is a primary goal, or for harvest programs where the potential for 

significant genetic interactions between hatchery and wild fish makes this the best strategy for meeting 

regional stock goals (for more information, see Appendix F, Technical Discussion Papers). 

A properly integrated program maintains fish that are adapted to the natural environment, in that the 

naturally-spawning component drives the adaptation of the composite population. Therefore, these fish 
8 Progress Report to Congress – April 2005 Applying Science 

may be appropriate for helping to rebuild declining wild populations. They should also survive in 

greater numbers than fish from a poorly integrated program, providing more fish for meeting either 

harvest or conservation goals. 

Successful integrated programs require healthy naturally-spawning populations and the functional 

habitats that sustain them. In this context, a hatchery should not be seen as a substitute for habitat, but 

rather as an extension of it—a productive tributary of the watershed in which it resides. 

The HSRG’s approach affects more than just hatcheries. It requires a new approach to managing 

salmon and steelhead—one that begins with goals for and understanding of the status of naturallyspawning stocks and then designing hatchery programs consistent with conservation and harvest goals 

for those stocks. Far from seeing hatcheries as a substitute for habitat, hatchery reform recognizes that 

healthy, abundant habitat is essential to the success of hatchery programs that seek to meet these goals. 

The size and health of natural populations and the habitat on which they depend controls what 

hatcheries can do to boost natural spawning and/or provide a harvestable surplus. Hatchery reform 

means managing a holistic, science-based system that results in more adult fish returning to both 

maintain healthy, fit natural populations and provide harvest opportunities. 

2004 PROJECT ACCOMPLISHMENTS 

The Puget Sound and Coastal Washington Hatchery Reform Project brings together a unique 

combination of independent science, manager coordination, political support and third-party project 

coordination/facilitation that has proven to be a highly effective formula. The partnership is guided by 

the assumption that the best way to help the managers succeed in moving their hatchery system 

forward is to let the scientists focus on science and the managers on management. The scientific 

recommendations assess benefits and risks, but leave the “how-to’s” to the managers. Each member of 

this partnership achieved significant accomplishments in 2004, which are described below (2004 

expenditures are detailed in Appendix A). 

HSRG Principles and Recommendations Report

In April 2004, the HSRG completed the regional review phase of the Hatchery Reform Project by 

publishing a report containing over 1,000 recommendations for change at individual hatcheries, 

along with 18 recommendations to be applied across the entire system. The HSRG also provided 

three principles to guide hatchery management in the future: 

1. Goals for all stocks must be quantified and expressed in terms of values to the community 

(harvest, conservation, education, research, etc.) 

2. The purpose, operation and management of each hatchery program must be scientifically 

defensible and consistent with current scientific knowledge. 

3. Decisions must be informed and modified by continuous evaluation and new scientific 

information. 

The report was released at a news conference in Seattle. At the news conference, WDFW Director 

Jeff Koenings and Northwest Indian Fisheries Commission (NWIFC) Chair Billy Frank, Jr. 
Applying Science Progress Report to Congress – April 2005 9 

pledged to implement the recommendations. Washington Governor Gary Locke pledged to include 

funding for hatchery reform in his proposed 2005–07 biennial budget. Congressman Norm Dicks, 

D-WA, applauded the progress achieved. The report was widely praised in extensive media 

coverage (see Publications page of the project’s web site, www.hatcheryreform.org). 

The report also included a set of tools developed by the HSRG for the regional review process, 

which can be used by the managers to apply science to decision making about hatcheries into the 

future. Those tools (all available from the project’s web site) include: 

Scientific Framework 

Organizes the current state of knowledge about how actions associated with hatcheries affect 

the environment and fish resources. Forms the basis for all of the HSRG’s tools, processes and 

recommendations. First published in 2000, after review by over 200 scientists and 

stakeholders. Updated in 2004. 

Benefit/Risk Assessment Tool 

Adapted from a tool developed by the co-managers, allows the user to evaluate the relative 

benefits and risks associated with specific actions and choices in hatchery management. 

Central to the regional review effort. 

Hatchery Operational Guidelines 

Describe operational practices to meet conditions for success, as defined in the Scientific 

Framework. 

Annual Research Grant Program 

A competitive grant program funding research projects to address knowledge gaps identified 

in the Scientific Framework. 

Emerging Issues in Hatchery Reform 

White papers on emerging issues critical to 21st-century hatchery management, such as the 

effects of changing ocean conditions on fisheries, preventing hatchery fish from preying on 

wild fish, and methods for preserving genetic diversity and fitness in hatchery populations. 

Technical Discussions and Workshops, Tools 

Developed

The state and tribal co-managers of Washington’s salmon and steelhead asked the HSRG to work 

with them in 2004 to develop tools for managing hatcheries consistent with the new context 

described in the HSRG’s principles and recommendations. Building on the tools developed during 

the review process (see above), the HSRG held technical discussions with WDFW and NWIFC 

scientists in the spring of 2004 that resulted in several important products. The first were technical 

discussion papers refining, and providing guidelines for implementing, the integrated and 

segregated hatchery program concepts (see Appendix F, Technical Discussion Papers). 
10 Progress Report to Congress – April 2005 Applying Science 

This scientific work provided a foundation for development of the “All H Analyzer” (AHA) 

management tool. AHA was used in a series of HSRG/co-manager technical workshops that were 

held in all ten Puget Sound and coastal Washington regions in the summer of 2004. The purpose 

of the workshops was to apply the guidelines for integrated and segregated hatchery programs to 

regional case studies, preparing the co-managers for decision-making meetings about 

implementing reform. AHA was applied to 27 case studies during the workshops. The managers 

found it to be a useful tool for understanding the implications of management alternatives and 

actions. AHA has generated a great deal of interest, because it is the only tool currently available 

for assessing the likely results of habitat, harvest and hatchery actions and alternatives together on 

a specific stock (a generic example of AHA is included as Appendix G). 

AHA is a management decision-making tool, built on recent work by HSRG, WDFW, NWIFC, 

National Oceanic and Atmospheric Administration (NOAA) Fisheries and other scientists, that 

allows the user to: 

• Use current habitat productivity/capacity, harvest rates and hatchery operations in a watershed 

and consider what will result from that set of factors, in terms of the number of fish returning 

to the habitat, harvest and hatchery, and the amount of influence the natural environment 

should have on integrated natural/hatchery populations. 

• Examine how these results could be modified in the short- and long-terms if habitat, harvest 

and/or hatchery programs are changed. 

• Confirm current conditions, describe a goal for the long-term future of the population, and 

develop one or more scenarios for achieving or moving toward the goal. 

• Apply a scientific approach in the face of the uncertainty always present in natural resource 

management. 

• Move from general management guidelines to strategies specifically tailored to unique 

watershed conditions and circumstances identified during the regional reviews. 

The management tool itself: 

• Allows managers to take a more sophisticated approach by considering the habitat, harvest 

and hatchery factors together. 

• Is basically an accounting tool that uses the best available scientific information to predict 

implications, quantifies and tracks fish produced naturally and in hatcheries, fish removed for 

harvest or hatchery broodstock, and the likely results of hatchery/natural fish interactions in 

the natural environment. 

• Fosters accountability, by documenting goals, assumptions, scientific hypotheses, 

relationships, management decisions and the rationale behind these decisions. The 

assumptions can then be verified by monitoring and evaluation; the hypotheses can be tested 

by research. In this way, AHA can be used to help identify areas where better science will 

make a difference in decision making. 
Applying Science Progress Report to Congress – April 2005 11 

• Tests a key hypothesis about whether fitness loss can be addressed without losing 

demographic benefits from hatcheries. Because this is an area of uncertainty, the effects of 

fitness gain or loss can be adjusted or turned off in AHA. The HSRG is also funding research 

on this topic (see chapter on research in the HSRG’s April 2004 report). 

The spring 2004 technical discussions also lent momentum to an effort by HSRG, NWIFC and 

WDFW scientists to provide the managers with a practical and cost-effective set of variables to 

monitor, in order to ensure hatchery programs are accountable for their results, successfully 

meeting goals, and adaptively managed to improve performance and adjust to changing 

circumstances. The HSRG, seeing this as a critical element of successful hatchery reform, has 

continued to work on this tool. The result will be a management tool entitled “Managing for 

Success and Accountability at Hatcheries.” Moving forward on this tool will be a central task for 

the project in 2005. 

Research and Scientific Publications

The HSRG continues to oversee a competitive grant program to fund research projects that fill 

knowledge gaps about using hatcheries to meet harvest and/or conservation goals. In February 

2004, the HSRG held its annual research review meeting at the NOAA Fisheries Science Center in 

Seattle, receiving reports from funded researchers. Over 40 state, tribal, federal, academic and 

private scientists and technical staff attended. Following this review, the HSRG decided to 

continue funding for five projects (research project reports are available at the project’s web site). 

In May 2004, the HSRG responded to a request from the Alaska Department of Fish and Game 

and the University of Alaska-Fairbanks to co-host scientific workshops in Juneau and Anchorage, 

Alaska. These workshops presented an overview of the Hatchery Reform Project and the work of 

the HSRG, and allowed an exchange of information and research results on hatchery-related issues 

with Alaskan researchers, managers and policy makers. The presentations made at the workshops 

are available on the project’s web site. 

In the fall of 2004, the HSRG began preparing a series of manuscripts to be submitted to the peerreviewed, scientific literature, on topics including the integrated/segregated concept, quantification 

of fitness loss, guidance on when to consider conservation hatchery programs, and others. One 

will apply the AHA tool to analyze the implications of integrated hatchery programs in western 

Washington. The first manuscript accepted for publication is Hatchery Reform in Washington 

State: Principles and Emerging Issues. It will be published in the American Fisheries Society’s 

Fisheries magazine in June 2005. The HSRG will continue to put an emphasis on scientific 

publications. Manuscripts will be made available electronically, once submitted for publication. 

Agency Science Teams 

Information below provided by the Washington State Department of Fish and Wildlife 

Major 2004 hatchery reform accomplishments for the WDFW hatchery science team include 

participating in development of AHA (see above). Also, all anadromous Puget Sound 

hatcheries were assessed and estimated costs generated by professional engineers for 

intake/passage and abatement compliance, implementation of HSRG recommendations, and 
12 Progress Report to Congress – April 2005 Applying Science 

capital needs to maintain current production for the next ten years. Severe hatchery fish losses 

to avian and mammalian predators were curtailed through installation of predator control 

devices at Marblemount, Palmer, Sol Duc and Bogachiel hatcheries. 

In addition, 12 multi-year, hatchery research studies supported by hatchery reform funding 

were continued in 2004, including work on hatchery/wild interactions, survival and diet 

studies. New hatchery technology necessary to implement reform was acquired and integrated 

into hatchery operations, including brood stock handling machines, an automated fish snout 

snipper for coded-wire tag recovery, and carbon dioxide stunner units used with adult fish 

pumps. Twenty previously-untagged hatchery stocks were coded-wire tagged, so important 

information on survival, harvest and return distributions can be ascertained. 

Information below provided by the Northwest Indian Fisheries Commission 

Tribal hatchery reform funding not devoted to implementation projects at tribal facilities (see 

section below on implementation funding provided/still needed) has been used to support the 

tribal hatchery science team within the Enhancement Services Division at NWIFC, as well as 

the tribal representative to the HSRG, based at the Nisqually Tribe. The NWIFC hatchery 

reform-funded science team consists of a geneticist, a biometrician and a salmon ecologist, 

who are supervised by a senior geneticist. The geneticists provide technical support for 

commission and tribal staff on issues involving genetics and salmon recovery including: 

appropriate uses of hatcheries in salmon recovery programs; planning, implementation and 

monitoring of hatchery research; risk assessment; and mixed stock fishery analysis using 

genetic data. The salmon ecologist provides technical support for tribal programs on issues 

involving ecology and artificial production such as the role of fish behavior, interspecies 

interactions and freshwater and nearshore habitats in designing hatchery programs; planning, 

implementation and monitoring of research for hatchery activities; and risk assessment of 

hatchery programs. The biometrician provides technical support for NWIFC and tribal 

enhancement staff on experimental design and monitoring, statistical analysis and database 

maintenance. 

FY 2004 tribal science team work activities: 

• NWIFC staff geneticists worked with tribes on genetic issues associated with the 

development of hatchery management and reform plans; helped collect and analyze 

morphological and DNA data on threatened Nooksack River and Stillaguamish River wild 

Chinook; developed tribal research to evaluate genetic changes in hatchery and wild 

populations; reviewed HSRG guidelines and developed models for the HSRG to use with 

the co-managers in deciding when to start hatchery programs and how to integrate 

hatchery and wild production consistent with sustainable natural production; coordinated 

information exchange between the co-managers, the HSRG, other independent scientific 

review groups such as the Recovery Science Review Panel, federal regulatory agencies, 

and the Shared Strategy for Salmon Recovery in Puget Sound; secured a grant and began 

developing a quantitative risk assessment model for hatcheries. 

• The NWIFC staff biometrician worked with the tribes to develop statistical techniques for 

assessing the contribution of hatchery and wild fish to natural spawning aggregations; 
Applying Science Progress Report to Congress – April 2005 13 

analyzed data on returns of hatchery fish, which is useful for evaluating the success of 

hatchery programs; and provided statistical consulting on tribal research and monitoring 

projects. The biometrician has assisted the HSRG in developing monitoring and 

evaluation criteria that can be used to determine the success of a hatchery program in 

meeting its goals and objectives. These criteria will also consider what data is needed for 

future research on hatcheries. The biometrician has also begun work with participants in 

regions already reviewed by the HSRG, to aid them in tailoring monitoring and evaluation 

criteria to the features and circumstances of their region. 

• The NWIFC salmon ecologist helped tribes develop and implement estuary research for 

investigating co-occurrence between hatchery and wild fish; continued to build upon a 

literature database on ecological interactions; and is developing a database of tribal 

hatchery reform recommendations and completed hatchery reform projects. The ecologist 

also worked with individual tribes to assist in development and implementation of 

ecological studies funded through the Hatchery Reform effort. 

• New hatchery management software and a database have been developed and distributed, 

to greatly improve the amount of information available to hatchery managers. The 

software, called HatPro, improves monitoring, management and planning capabilities for 

hatchery managers, as well as allowing on-site electronic transfer of key hatchery data 

directly to state, tribal and federal agencies. Four group training workshops, and numerous 

on-site training sessions, have been provided to tribal hatchery managers. 

Information below provided by the US Fish and Wildlife Service 

FY 2004 USFWS science team work activities included: 

• Participation of a USFWS fish geneticist as a member of the HSRG, including preparation 

of reports and scientific papers. 

• Conduct of a science support project by a USFWS fish nutrition specialist concerning 

analysis and quality control of fish feed at Olympic Peninsula fish hatcheries. 

Regional Implementation Progress Report to Congress – April 2005 15 

Regional Implementation Progress 

Reports 

Implementing the HSRG’s recommendations and putting into practice the new approach to salmon 

and steelhead management will require capital investment, a continuing commitment to new hatchery 

practices, and accountability to ensure goals are being achieved. The state and tribal co-managers have 

agreed with the vast majority of the recommendations and have implemented many of them. The state, 

tribal and federal managers have each developed databases for tracking the status of each 

recommendation. They are working with the HSRG and the facilitation team to design a long-term 

strategy for changing the way hatcheries are managed, and incorporating hatchery reform into other 

salmon recovery and harvest management processes. 

As described above, in 2004 that work included technical discussions that resulted in new 

management tools and papers refining key hatchery reform concepts; regional workshops where 

guidelines for integrated and segregated hatchery programs and tools such as AHA were applied to 

regional case studies; co-manager decision-making meetings on implementing reform in each region; 

and work by the HSRG to prepare manuscripts for the peer-reviewed scientific literature. 

In 2005, the co-managers are continuing to use AHA; wrapping up regional decision-making 

meetings; and incorporating the recommendations into recovery plans and other management 

documents and processes. The HSRG is completing its tools and scientific publications; developing an 

agenda to guide hatchery-related research; and preparing for a workshop on hatchery reform to be held 

in the second half of the year. 

Most of the co-managers have also provided the HSRG with draft reports that detail implementation 

progress to date in each region. What follow are a set of general observations, and then a synopsis of 

each regional draft report and analysis from the HSRG as to how the region is doing in implementing 

hatchery reform, based on those reports. The co-managers intend to publish their regional 

implementation progress reports in summer 2005. 

The HSRG asked the co-managers to respond to the following questions when preparing these reports: 

1. What are the management premises/goals for each salmonid stock and the role of hatcheries now 

and into the future (provide updates to the regional stock structure and management premises for 

biological significance, population viability, habitat and harvest; and hatchery program purpose 

[harvest, conservation, both, etc.] and type [integrated or segregated])?; 

2. What steps are the co-managers taking toward meeting these stock goals (for example, provide 

updates on progress toward meeting guidelines for proper genetic integration or segregation; can 

or will the proportion of natural-origin fish in the hatchery broodstock and hatchery-origin fish on 

the spawning grounds be determined and controlled?; what other changes have been or will be 

made to implement HSRG program-specific or system-wide recommendations in each region?)?; 
16 Progress Report to Congress – April 2005 Regional Implementation 

3. What steps are being taken in each region to ensure hatchery programs are managed for success 

over time (describe the process/strategy that is in place or under development to track progress 

toward achieving stock goals over time)?
Regional Implementation Progress Report to Congress – April 2005 17 

EASTERN STRAIT OF JUAN DE FUCA 

The regional implementation progress report for Eastern Straits was jointly authored by WDFW and 

the Jamestown S’Klallam, Lower Elwha Klallam, and Port Gamble S’Klallam tribes. They state that 

the report represents co-manager agreement at the policy and technical level. This region was 

reviewed by the HSRG in 2001. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

This region contains a complex of watersheds that drain the northeastern slopes of the Olympic 

mountain range, including the Dungeness and Elwha rivers and several smaller watersheds. 

Although each of these sub-regions currently have much habitat of poor quality, they are still 

producing some level of Chinook, coho, pink, chum, cutthroat and steelhead over portions of the 

region. 

Habitat in the Dungeness drainage is considered poor to fair for salmonids, but is expected to 

improve if efforts to modify the Dungeness River dikes, to return the river to its meander channels 

are successful. Major habitat concerns include the diversion of instream flow for irrigation, loss of 

functional floodplain and estuary in the lower watershed, lack of habitat complexity, substrate 

instability, and poor riparian condition. Upper watershed tributaries in the Olympic National Park 

remain in good condition. Significant habitat restoration efforts are underway in the mainstem, 

where islands of high-quality habitat warrant protection or have high restoration potential for 

producing naturally spawning salmonids. Both hatcheries in the Dungeness sub-region focus on 

the conservation of severely depleted salmonids, notably ESA-listed Dungeness spring Chinook. 

They also maintain a coho program for harvest purposes. 

Natural salmonid production in the Elwha River watershed is currently severely impaired due to 

the presence of the Elwha and Glines Canyon dams. Habitat in the upper watershed is within the 

Olympic National Park and remains pristine, but fish access is limited to only the lower 4.9 miles 

of what was historically a 77 mile range. Removal of the dams has been authorized and funded by 

the US Congress. Habitat condition downstream of Elwha Dam is severely impaired, due to loss of 

suitable spawning substrate and channel complexity. As in the Dungeness Basin, the emphasis of 

this sub-region’s hatchery programs is on conservation of the remaining stocks of salmonids, 

including the ESA-listed Elwha fall Chinook. A coho program is maintained primarily for harvest. 

In recent years, winter steelhead or coho salmon rearing has also taken place. 

General Overall Comment about the Co-Manager Report: 

The co-managers in this region have taken actions in the past year and half consistent with 

hatchery reform objectives of improving efficiency and effectiveness of hatchery operations, 

supporting fisheries, and conserving naturally-spawning stocks. Overall, the response of the 

Eastern Straits co-managers has been good in meeting the HSRG’s recommendations. The effort 

has been a cooperative process by the co-managers to clearly elucidate hatchery reform issues at 

both the technical and policy levels. Stock goals and purposes of hatchery programs have been 
18 Progress Report to Congress – April 2005 Regional Implementation 

clearly stated. Managers have identified whether the programs intend to integrate the hatchery 

populations with, or segregate them from, the naturally spawning segment of the populations, and 

have incorporated HSRG-recommended hatchery protocols and modifications required for 

achieving those goals. They have employed new co-manager tools in both the Dungeness and 

Elwha basins to describe and analyze complex interactions of hatchery fish with natural fish, and 

have suggested methods to improve the efficiency and effectiveness of hatchery operations in the 

region. In most cases, these methodologies are being put into practice. The comments below do 

not pertain to steelhead programs. As discussed elsewhere, the co-managers are reviewing the 

HSRG’s system-wide recommendations for steelhead and will address them in a forthcoming 

white paper. 

1. Stock Goals and the Role of Hatcheries 

a) Are short- and long-term management goals/premises for habitat, 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reported goals for most natural and hatchery stocks in the region, 

and confirmed the goals upon which the HSRG recommendations are based. The majority 

of HSRG recommendations have been met, or acceptable alternatives proposed. However, 

no specific goals have been identified for the naturally-spawning coho population in the 

Dungeness River. The HSRG recommends that the co-managers develop and explicitly 

state goals for this stock. The co-managers have stated that HSRG recommendations for 

habitat restoration and subsequent integration of hatchery coho and Chinook on the 

Dungeness River must await a basin-wide life history study that is proposed by the comanagers, for which funding is being solicited. Information derived from the life history 

study will apply to all salmonids in the Dungeness Basin. The HSRG strongly supports the 

proposed study, and recommends that funds be made available as soon as possible. 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

The purposes for all hatchery programs are adequately defined and the co-managers have 

proposed no changes in the purposes of the individual programs since the HSRG’s review. 

The co-managers have answered all HSRG questions related to program purposes. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

All programs are identified as either integrated or segregated, and all HSRG 

recommendations satisfactorily addressed. The co-managers have suggested an acceptable 

alternative to the HSRG’s recommendation that the Elwha Restoration Team (ERT) 
Regional Implementation Progress Report to Congress – April 2005 19 

consider captive broodstocks, in order to reduce risk of demographic loss during dam 

removal. Instead, they plan to create a reserve population using off-station plants and 

acclimation techniques in Morse Creek, habitat historically used by Elwha salmonids. The 

purpose is to reduce demographic, ecological and genetic risks associated with dam 

removal by creating refugia for Elwha stocks in Morse Creek. These populations will be 

monitored, with captive broodstocking and other artificial propagation measures invoked 

only if necessary. 

2. Steps Taken (Decisions Made and Actions Taken) Towards Meeting Short- and LongTerm Expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

The co-managers applied the AHA tool to the hatchery program for Dungeness Chinook 

and concluded that, under current habitat conditions, integrating hatchery- and naturallyspawning broodstock at this time would result in increased demographic risk of extinction. 

The aim of the hatchery program is to conserve this severely depleted population in a 

hatchery gene bank, pending improvements in habitat. An AHA analysis of the segregated 

Dungeness coho hatchery program gave similar results, demonstrating that poor habitat 

condition does not allow integrating the hatchery program at this time. It will remain as a 

segregated conservation program. This is a logical, scientific approach, given current 

conditions. To integrate the program today would require a significant reduction in smolt 

production, because of the difficulty in obtaining a sufficient number of natural-origin 

returning fish for the hatchery broodstock. However, as conditions improve and 

abundance increases, the managers should consider converting to an integrated program. 

According to the co-managers, the final decision to integrate hatchery production for coho 

and Chinook at the Dungeness hatchery awaits the outcome of a proposed life history 

study, and determination of the productivity and capacity of wild salmonids in the 

Dungeness River Basin. 

At the request of ERT, the HSRG reviewed the Elwha River Restoration Plan. However, 

neither this plan nor the co-managers’ implementation progress report for the Elwha subregion included specific strategies for achieving desired hatchery- and naturally-spawning 

proportions in the hatchery broodstock and on the spawning grounds for integrated and 

segregated programs. The HSRG recommends that broodstock management strategies for 

all stocks affected by the restoration plan be developed prior to its implementation. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

By and large, the co-managers have met HSRG recommendations to size programs 

consistent with goals for all hatchery- and naturally-spawning stocks. They have 
20 Progress Report to Congress – April 2005 Regional Implementation 

developed an alternative conservation hatchery program following closure of the Chinook 

captive broodstock at Hurd Creek hatchery. This new hatchery program gets eggs from 

naturally-spawning stocks and produces a mix of zero-age and yearling smolts, as per 

HSRG recommendations. While progress has been made, the managers in this region have 

generally not developed goals for harvest contribution of hatchery programs explicit 

enough to specifically size the programs to meet these needs. 

The HSRG notes that the Dungeness fall pink program at Hurd Creek Hatchery has been 

terminated for lack of funds. This stock, which is the only pink salmon stock in the lower 

Dungeness River, is recognized by the managers to be of high biological significance and 

at critical population viability. In addition, riverine habitat is inadequate and the shortterm prognosis for habitat restoration is poor. In light of these factors, the HSRG 

recommends that the co-managers review program options or alternatives to reinstitute the 

conservation hatchery program for this depleted population. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

Operational guidelines for natural rearing protocols, selection of broodstocks, densities, 

flows, spawning matrices, proportional mixes of zero-age and yearling smolts, etc., have 

been met. The Lower Elwha Klallam Tribe is to be commended for its successful 

implementation of an enriched rearing environment in the earthen pond at the tribal 

hatchery. 

3. Steps Taken to Track Progress toward Expected Outcomes 

Please see general HSRG comments about managing for success. 

a) Will the status of major stocks (e.g., harvest and escapement) be monitored 

over time? 

The Elwha River Restoration Plan includes provisions for monitoring recovery 

(escapement) of Elwha River stocks following dam removal. However, no specific 

discussion on monitoring the status of stocks was presented in the implementation 

progress report for the Eastern Straits region. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

No report was given on methodologies (tagging, marking, etc.) to be used in assessing 

contribution of hatchery programs to conservation or harvest. There was no discussion on 

methods to assess the proportion of hatchery- or natural-origin fish on the spawning 

grounds. 
Regional Implementation Progress Report to Congress – April 2005 21 

There was no discussion of whether the system will be adaptively managed. Suffice to say 

that the Elwha managers will make appropriate mid-course corrections as data becomes 

available during dam removal. The co-managers have made the most of their available 

resources in this region. However, the potential need to expand spawning ground surveys 

and stock identification sampling programs, in particular, should be reviewed as a part of 

the development of a comprehensive monitoring plan for the region. Stable funding is 

needed for long-term monitoring of stock composition on the spawning grounds. The 

monitoring of hatchery contributions to harvest and natural spawning escapement is 

critical for tracking the success of both integrated and segregated programs. 

c) Will contributions of hatchery-origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

There was no discussion of methodologies that will be used to ensure that data gathered 

will have the desired accuracy or precision. It is likely that additional spawning surveys 

and biosampling will be needed in this region, as in others, in order for adequate accuracy 

and precision to be achieved. 
22 Progress Report to Congress – April 2005 Regional Implementation 

SOUTH PUGET SOUND 

The regional implementation progress report for South Sound was authored by WDFW, with a 

separate report on the Nisqually sub-region provided by the Nisqually Tribe. No report was provided 

by the Squaxin Island Tribe. WDFW states that the response was based upon co-manager technical 

discussions, but not policy review or agreement. This region was reviewed by the HSRG in 2001. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

Chinook and coho stocks in this region have historically been harvested at rates appropriate for 

hatchery stocks, with natural escapements being a secondary consideration. Consequently, the 

main purpose for most hatchery programs in this region is harvest. The Nisqually River coho and 

Chinook programs have secondary conservation goals. A few stocks, like Deschutes coho and 

White river spring Chinook, have received special protection due to their low abundance, and 

some stock goals are currently under revision. In the Nisqually River, for instance, the comanagers are developing specific goals for Nisqually fall Chinook, and are considering a change in 

the management strategy for coho that elevates its conservation status. The biggest challenge for 

managers in this region will be developing strategies to modify historically large harvest programs 

to be consistent with new conservation goals. 

General Overall Comment about the Co-Manager Report: 

The co-managers in this region have made good progress in regard to sizing hatchery programs to 

meet specific harvest or conservation needs. The HSRG commends the co-managers for reducing 

and/or closing several programs in this region, as recommended by the HSRG. The HSRG also 

commends and supports the Nisqually Tribe for evaluating multiple ways to implement improved 

broodstock management strategies (integrated or segregated hatchery programs) in the basin. 

WDFW and the Squaxin Island Tribe are also making significant progress in the development of 

alternatives for bringing Deschutes River hatchery facilities into regulatory compliance and 

implementing HSRG recommendations. The comments below do not pertain to steelhead 

programs. As discussed elsewhere, the co-managers are reviewing the HSRG system-wide 

steelhead recommendations and will address them in a forthcoming white paper. 

1. Stock goals and the role of hatcheries. 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have separately reviewed and confirmed the goals for their regional 

stocks that formed the premise for the HSRG’s recommendations. The co-managers have 

not yet reached agreement on all stock goals. 
Regional Implementation Progress Report to Congress – April 2005 23 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

The co-managers explicitly stated the purposes of all hatchery programs in the region 

during the regional review process. It is not clear if they have revisited these purposes 

since the regional review. Most questions raised by the HSRG have been fully addressed. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Every hatchery program in the region was clearly identified as either integrated or 

segregated during the regional review process. It is not clear if the co-managers have 

revisited these program types since the regional review. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long-term 

expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

The HSRG guidelines for integration and segregation have been largely met in the region. 

Exceptions include Squaxin Net pen coho, where the level of straying is being studied, 

and the Nisqually Chinook and coho programs, where the Nisqually Tribe is evaluating 

management alternatives. The Nisqually Tribe has taken positive action by investigating 

the feasibility of a mainstem weir as an option for achieving proper integration or 

segregation, if they intend to maintain the program at its current size. The HSRG supports 

this as a high priority for funding, if this strategy is selected. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

The HSRG commends the co-managers for appropriately sizing most of the programs in 

this region. The HSRG recommended during the regional review that eight programs and 

one hatchery in this region be discontinued or reduced in size (number smolts released). 

McAllister Creek hatchery was closed and the Chambers Creek Chinook, Garrison 

Springs chum, Nisqually coho, Coulter Creek Chinook, and Minter Creek pink programs 

were either reduced or discontinued. The Minter Creek chum and White River (Hupp 

Springs) programs were not eliminated as recommended. The HSRG also recommended 

that the co-managers evaluate regional carrying capacity, especially for coho. It is not 

clear whether this evaluation is taking place. While progress has been made, the managers 
24 Progress Report to Congress – April 2005 Regional Implementation 

in this region have generally not developed goals for harvest contribution of hatchery 

programs explicit enough to specifically size the programs to meet these needs. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

The co-managers have addressed most recommendations, to the extent available funds 

have allowed. They are committed to implementing most reforms and to meeting HSRG 

operational guidelines. Stable funding for facilities and operations must be a high priority, 

to sustain hatchery reform over time. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 

Regional catch contributions and spawning escapement estimates are made annually. All 

hatchery Chinook and coho releases in this region have been adipose fin marked or 

tagged, in order to understand the spawner composition. Hatchery releases are also well 

represented, with tagged groups for estimating harvest contribution. There have also been 

increased efforts to survey spawning grounds, in response to an increased emphasis on 

natural production in the region. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

The co-managers have made the most of their available resources in this region, however 

the potential need to expand spawning ground surveys and stock identification sampling 

programs, in particular, should be reviewed as a part of the development of a 

comprehensive monitoring plan for the region. A weir in the Nisqually Basin would be a 

useful tool for monitoring purposes, in addition to broodstock management. Stable 

funding is needed for long-term monitoring of stock composition on the spawning 

grounds. The monitoring of hatchery contributions to harvest and natural spawning 

escapement is critical for tracking the success of both integrated and segregated programs. 

c) Will contributions of hatchery-origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

As previously mentioned, a weir in the Nisqually Basin would increase the accuracy and 

precision of estimates of abundance and stock composition. It is likely that additional 

spawning surveys and biosampling will be needed in this region, as in others, in order for 

adequate accuracy and precision to be achieved. 
Regional Implementation Progress Report to Congress – April 2005 25 

STILLAGUAMISH/SNOHOMISH RIVERS 

The regional implementation progress report for Stillaguamish/Snohomish was jointly authored by 

WDFW and the Stillaguamish and Tulalip tribes. They state that the response was coordinated at both 

the co-manager technical and policy levels. This region was reviewed by the HSRG in 2001. 

HSRG Response and Synopsis 

General Description of Region and Hatchery Programs/Issues: 

The co-managers in the Stillaguamish/Snohomish region have traditionally placed a strong 

emphasis on natural production. The region is home to large natural stocks, and large and small 

hatchery programs. The Snohomish Basin has the largest naturally-producing coho population in 

the state of Washington. Together with Tulalip Bay, it also includes large Chinook, coho and chum 

harvest programs. A primary challenge here is to meet harvest goals, while rebuilding or 

maintaining naturally-spawning stocks. The co-managers appear to be meeting this challenge. 

Salmon stocks in the Stillaguamish are less productive and conservation issues dominate. Habitat 

protection and restoration are under way in both basins. The co-managers are managing hatcheries 

on the premise of improved habitat conditions. 

General Overall Comment about the Co-Manager Report: 

The HSRG commends the co-managers for their thorough consideration of all advice and 

recommendations provided by the HSRG during the regional review. It is clear that the comanagers in the Stillaguamish/Snohomish region fully understand and subscribe to the principles 

and concepts developed in the Hatchery Reform Project. Goals are clearly articulated, credible 

progress has been made (or will soon be made) to implement reforms and the infrastructure 

necessary to track progress and assure success over time is evolving. The comments below do not 

pertain to steelhead programs. As discussed elsewhere, the co-managers are reviewing the HSRG’s 

system-wide recommendations for steelhead and will address them in a forthcoming white paper. 

Operational recommendations for steelhead have generally been met for all regional programs. 

1. Stock goals and the role of hatcheries. 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reviewed the goals for all stocks in the region and confirmed the 

goals that formed the premise for the HSRG’s recommendations. In the few instances 

where the stock goals have been modified (e.g., for Stillaguamish coho), the new goals are 

clearly articulated. All recommendations of the HSRG have been met. 
26 Progress Report to Congress – April 2005 Regional Implementation 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

The co-managers have explicitly stated the purpose of all hatchery programs in the region. 

All questions raised by the HSRG have been fully addressed. Where the program purpose 

has changed since the original HSRG review, HSRG guidelines for the revised program 

have been met. An example of this is the North Fork Stillaguamish chum program, which 

was changed from a conservation program to an integrated education program, and 

reduced in size. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Every hatchery program in the region is clearly identified as either integrated or 

segregated. The co-managers have developed a particularly creative solution for the 

segregated Tulalip Bay Chinook and coho programs, where the broodstock is taken from 

the integrated hatchery returns to the Wallace Hatchery. The HSRG applauds this 

initiative. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long term 

expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

The HSRG guidelines for integration and segregation have either been met or plans are in 

place to meet them. The HSRG supports the co-managers’ request for adequate funding to 

upgrade facilities and for on-going management and monitoring of stock composition on 

the spawning grounds and in the hatchery broodstock. Co-managers in this region have 

made effective use of available funds, including tribal hatchery reform funding, but 

permanent funding is needed to ensure that the benefits of proper integration and 

segregation will continue into the future. In particular, resources needed to safely collect 

and transport representative samples of natural-origin spawners for incorporation in 

hatchery broodstock must be a high priority. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reviewed and resized hatchery programs to be consistent with all 

stock goals. They intend to evaluate the programs on an ongoing basis through adaptive 

management. For example, the release of non-native Chinook stock has been suspended, 
Regional Implementation Progress Report to Congress – April 2005 27 

the South Fork Stillaguamish chum program has been suspended, and several programs 

have been reduced (fewer smolts released). In all instances, the questions raised by the 

HSRG have been adequately addressed. The co-managers in this region are developing 

goals for harvest contribution of hatchery programs explicit enough to allow them to size 

the programs to meet these needs. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

The co-managers have addressed all recommendations, to the extent available funds have 

allowed. They are committed to implementing all reforms and to meeting HSRG 

operational guidelines. For example, all programs now employ five-by-five matrix 

spawning protocols, to maximize effective population size. Significant facility 

improvements have been made in the Stillaguamish Basin, where many of the HSRG’s 

recommendations have been implemented. Stable funding for facilities and operations to 

sustain hatchery reform over time must be a high priority. For example, funds are needed 

to improve the handling and sorting of coho and Chinook broodstock at the Wallace 

Hatchery, to fully integrate those programs. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. The co-managers in this 

region are working on developing a comprehensive monitoring plan to ensure continued 

success of their hatchery programs through adaptive management. This plan has the potential 

to serve as a model for hatchery monitoring programs state-wide. 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 

Catch contributions and spawning escapement estimates for stocks in the region are made 

annually. The HSRG presumes that the evolving adaptive management plan for the region 

will include an assessment of the need to improve the accuracy and precision of these 

estimates. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

The co-managers have made the most of their available resources in this region, however 

the potential need to expand spawning ground surveys and stock identification sampling 

programs, in particular, should be reviewed as a part of the development of a 

comprehensive monitoring plan for the region. Stable funding is needed for long-term 

monitoring of stock composition on the spawning grounds. The monitoring of hatchery 

contributions to harvest and natural spawning escapement is critical for tracking the 

success of both integrated and segregated programs. 
28 Progress Report to Congress – April 2005 Regional Implementation 

c) Will contributions of hatchery origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

Extensive stock identification programs have been developed and implemented that meet 

statistical standards for precision and accuracy, using a range of marking methods to track 

the performance of hatchery stocks over time. As the needs associated with the 

implementation of new hatchery integration policies are evaluated, the need for additional 

marking and mark sampling will be revisited. Funds should be provided for genetic stock 

identification sampling and analysis for chum programs. It is likely that additional 

spawning surveys and biosampling will be needed in this region, as in others, in order for 

adequate accuracy and precision to be achieved. 
Regional Implementation Progress Report to Congress – April 2005 29 

SKAGIT RIVER 

The regional implementation progress report for Skagit was authored by WDFW. WDFW states that 

the response was coordinated at the co-manager technical level. Although it was not specifically 

reviewed and agreed to at the policy level, WDFW believes it would be consistent at that level as well. 

This region was reviewed by the HSRG in 2002. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

Management in the Skagit region is primarily directed towards the needs of natural production. 

Portions of its headwaters are relatively pristine, with altered habitat downstream that is prone to 

flooding. There are only a few harvest-oriented hatchery programs in this region. Most Skagit 

River hatchery stocks have the primary purpose of serving as US/Canada Treaty indicator stocks, 

with secondary harvest and conservation goals. The Baker River programs are mitigation for two 

dams. Currently, the managers are also considering whether to institute a conservation program for 

spring Chinook in the Sauk and Suiattle rivers. 

General Overall Comment about the Co-Manager Report: 

The co-managers have considered all HSRG recommendations, and have taken positive action on 

some. They have made significant changes to the Baker River programs, under a new re-licensing 

agreement. The HSRG recommended that they evaluate whether surrogate indicators stocks could 

obviate the need for the indicator stock hatchery programs in this region. The managers are 

currently conducting this evaluation, and will decide on a course of action when that evaluation is 

complete. The comments below do not pertain to steelhead programs. As discussed elsewhere, the 

co-managers are reviewing the HSRG’s system-wide recommendations for steelhead and will 

address them in a forthcoming white paper. 

1. Stock goals and the role of hatcheries 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reviewed and confirmed the goals for all stocks in the region that 

formed the premise for the HSRG’s recommendations. For example, the co-managers are 

no longer pursuing a conservation purpose for the Skagit hatchery spring Chinook 

program, as recommended by the HSRG. 
30 Progress Report to Congress – April 2005 Regional Implementation 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

The co-managers have explicitly stated the purpose of all hatchery programs in the region. 

Questions raised by the HSRG have not been addressed in many cases. The progress 

report states that this is because data are not yet available to support alternatives, such as 

using stocks other than existing Skagit hatchery stocks as indexes for harvest 

management. The HSRG continues to believe that better alternatives may exist to the 

current programs that are operated primarily to serve as indicator or double index stocks. 

These alternatives may also be more cost-effective than the current approach. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Every hatchery program in the region is clearly identified as either integrated or 

segregated. The co-managers changed Skagit River coho from a segregated to integrated 

program, as recommended by the HSRG. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long-term 

expectations. 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

The HSRG guidelines for broodstocking of integrated and segregated programs have been 

met in most instances. Broodstock for the Skagit River summer and fall Chinook 

programs are comprised almost entirely of natural-origin adults. The co-managers have 

made plans to start incorporating natural-origin broodstock into the Skagit River coho 

broodstock, as recommended by the HSRG. The HSRG supports the co-managers’ request 

for funding to monitor stock composition on the spawning grounds and in the hatchery 

broodstock. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reviewed the HSRG’s recommendations to reduce the release 

numbers for the Skagit River chum or Baker/Skagit coho hatchery programs. They 

decided that both programs are already an appropriate size. 
Regional Implementation Progress Report to Congress – April 2005 31 

c) Have steps been taken to better met hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed/ 

The co-managers have addressed several recommendations, to the extent available funds 

have allowed. Fish passage by the hatchery intake for Skagit River chum was improved, 

as recommended. Many of the HSRG’s recommendations for the Baker River programs 

will be addressed under a new re-licensing agreement. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 

The co-managers are currently collecting data that will be available to make comparisons 

for determining whether Skagit index stocks can be represented by other stocks. Catch 

contributions and spawning estimates for stocks in the region are made annually. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

The co-managers have made the most of available resources in this region, however the 

potential need to expand spawning ground surveys and stock identification sampling 

programs, in particular, should be reviewed as a part of the development of a 

comprehensive monitoring plan for the region. The monitoring of hatchery contributions 

to harvest and natural spawning escapement is critical for tracking the success of both 

integrated and segregated programs. Hatchery index releases are tagged at rates sufficient 

to estimate harvest rates. However, Chinook index escapement estimates lack precision 

for most brood years, due to mainstem spawning and the inability to recover sufficient 

numbers on carcasses. Stable funding is needed for long-term monitoring of stock 

composition on the spawning grounds. 

c) Will contributions of hatchery-origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

It is likely that additional spawning surveys and biosampling will be needed in this region, 

as in others, in order for adequate accuracy and precision to be achieved. 
32 Progress Report to Congress – April 2005 Regional Implementation 

NOOKSACK/SAMISH RIVERS 

The regional implementation progress report for Nooksack/Samish was authored by WDFW. WDFW 

states that the response was coordinated at the co-manager technical level. Although it was not 

specifically reviewed and agreed to at the policy level, WDFW believes it would be consistent at that 

level as well. This region was reviewed by the HSRG in 2002. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

The Nooksack/Samish region includes programs with harvest, conservation and educational 

purposes. Co-managers in this region face difficult decisions when balancing the needs for 

conservation against the economic and cultural needs for fisheries. Chinook programs in this 

region include ESA-listed stocks (such as North Fork/Middle Fork Nooksack spring Chinook) and 

segregated programs with harvest goals (such as Lummi Bay Hatchery summer/fall Chinook and 

Mainstem Nooksack Hatchery summer/fall Chinook). The co-managers’ challenge is to 

successfully conduct these diverse programs, while minimizing straying among programs. 

Discussion is currently underway among the co-managers to initiate a conservation program for 

the South Fork Nooksack stock, but reducing the stray rate from other Chinook programs in the 

region must be a primary objective in any conservation effort. The management of coho is also 

complicated by the objectives of conducting both integrated conservation and segregated harvest 

programs. The biggest challenge for managers in the region will be developing strategies to 

operate large programs to meet their harvest needs, while meeting conservation goals for stocks 

with limited natural habitat productivity. 

General Overall Comment about the Co-Manager Report: 

The co-managers in this region have carefully considered the HSRG’s recommendations and 

principles of hatchery reform. Stock goals are clearly stated, implementation is proceeding in a 

scientifically defensible manner, and the co-managers are incorporating new information as it 

becomes available. To meet regional goals, programs have been reduced in size, a high proportion 

of hatchery releases are being marked and tagged, and monitoring has been increased. The 

programs at Bellingham Technical College’s Whatcom Creek Hatchery have been changed, to 

focus more on education and less on producing fish for harvest. 

1. Stock goals and the role of hatcheries. 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reviewed the goals for all stocks in the region, and confirmed the 

goals that were developed during the regional reviews. However, there appears to be a 
Regional Implementation Progress Report to Congress – April 2005 33 

lack of agreement among the co-managers about goals for the naturally-spawning 

component of the fall Chinook population in the Nooksack River. This has implications 

for several regional hatchery programs. In addition, it appears that the co-managers’ goals 

for natural coho stocks in this region may be in transition, and are currently unresolved. In 

the absence of agreement, programs cannot be designed that are consistent with goals for 

these stocks. 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

The co-managers have identified the purpose of each hatchery program, and addressed the 

majority of questions raised during the regional review. The co-managers have agreed that 

the major focus of the Whatcom Creek Hatchery should be education, and the curriculum 

is being modified to teach the best operational and fish culture practices. The co-managers 

have requested, and the HSRG will provide, assistance in developing a conservation 

program for South Fork Nooksack spring Chinook. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Every hatchery program within the region is identified as integrated or segregated. In most 

cases, no changes to program types were noted by the co-managers. However, the 

program type of the Skookum Creek Hatchery Coho is under evaluation. This was 

reviewed as a segregated harvest program. The co-managers are investigating interactions 

with wild coho, but have not yet developed a broodstock management strategy for this 

program consistent with guidelines for integrated or segregated programs. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long-term 

expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

Throughout the region, the co-managers have made significant progress in achieving 

desired spawning proportions. Hatchery releases are marked, using a combination of 

adipose fin clips, otolith marks and coded wire tags. The North Fork/Middle Fork 

Nooksack spring Chinook program has been reduced by more than half, to allow 

evaluation and potentially reduce straying to the South Fork. Information is being 

gathered on timing and the propensity to stray. Release strategies have also been changed. 

The co-managers have terminated the North Fork Nooksack Chum program, which was 

not meeting the guidelines for proper integration. The Mainstem Nooksack hatchery 

summer/fall Chinook has not been suspended, as recommended by the HSRG. However, 
34 Progress Report to Congress – April 2005 Regional Implementation 

hatchery production is differentially marked, and spawning ground surveys are underway 

as conditions permit, to identify hatchery strays in the South Fork. Tissue sampling for 

DNA analysis of outmigrating juveniles from the South Fork has been conducted, but 

progress on developing baselines has been hindered by a lack of samples. A lack of 

funding has also limited the DNA analysis. While the co-managers deserve credit for the 

changes made to date, the HSRG still believes this outplanting program should either be 

discontinued, or other actions taken to reduce the risks it poses to South Fork spring 

Chinook (a stock for which the co-managers are proposing a new conservation hatchery 

program). 

Various strategies are underway to improve collection facilities and reduce potential 

straying for Lummi Bay Hatchery Summer/Fall Chinook. Although hatchery reform funds 

have not been made available, the co-managers are improving ponds using limited 

existing funds and are continuing efforts to secure additional funds. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

Two hatchery programs have been discontinued—North Fork Nooksack Chum and 

Samish Chum. Significant reductions have been made to the North Fork/Middle Fork 

Nooksack spring Chinook and Whatcom Creek Hatchery Pink programs, to better achieve 

the goals for these stocks. As recommended, the program size for the Lummi Bay 

Hatchery coho program is being reviewed, but no changes have been implemented. While 

progress has been made, the co-managers in this region have generally not developed 

goals for harvest contribution of hatchery programs explicit enough to specifically size the 

programs to meet these needs. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

Throughout the region, spawning protocols have been adjusted to follow HSRG 

guidelines. Various release strategies are under evaluation for North Fork/Middle Fork 

Nooksack spring Chinook, to better meet conservation goals for this stock. Disease 

prevention is being actively addressed for several programs, including pond modifications 

for Lummi Bay Hatchery coho and new rearing ponds for Samish summer/fall Chinook. 

Evaluation of the potential impact of yearling releases is ongoing for Samish summer/fall 

Chinook. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 
Regional Implementation Progress Report to Congress – April 2005 35 

The co-managers have ongoing monitoring programs in place for numerous stocks. For 

example, extensive marking programs are ongoing for Lummi Bay Hatchery summer/fall 

Chinook and Nooksack North Fork/Middle Fork spring Chinook, to monitor potential 

interactions with South Fork Nooksack spring Chinook. Marking programs are also 

ongoing for Samish summer/fall Chinook, to evaluate stray rates and contribution to 

fisheries. DNA baselines are being developed, as funding permits. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

The co-managers are making management changes for North Fork/Middle Fork spring 

Chinook, as new biological information becomes available. Monitoring programs are in 

place in the Nooksack and Samish drainages. Monitoring programs for coho in the 

Nooksack drainage have been increased, to improve information available for Kendall 

Creek coho. The co-managers have made the most of their available resources in this 

region, however the potential need to expand spawning ground surveys and stock 

identification sampling programs, in particular, should be reviewed as a part of the 

development of a comprehensive monitoring plan for the region. Stable funding is needed 

for long-term monitoring of stock composition on the spawning grounds. The monitoring 

of hatchery contributions to harvest and natural spawning escapement is critical for 

tracking the success of both integrated and segregated programs. 

c) Will contributions of hatchery-origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

Although not specifically addressed, marking and tagging proportions are high throughout 

the region. It is likely that additional spawning surveys and biosampling will be needed in 

this region, as in others, in order for adequate accuracy and precision to be achieved. High 

stray rates from all Chinook programs into the South Fork Nooksack have been a 

particular concern. Programs to monitor straying into this system are ongoing to assess 

effects on the South Fork Nooksack spring Chinook stock. 
36 Progress Report to Congress – April 2005 Regional Implementation 

CENTRAL PUGET SOUND 

The regional implementation progress report for Central Sound was authored by WDFW, with a 

separate report on the East Kitsap sub-region provided by the Suquamish Tribe. WDFW states that the 

response was WDFW’s interpretation of co-manager technical meetings and subsequent agreements 

and that opportunity for review was provided to the tribal co-managers. This region was reviewed by 

the HSRG in 2002. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

The Central Puget Sound region is one of the largest regions reviewed by the HSRG. It contains 

four sub-regions—Puyallup River, Green River, Lake Washington and East Kitsap. Each subregion is different in terms of its harvest goals, habitat conditions and hatchery programs, but the 

region’s hatchery programs predominantly have harvest as their primary goal. Most hatchery 

programs in the region are large, harvest-oriented Chinook and coho programs, but there are also 

several smaller, harvest-oriented chum programs. Few conservation programs exist in the region, 

but there are important conservation programs for spring Chinook in the Puyallup system and a 

conservation-oriented, harvest program for sockeye in the Lake Washington sub-region. The 

region includes two of the three largest cities in the state of Washington. Habitat through the 

region has been negatively affected by population growth, industrial development in estuarine 

areas, hydroelectric and water supply impoundments. The biggest challenge for co-managers in the 

region will be developing strategies to operate large programs to meet harvest needs, while 

meeting conservation goals for stocks with limited natural habitat productivity. 

General Overall Comment about the Co-Manager Report: 

Based on the implementation progress report, it appears that the sub-regions have progressed at 

different paces, in terms of implementing hatchery reform. Specifically, the co-managers in the 

Green River, Lake Washington and East Kitsap sub-regions seem to have made good 

implementation progress. However, a major shortcoming in the region is the inability to identify 

hatchery-origin fish. The managers in the Puyallup watershed have made some progress, but 

appear to still be in the discussion and planning stage for many of the important elements of 

hatchery reform. No report was received about the White River drainage of the Puyallup subregion, therefore the HSRG cannot comment on progress in that drainage. The progress report 

addressed only the HSRG’s program-specific recommendations. Focusing only on those 

recommendations makes it difficult to assess progress in regard to developing clear stock goals or 

determining how programs will be managed over time. Follow-up conversations with authors of 

the report, however, indicate that progress in these two areas is again different across the subregions, with good progress made in the Green River and Lake Washington sub-regions, and less 

progress in the Puyallup and East Kitsap sub-regions. 

The comments below do not pertain to steelhead programs. As discussed elsewhere, the comanagers are reviewing the HSRG’ system-wide recommendations for steelhead and will address 
Regional Implementation Progress Report to Congress – April 2005 37 

them in a forthcoming white paper. Operational recommendations for steelhead have generally 

been met for all programs in the region. 

1. Stock goals and the role of hatcheries 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

Specific information was not provided to answer this question in the implementation 

progress report. Follow-up discussions with one sub-basin author indicated that, in at least 

some sub-regions, this has occurred. Specifically, the co-managers in the Green River and 

Lake Washington sub-basins have reviewed goals and are in technical agreement. It 

appears that, in the Puyallup and East Kitsap sub-regions, individual managers are 

reviewing these goals, but active co-manager discussion has not occurred. 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

Again, specific information was not provided to answer this question in the 

implementation report. Follow-up discussions with one sub-basin author indicated that, in 

at least some sub-basins, this has occurred. Specifically, the co-managers in the Green 

River and Lake Washington sub-basins have reviewed the purpose of each hatchery 

program and are in technical agreement. Again, it appears that in the Puyallup and East 

Kitsap sub-regions, individual managers are reviewing the purpose of their programs, but 

active co-manager discussion has not occurred. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Specific information was not provided to answer this question in the implementation 

report. Follow-up discussions with one sub-region author indicated that, in at least some 

sub-basins, this has occurred. Specifically, the co-managers in the Green River and Lake 

Washington sub-basins have reviewed the program type for of each hatchery program and 

are in agreement. In the Lake Washington watershed, the broodstock management strategy 

for the fall Chinook program has been modified to an integrated strategy. Again, it 

appears that in the Puyallup and East Kitsap sub-regions, individual managers are 

reviewing their broodstock management strategy, but active co-manager discussion has 

not occurred. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long-term 

expectations 
38 Progress Report to Congress – April 2005 Regional Implementation 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

Comments on this question are confined to the Green River, Lake Washington, East 

Kitsap and Puyallup River watersheds, where progress reports have been provided. Good 

progress has been made in the Green River and Lake Washington sub-regions toward 

implementing effective broodstock management principles for Green River fall Chinook 

and coho, and Lake Washington fall Chinook and coho. In the Green River, the hatchery 

fall Chinook broodstock includes approximately 20–30% natural-origin recruits, and some 

hatchery-origin strays are being removed from the spawning population by a weir at Icy 

Creek. In order to accomplish the goals of allowing the natural-origin segment to drive the 

adaptation of this stock, however, additional efforts are likely to be needed to control 

hatchery straying, and/or to incorporate additional natural-origin fish into the broodstock. 

For Green River coho, unmarked fish are being incorporated into the hatchery broodstock 

at a rate of up to 70%. However, since a major portion of the hatchery releases that can 

contribute to escapement in this watershed are not marked, it is impossible to determine 

the composition of the hatchery broodstock or the naturally-spawning population. 

Additionally, the managers report that little effort has been put into evaluating the 

hatchery stray rate from various coho programs in the watershed. The HSRG strongly 

supports additional marking and evaluation of the composition of natural spawning, if the 

co-managers want to effectively integrate this stock. 

Good progress has also been made in the East Kitsap sub-region toward implementing 

effective broodstock management principles. The fall Chinook harvest program in this 

sub-region had already met these principles, but the HSRG had concerns about the 

effectiveness of these strategies for the coho net pen and fall chum programs. Since the 

review, the co-managers have suspended all coho net pen releases. While this decision 

was not driven solely by the desire to more effectively segregate the program, suspension 

of the program effectively eliminates any straying risks that may have occurred. Should 

this program be reactivated, the HSRG suggests that the co-managers review their harvest 

and conservation goals for coho stocks in the sub-region and design a program that is 

consistent with those goals. The co-managers also recognize the need to begin 

incorporating natural-origin fish into the hatchery broodstock for the East Kitsap fall 

chum program. The implementation report indicates that this will be accomplished as 

program funding allows. The HSRG supports funding for implementation of this 

broodstock policy. However, alternate goals or enhancement strategies may need to be 

developed for this stock, if funding to implement the preferred option is not available. 

In the Lake Washington sub-region, good progress has been made for many programs. 

The Lake Washington sockeye program is probably the model for broodstock 

management, monitoring and evaluation and adaptive management in the entire region. In 

addition, efforts are being made at Lake Washington fall Chinook and coho programs to 

integrate the hatchery broodstock with natural stocks in the sub-region. The progress 

report states that, in both of these programs, approximately 10% of the hatchery 

broodstock is now made up of natural spawners. However, since the level of current 
Regional Implementation Progress Report to Congress – April 2005 39 

hatchery straying was not reported, it is impossible to determine if this approach will 

effectively integrate the hatchery and natural populations. Additional efforts to limit 

hatchery straying, or further incorporate natural-origin recruits into the broodstock, are 

likely needed. In particular, the integration of the Lake Washington fall Chinook program 

will likely require further collection of broodstock from the natural populations in north 

Lake Washington tributaries. 

In the Puyallup River, the report points to progress in reducing straying risks from some 

programs, but actions to improve stock integration have yet to occur. The report says that 

discussions are occurring regarding collection of natural-origin broodstock for the fall 

Chinook and coho program, but final decisions on the exact approach have not been made. 

The Puyallup Tribe has constructed a new facility that should reduce straying of returning 

fall Chinook. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

In the East Kitsap sub-region, several programs have been resized to be more consistent 

with stock goals for harvest and conservation. Most notably, the coho net pen program has 

been suspended, partially as the result of changing harvest goals. Permanent reduction is 

being considered for fall Chinook releases from satellite locations at Grovers, Dogfish and 

Clear creeks. In addition, fry releases have been reduced both in number and location in 

for East Kitsap coho, to be more consistent with the primarily educational purpose of the 

program. Chum programs are also being discontinued in central and south Kitsap streams, 

where populations no longer appear to need supplementation. While progress has been 

made, the managers in this region have generally not developed goals for harvest 

contribution of hatchery programs explicit enough to specifically size the programs to 

meet these needs. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

Many of the recommended changes in hatchery operational guidelines are being 

implemented. The report indicates that most other operational changes will be adopted as 

facilities are improved. For example, spawning guidelines have been adopted to increase 

effective population sizes in most hatchery programs, and efforts are being made to 

incorporate all portions of the run timing into the hatchery broodstock. Infrastructure 

improvements at the Green River Hatchery should significantly improve the ability to 

meet suggested operational changes, such as allowing volitional releases of hatchery fish. 

A major shortcoming in the region is the inability to identify hatchery-origin fish. In 

certain watersheds, for example the Green River, a major portion of hatchery coho 

releases has not been marked. In order to accurately estimate the composition of hatchery 

fish spawning naturally, and to accurately collect natural-origin spawners for hatchery 

broodstock, all major releases of coho need to be marked. 
40 Progress Report to Congress – April 2005 Regional Implementation 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. The progress report 

provided no information in regard to developing a monitoring and evaluation or adaptive 

management plan for the region, necessary elements for managing for success into the 

future. Therefore, the HSRG can make no comment in regard to the co-managers’ 

progress in this area. The HSRG strongly recommends the development of an adaptive 

management plan, as well as a comprehensive monitoring and evaluation program. 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 

No information was provided on this topic; therefore, the HSRG can make no comment in 

regard to this question (see above). 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

No information was provided on this topic; therefore, the HSRG can make no comment in 

regard to this question (see above). Stable funding is needed for long-term monitoring of 

stock composition on the spawning grounds. The monitoring of hatchery contributions to 

harvest and natural spawning escapement is critical for tracking the success of both 

integrated and segregated programs. 

c) Will contributions of hatchery-origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

Catch contribution and spawning escapement estimates are made annually for stocks in 

the region. Although not specifically addressed, marking and tagging proportions are high 

throughout the region. As noted earlier, however, the managers report that little effort has 

been put into evaluating the hatchery stray rate from various coho programs in the Green 

River watershed. They also note that additional funding will be required to expand 

assessment efforts, including accurately determining stock composition of natural 

spawners, as well as collection of natural-origin recruits for incorporation into hatchery 

broodstocks. It is likely that additional spawning surveys and biosampling will be needed 

in this region, as in others, in order for adequate accuracy and precision to be achieved. 
Regional Implementation Progress Report to Congress – April 2005 41 

HOOD CANAL 

The regional implementation progress report for Hood Canal was jointly authored by WDFW, the 

Skokomish, Jamestown S’Klallam, Lower Elwha Klallam, and Port Gamble S’Klallam tribes and 

USFWS. They state that the report represents co-manager agreement at the policy and technical level. 

This region was reviewed by the HSRG in 2003. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

Hood Canal is a fjord between the Olympic Mountains and the Kitsap Peninsula in the western 

Puget Sound area. Three state hatcheries, one federal hatchery, several tribal facilities and one 

non-government organization hatchery exist in this region. The HSRG identified two major 

problems in the Hood Canal region: 1) overproduction of chum, coho and Chinook; and 2) high 

stray rates of returning coho released from net pens and hatcheries at the northern end of Hood 

Canal that pose genetic risks to natural populations. Large surpluses of unharvested, returning 

adults must be handled by hatchery personnel. Carcasses resulting from large numbers of 

unharvested adults may also contribute to nutrient load and low dissolved oxygen problems in the 

marine environments of Hood Canal. The biggest challenge for co-managers in the region will be 

developing strategies to operate large programs to meet their harvest needs, while meeting 

conservation goals for stocks with limited natural habitat productivity. 

General Overall Comment about the Co-Manager Report: 

Co-managers in the Hood Canal region agreed with most of the changes recommended by the 

HSRG, and have responded aggressively. For example, they have substantially reduced the 

number of fall chum and other species released into Hood Canal. The co-managers have not 

agreed with the HSRG’s assessment of the scope and seriousness of straying from coho programs 

at the northern end of Hood Canal. They have implemented more extensive spawning ground 

surveys, to quantify the problem, and are planning to conduct genetic and other studies to 

investigate these concerns and the feasibility of implementing the HSRG’s recommendations on 

this subject. These recommendations include developing a new hatchery broodstock for coho and 

other major, programmatic changes. An unresolved problem is the lack of marking on a sufficient 

number of fish from large hatchery programs—such as the fall chum program and the Skokomish 

River fall Chinook program—to accurately determine the abundance and productivity of 

potentially-affected natural stocks. 

1. Stock goals and the role of hatcheries. 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 
42 Progress Report to Congress – April 2005 Regional Implementation 

The co-managers have reviewed conservation and harvest goals for all stocks in the region 

and have made a number of changes as a result. Habitat goals appear to not be as welldefined, particularly in the Skokomish River. 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

The purpose of each program is clearly stated. For example, the co-managers have 

developed a comprehensive strategy for using artificial propagation to help recover 

summer chum throughout Hood Canal, a species currently listed as threatened under the 

Endangered Species Act. In contrast, hatchery programs for fall chum are intended to 

support harvest. Most questions raised by the HSRG have been addressed. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Every hatchery program in the region is clearly designated as either integrated or 

segregated. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long-term 

expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

There have been substantial reductions in the number of chum released from segregated 

programs. The co-managers have terminated steelhead outplants across the region. They 

have also reduced the number of pink salmon released from Hoodsport Hatchery from one 

million to 500,000 fry. These changes are expected to reduce the proportion of hatcheryorigin fish on natural spawning areas. No changes have yet been implemented to reduce 

stray rates from north Hood Canal coho programs. The co-managers are investigating 

alternative strategies to meet the intent of the HSRG’s coho recommendations. 

Fall chum, pink and the majority of Chinook are released from hatcheries unmarked, thus 

precluding the ability to understand or control the proportion of hatchery- and naturalorigin fish from these segregated programs in broodstocks and on the spawning grounds. 

The HSRG recognizes the concern of the Skokomish Tribe about the potential harvest 

implications of applying 100% adipose fin clips to fall Chinook releases in the region. 

However, without applying a “mass mark” of some sort, the status of the natural fall 

Chinook population in the Skokomish River will never be understood. The HSRG 

therefore recommends that the co-managers come to agreement on and implement a 

marking (external or otherwise) and mark recovery protocol that will allow the 

identification of hatchery- versus natural-origin fall Chinook in this watershed. 
Regional Implementation Progress Report to Congress – April 2005 43 

Additionally, the lack of marking also precludes understanding the stray rate from large 

hatchery programs for fall chum in the entire region. The HSRG therefore makes the same 

recommendation for these programs. 

The co-managers have used the All-H Analyzer (AHA) tool to investigate the feasibility 

of developing integrated hatchery broodstocks for Chinook on the Skokomish River 

(George Adams Hatchery) and coho at Big Beef Creek, as recommended by the HSRG. 

Preliminary analyses of coho in Big Beef Creek indicate that this population can support 

an integrated hatchery broodstock, which could then provide harvestable fish for the Port 

Gamble net pens, and perhaps elsewhere in Hood Canal, as recommended by the HSRG. 

On the other hand, AHA analysis indicates that poor habitat conditions in the Skokomish 

River preclude meeting the guidelines for an integrated hatchery program for Chinook 

salmon at the George Adams Hatchery at this time. However, this recommendation by the 

HSRG remains a long-term goal of the co-managers, pending habitat improvements. The 

HSRG recommends incorporating natural-origin fish into the hatchery broodstock for this 

program, as the health of the natural population allows, to increase the degree of 

adaptation to the natural environment of this population. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

While progress has been made, the managers in this region have generally not developed 

goals for harvest contribution of hatchery programs explicit enough to specifically size the 

programs to meet these needs. 

In response to HSRG recommendations, the co-managers have significantly reduced the 

total number of fish released from Hood Canal hatcheries. For example, overall hatchery 

production of chum fry in Hood Canal has been reduced from 33.7 million to 22.5 million 

fry, a 33% decrease. These reductions have been accomplished by terminating fall chum 

programs at Quilcene National Fish Hatchery (NFH) (2.2 million fry) and at George 

Adams Hatchery (five million fry), and reducing fall chum production at the Little Boston 

Tribal Hatchery (from one million to 500,000 fry) and at the Hoodsport Hatchery (from 15 

million to 12 million fry). These reductions should significantly reduce the large number 

of surplus fall chum adults returning to Hood Canal hatcheries. The co-managers have 

also followed the HSRG recommendation to terminate the Chinook program at Big Beef 

Creek (200,000 fry), but have only modestly reduced production of Chinook at Hoodsport 

Hatchery, from three million to 2.8 million sub-yearlings (a seven percent reduction) and 

from 250,000 to 120,000 yearlings, in response to the HSRG recommendation to address 

loading and density concerns at that hatchery. They have also reduced pink production 

from one million to 500,000 fry at Hoodsport Hatchery and have agreed to terminate all 

steelhead outplants into Hood Canal streams, while retaining the Hamma Hamma River 

steelhead conservation and recovery program (as the HSRG recommended). 

Consistent with HSRG recommendations, the coho program at George Adams Hatchery 

was reduced from 500,000 to 300,000 smolts released annually, to reduce the number of 
44 Progress Report to Congress – April 2005 Regional Implementation 

unharvested surplus adults returning to that facility. In order to reduce straying, the HSRG 

recommended discontinuing the Quilcene Bay net pen program and either reducing net 

pen releases of coho into Port Gamble Bay or increasing the harvest on these fish. The 

Port Gamble S’Klallam Tribe has successfully restored its fishery in Port Gamble Bay, 

and non-treaty fishers are also harvesting these fish. The Quilcene Bay program has not 

been discontinued. The co-managers will also consider adjustments to the net pen program 

size, based on results of monitoring harvests and escapements. The HSRG remains 

concerned about the level of straying and believes that the co-managers need to continue 

pursuing a combination of hatchery and harvest actions to reduce straying to an acceptable 

level. Given the high surplus returns to Quilcene NFH, the Quilcene Bay net pen program 

appears to provide marginal additional benefits, while posing significant straying risks. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

The co-managers have addressed many facility recommendations, to the extent funds have 

allowed. For example, they have acquired a new groundwater source (200 gallons per 

minute) for egg incubation at Hoodsport Hatchery. However, limited floor/building space 

has prevented them from expanding incubation facilities to meet egg incubation needs for 

chum salmon. Consequently, the co-managers have chosen not to follow the HSRG 

recommendation to terminate chum fry transfers from McKernan and George Adams 

hatcheries to Hoodsport Hatchery, because of continuing shortages of egg incubation 

space at Hoodsport. Additional incubation space at Hoodsport, or further reductions of the 

chum program there, should be high priorities for implementation. The co-managers 

report that the majority of HSRG facility recommendations remain unimplemented 

because of funding constraints, such as installation of pollution abatement ponds at 

George Adams Hatchery. The co-managers have increased the incorporation of “jacks” 

into coho broodstocks at Quilcene NFH and Hoodsport Hatchery from two to ten percent 

of all males spawned, as recommended by the HSRG. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. The co-managers in 

Hood Canal have initiated some additional marking and coded-wire tagging programs, 

particularly for Chinook released from Hoodsport Hatchery. However, monitoring of 

natural- and hatchery-origin Chinook in the Skokomish River will require a substantial 

increase in marking of fish released from George Adams Hatchery. Additional monitoring 

and evaluation appears to be limited by availability of funds (e.g., genetic studies, 

additional monitoring equipment). 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 

Monitoring of summer chum recovery and contributions of hatchery-origin coho to 

harvest will continue. All hatchery-origin summer chum are otolith marked prior to 
Regional Implementation Progress Report to Congress – April 2005 45 

release, and all coho are adipose fin clipped. At the present time, no fall chum or pink are 

marked (e.g. with otolith marks), and only a small portion of Chinook are marked or 

tagged. The co-managers need to agree on and implement a strategy for distinguishing all 

hatchery- and natural-origin fish in the region. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

Monitoring of progress towards achievement of conservation goals will continue for 

winter steelhead and fall Chinook in the Hamma Hamma River, and summer chum 

throughout Hood Canal. Contributions to harvest of coho released from Quilcene NFH, 

Quilcene Bay net pens, and Port Gamble net pens will continue. Monitoring of hatcheryorigin Chinook escapement into the Skokomish River will be difficult without a 

substantial increase in marking effort and resources. As noted above, all releases of fall 

chum and pink within Hood Canal are unmarked (e.g. via otoliths) and, hence, 

contributions to harvest and escapement cannot be estimated directly. The co-managers 

have made the most of their available resources in this region, however the potential need 

to expand spawning ground surveys and stock identification sampling programs, in 

particular, should be reviewed as a part of the development of a comprehensive 

monitoring plan for the region. Stable funding is needed for long-term monitoring of stock 

composition on the spawning grounds. The monitoring of hatchery contributions to 

harvest and natural spawning escapement is critical for tracking the success of both 

integrated and segregated programs. 

c) Will contributions of hatchery-origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

Accurate estimates of escapement and contributions to harvest and broodstock are 

obtainable for hatchery-origin coho, Hamma Hamma steelhead, summer chum, and 

partially for fall Chinook released from Hoodsport Hatchery. Such estimates are currently 

not possible for fall chum, pink and fall Chinook released from the George Adams 

Hatchery into the Skokomish River (see comment above). It is likely that additional 

spawning surveys and biosampling will be needed in this region, as in others, in order for 

adequate accuracy and precision to be achieved. 
46 Progress Report to Congress – April 2005 Regional Implementation 

WILLAPA BAY 

The regional implementation progress report for Willapa Bay was authored by WDFW. There are no 

tribal co-managers in this region. This region was reviewed by the HSRG in 2003. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

The Willapa Bay region, located in coastal southwest Washington, drains numerous rivers and 

creeks. The watershed is noted for an abundance of rainfall and timber harvest, the latter of which 

has resulted in habitat degradation. Hatcheries are located on each of the three largest rivers—the 

Willapa, Naselle and Nemah. Unlike all other regions reviewed by the HSRG, Willapa Bay does 

not have tribal harvest, and there is no commercial harvest of steelhead. Unlike the Puget Sound 

and Hood Canal regions, there are no ESA-listed stocks in this region. Much of the fish harvest is 

commercial, and there are large hatchery Chinook and coho programs. Hatcheries in this region 

require considerable capital construction to comply with passage/intake requirements and pollution 

abatement, or just to continue to operate. Naselle Hatchery (which has difficulty trapping 

Chinook) needs to be either completely rebuilt or abandoned. Nemah Hatchery impairs wild chum 

during coho returns. The biggest challenge for managers in the region will be to develop strategies 

to operate large programs to meet their harvest needs, while meeting conservation goals for stocks 

with limited natural habitat productivity. 

General Overall Comment about the Manager Report: 

Progress has been made in some areas in this region, including improved monitoring and 

identifying hatchery programs as integrated or segregated. However, it appears that less progress 

has been made in implementing hatchery reform in this region than in many others. Of particular 

concern is the uncertainty as to whether clear goals have been defined for each of the stocks within 

the region. Another major obstacle is the continued lack of ability to identify hatchery- and 

natural-origin adults. WDFW cites the time requirements necessary to implement significant 

capital improvements and limited resources as the principal constraints to complete 

implementation of HSRG recommendations. The HSRG recommendations have been used to 

garner funding, and many recommendations have been implemented. Funding has been identified 

for marking fish to ascertain hatchery/wild run compositions, beginning in 2006. The comments 

below do not pertain to steelhead programs. As discussed elsewhere the co-managers are 

reviewing the HSRG system-wide recommendations for steelhead and will address them in a 

forthcoming white paper. Operational recommendations for steelhead have generally been met for 

all programs in the region. 

1. Stock goals and the role of hatcheries 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 
Regional Implementation Progress Report to Congress – April 2005 47 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

Goals for all hatchery- and naturally-spawning stocks in this region were identified during 

the regional review process. The progress report provided by WDFW addressed the 

HSRG’s program-specific recommendations. Focusing only on those recommendations 

makes it difficult to assess progress in regard to developing clear stock goals or 

determining how programs will be managed over time. The managers state that until fish 

are marked and adult fish return, clear goals cannot be defined. The managers also state 

that decisions about the role of hatcheries in this region are complicated by the fact that an 

engineers’ assessment of Naselle Hatchery recommended either abandoning or completely 

rebuilding the facility. This assessment of the facility is consistent with the HSRG’s 

review. The managers need to be clear what they will do if funds are not provided for 

improving this facility. It is not clear to the HSRG whether the managers in this region 

clearly understood the distinction between stock goals and hatchery program types 

(integrated or segregated). The managers should clarify goals for all stocks in this region 

and develop interim plans for operating programs while better information is collected 

that will allow them to refine stock goals and hatchery program roles. 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

Purposes for all hatchery programs in this region were identified during the regional 

review process. Most questions raised by the HSRG regarding the purposes of hatchery 

programs have been addressed. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Every hatchery program in the region was designated as either integrated or segregated 

during the regional review process. WDFW reports that these designations are being 

reviewed for programs across the region, and this may result in major changes. For 

example, a plan for integrating Willapa Basin hatchery winter steelhead is being 

considered. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long term 

expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 
48 Progress Report to Congress – April 2005 Regional Implementation 

WDFW has adopted the HSRG’s guidelines for integration and segregation. All hatchery 

Chinook releases in the region will be identified through adipose fin clipping beginning in 

2006. This will help to resolve uncertainty as to the degree of integration in many stocks 

(Chinook in particular). A process for documenting hatchery and wild coho in hatchery 

broodstock has begun. Spawning surveys have been increased. Significant strides have 

been made in identifying stocks via coded-wire tagging; Willapa, Nemah and Naselle 

river fall Chinook, and Nemah and Naselle river coho are now being coded-wire tagged. 

The HSRG strongly supports WDFW’s request for adequate funding to upgrade facilities 

and on-going management and monitoring of stock composition on the spawning grounds 

and in the hatchery broodstock. 

WDFW has made good use of available funds, including hatchery reform funding, but 

stable funding is needed to ensure that the benefits of proper integration and segregation 

continue into the future. In particular, resources needed to safely collect and transport 

natural-origin spawners, for incorporation in hatchery broodstock, must be a high priority. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

No information has been provided regarding whether WDFW has resized or will resize 

hatchery programs in this region. The managers in this region have generally not 

developed goals for harvest contribution of hatchery programs explicit enough to 

specifically size the programs to meet these needs. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

WDFW reports that it is committed to implementing HSRG operational guidelines. All 

programs in this region now employ single pair mating protocols, to maximize effective 

population size. The spawning protocol of using ten percent jacks for coho (as 

recommended by the HSRG) will commence in 2005. Stable funding for facilities and 

operations to sustain hatchery reform over time must be a high priority. For example, 

funds are needed to improve the handling and sorting of coho and Chinook broodstock at 

all three regional facilities, in order to allow those programs to operate as properly 

integrated. WDFW is to be complemented for conducting a steelhead recycling study at 

Forks Creek Hatchery in a timely manner, consistent with the HSRG’s recommendations. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. In this region, WDFW is 

working on developing a comprehensive monitoring plan to ensure continued success of their 

hatchery programs through adaptive management. 
Regional Implementation Progress Report to Congress – April 2005 49 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 

Harvest information will be greatly enhanced with the recent addition of coded-wire 

tagging of Naselle and Nemah stocks. There are increased spawning escapement surveys 

for stocks in the region. Marking of Chinook will increase the value of these surveys. The 

HSRG presumes that the evolving adaptive management plan for the region will include 

an assessment of the need to improve the accuracy and precision of these estimates. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

The monitoring of hatchery contributions to harvest and natural spawning escapement is 

critical for tracking the success of both integrated and segregated programs. The comanagers have made the most of their available resources in this region, however the 

potential need to expand spawning ground surveys and stock identification sampling 

programs, in particular, should be reviewed as a part of the development of a 

comprehensive monitoring plan for the region. Stable funding is needed for long-term 

monitoring of stock composition on the spawning grounds. The monitoring of hatchery 

contributions to harvest and natural spawning escapement is critical for tracking the 

success of both integrated and segregated programs. 

c) Will contributions of hatchery origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

Extensive stock identification programs need to be developed and implemented that meet 

statistical standards for precision and accuracy, using a range of marking methods to track 

the performance of hatchery stocks over time. As the needs associated with the 

implementation of new hatchery integration policies are evaluated the need for additional 

marking and mark sampling will be revisited. It is likely that additional spawning surveys 

and biosampling will be needed in this region, as in others, in order for adequate accuracy 

and precision to be achieved. 
50 Progress Report to Congress – April 2005 Regional Implementation 

NORTH COAST 

The regional implementation progress report for North Coast was authored by WDFW, with separate 

reports provided to the HSRG by the Quinault Indian Nation and the Hoh and Makah tribes. WDFW 

states that the report is based upon technical discussions, but not policy review or agreement. This 

region was reviewed by the HSRG in 2003. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

This region includes the coastal drainages west of—and including—the Hoko River and north of 

Grays Harbor. Most of the land base within this region consists of public and private timberlands, 

Indian reservations and Olympic National Park. The region is sparsely inhabited, with the City of 

Forks representing the largest population center. This report covers implementation progress made 

by the co-managers in response to the HSRG’s recommendations with respect to 15 hatchery 

programs (five Chinook, seven coho, two sockeye, and one chum) reviewed by the HSRG in 2003. 

An additional 12 hatchery programs were also reviewed in the region in 2003, but, for the reasons 

described below, the comments that follow do not apply to them. 

General Overall Comment about the Co-Manager Report: 

In general, the co-managers have considered the HSRG’s recommendations carefully and have 

indicated, with few exceptions, a willingness to implement them. Indeed, many of the 

recommendations are already being implemented. However, full implementation will take time 

because of the funding that will be required. To this end, the co-managers need to develop a 

prioritized implementation plan and attach timelines to it. The comments below do not pertain to 

eleven steelhead programs. As discussed elsewhere, the co-managers are reviewing the HSRG 

system-wide recommendations regarding steelhead and will address them in a forthcoming white 

paper. Operational recommendations for steelhead have generally been met for all programs in the 

region, and some of the programs are already being operated according to the HSRG’s systemwide recommendations for steelhead. The comments also do not apply to the Hoko River fall 

Chinook program, for which there was no response to the HSRG’s request for an implementation 

update. 

1. Stock goals and the role of hatcheries. 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reviewed the goals for all stocks in the region and confirmed the 

goals that formed the premise for the HSRG recommendations. Most of the HSRG’s 

recommendations have been accepted by the co-managers. 
Regional Implementation Progress Report to Congress – April 2005 51 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

The co-managers have explicitly stated the purpose of all hatchery programs in the region. 

The HSRG questioned the need for a conservation program to supplement a seemingly 

healthy coho population (Queets River Coho). This program was subsequently suspended. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

The intent for every hatchery program in the region is clearly identified as either 

integrated or segregated. The co-managers have indicated, however, that the costs entailed 

in ensuring that hatchery programs are properly integrated or segregated are a major 

hindrance to immediate implementation of the intended strategy. The HSRG strongly 

supports requests for funding in support of the marking, monitoring and infrastructure 

needed to ensure that hatchery programs are properly integrated or segregated, because 

hatchery programs must be operated in one or other of these modes if hatchery reform is 

to be successful. 

2. Steps taken (decisions made and actions taken) towards meeting short -and long-term 

expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

The HSRG guidelines for integration and segregation are already being met for some of 

the programs (e.g., Lake Ozette sockeye and Quinault River fall Chinook). For others, the 

degree of marking and/or monitoring will have to be intensified, to ensure that proper 

integration or segregation is being achieved. As mentioned above, the co-managers report 

that effective broodstock management will be accelerated if additional state and federal 

funding is made available for implementing these strategies. 

b) Have steps been taken to size programs consistent with goals for all hatcheryand naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

The co-managers have reviewed and resized some hatchery programs to be consistent 

with stock goals and intend to evaluate the programs on an ongoing basis through adaptive 

management. Questions about proper sizing of some programs to avoid recent surplus 

hatchery returns have been resolved by either intensifying harvest, reducing the size of 

programs, or both (e.g., Educket Creek Hatchery coho and Queets/Salmon River coho). 

However, the managers in this region have generally not developed goals for harvest 
52 Progress Report to Congress – April 2005 Regional Implementation 

contribution of hatchery programs explicit enough to specifically size the programs to 

meet these needs in the future. The HSRG recommended discontinuing the Quillayute 

system hatchery spring Chinook program due to negative genetic interactions with native 

summer Chinook. While the co-managers have begun collecting DNA samples on these 

stocks, the program is continuing. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

With few exceptions, the co-managers are committed to implementing HSRG 

recommendations to meet operational guidelines. One exception is the Quillayute summer 

chinook program, where recommendations regarding flow, density and rearing/release 

protocols have not been addressed. The co-managers have addressed all 

recommendations, to the extent available funds have allowed. Recommendations 

pertaining to operational aspects of hatchery programs (e.g., use of proper spawning 

protocols, proper disposal of hatchery mortalities, reductions in program size, suspension 

of programs, etc.) are being met, but full implementation of recommendations that are 

more costly to put into effect will require time and continued funding. Non-acceptance of 

recommendations has been rare, and the basis has usually been reasonable. For example, 

the reluctance to go to the expense of monitoring stray rates of Quinault River Hatchery 

chum was because the biological significance of the wild stock in the neighboring 

watershed was considered low, and there were no management goals for the natural stock. 

Since the HSRG regional review was conducted, the facility built by the Quinault Indian 

Nation on the Queets River was partially closed, due to budget limitations. This led the 

Quinaults to return to their prior practice of rearing these fish in their Lake Quinault 

facility, necessitating the inter-watershed movements of fish and eggs between 

watersheds. Despite the precautions they plan to take, these fish transfers will still carry 

with them a risk of disease transfers. In light of these risks, the HSRG believes that 

obtaining the funding necessary to return to in-basin rearing should be a priority. 

Some facility improvements have been made in this region, but much remains to be done 

if HSRG recommendations are to be effectively carried out. Stable funding for facilities 

and operations to sustain hatchery reform over time must therefore be a high priority. For 

example, funds are needed to modify facilities at Sol Duc Hatchery and Makah National 

Fish Hatchery to permit volitional fish releases. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. The co-managers in this 

region recognize the need for having monitoring plan to ensure continued success of their 

hatchery programs through adaptive management. 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 
Regional Implementation Progress Report to Congress – April 2005 53 

Catch contributions and spawning escapement estimates for stocks in the region are made 

annually. 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

The co-managers have made the most of their available resources in this region, however 

the potential need to expand spawning ground surveys and stock identification sampling 

programs, in particular, should be reviewed as a part of the development of a 

comprehensive monitoring plan for the region. Stable funding is needed for long-term 

monitoring of stock composition on the spawning grounds. The monitoring of hatchery 

contributions to harvest and natural spawning escapement is critical for tracking the 

success of both integrated and segregated programs. 

c) Will contributions of hatchery origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

Extensive stock identification programs have been developed and implemented that meet 

statistical standards for precision and accuracy, using a range of marking methods to track 

the performance of hatchery stocks over time. As the needs associated with the 

implementation of new hatchery integration policies are evaluated, the need for additional 

marking and mark sampling will be revisited. It is likely that additional spawning surveys 

and biosampling will be needed in this region, as in others, in order for adequate accuracy 

and precision to be achieved. 
54 Progress Report to Congress – April 2005 Regional Implementation 

GRAYS HARBOR 

The regional implementation progress report for Grays Harbor was authored by WDFW. WDFW 

states that the report is based upon co-manager technical discussions, but not policy review or 

agreement. This region was reviewed by the HSRG in 2003. 

HSRG Synopsis and Response 

General Description of Region and Hatchery Programs/Issues: 

The Grays Harbor region is located along the central Washington coast and contains two major 

river basins—the Humptulips and Chehalis rivers. The latter is the second-largest basin in 

Washington state. In addition to stream habitat degradation from timber harvest, estuary habitat 

has been diminished with port and residential development. There are numerous cooperative 

salmon rearing programs and five hatcheries (Humptulips, Lake Aberdeen, Bingham Creek, 

Satsop Springs and Skookumchuck) in the region. Although there are efforts to understand stock 

status, the origin of naturally-spawning fish and fish used in hatchery brood stocks is often 

uncertain, due to lack of marking/tagging. The biggest challenge for managers in the region will be 

developing strategies to operate large programs to meet their harvest needs, while meeting 

conservation goals for stocks with limited natural habitat productivity. 

General Overall Comment about the Co-Manager Report: 

Progress has been made in some areas in this region, including goal identification, spawning 

ground surveying, and identifying hatchery programs as integrated or segregated. However, less 

progress has been made in implementing hatchery reform in this region than in many others. 

WDFW cites the time requirements necessary to implement significant capital improvements and 

limited resources as the principal constraints to complete implementation of HSRG 

recommendations. The HSRG recommendations have been used to garner funding, and many 

recommendations have been implemented. One major obstacle is the continued lack of ability to 

distinguish hatchery- and natural-origin adults. Funding has been identified for marking fish to 

ascertain hatchery/wild run compositions, beginning in 2006. The comments below do not pertain 

to steelhead programs. As discussed elsewhere the co-managers are reviewing the HSRG’s 

system-wide recommendations for steelhead and will address them in a forthcoming white paper. 

Operational recommendations for steelhead have generally been met for all regional programs. 

1. Stock goals and the role of hatcheries 

a) Are short- and long-term management goals/premises for habitat and 

conservation and harvest of all regional hatchery- and naturally-spawning 

salmonid stocks clearly stated? Have specific questions raised in the regional 

review been adequately addressed? 

Goals for all hatchery- and naturally-spawning stocks in this region were identified during 

the regional review process. The progress report provided by WDFW addressed the 
Regional Implementation Progress Report to Congress – April 2005 55 

HSRG’s program-specific recommendations. Focusing only on those recommendations 

makes it difficult to assess progress in regard to developing clear stock goals or 

determining how programs will be managed over time. WDFW states that until fish are 

marked and adult fish return, clear goals cannot be defined. It is not clear to the HSRG 

whether WDFW staff in this region clearly understood the distinction between stock goals 

and hatchery program types (integrated or segregated). The co-managers should clarify 

goals for all stocks in this region and develop interim plans for operating programs while 

better information is collected that will allow them to refine stock goals and hatchery 

program roles. 

b) Is the purpose (harvest, conservation, education, etc.) of each hatchery 

program stated? Have specific questions raised in the regional review been 

adequately addressed? 

Purposes for all hatchery programs in this region were identified during the regional 

review process. Most questions raised by the HSRG regarding the purposes of hatchery 

programs have been addressed. 

c) Is the program type (integrated vs. segregated) identified and explained for 

each hatchery program? Have specific questions raised in the regional review 

been adequately addressed? 

Every hatchery program in the region was designated as either integrated or segregated 

during the regional review process. WDFW reports that these designations are being 

reviewed for programs across the region, and this may result in major changes. 

2. Steps taken (decisions made and actions taken) towards meeting short- and long-term 

expectations 

a) Has significant progress been made to achieve desired hatchery- and 

naturally-spawning proportions in the hatchery broodstock and on the 

spawning grounds for integrated and segregated programs? 

WDFW has adopted the HSRG’s guidelines for integration and segregation. All hatchery 

Chinook releases in the region will be identified through adipose fin clipping beginning in 

2006. This will help to resolve the uncertainty as to the degree of integration in many 

stocks (Chinook in particular). A process for documenting hatchery and wild coho in 

hatchery broodstock has begun. Spawning surveys have been increased. Significant strides 

have been made in identifying stocks via coded wire tagging. Wynoochee Chinook, 

Bingham late coho, Satsop Springs Chinook, and Humptulips Chinook are now being 

coded wire tagged. The Satsop Springs Chinook program was 100% marked/tagged, 

which will allow summer and fall Chinook to be distinguished on spawning grounds and 

in the hatchery. However, Chinook still need to be mass marked and some stocks need to 

be coded wire tagged. The HSRG strongly supports WDFW’s request for adequate 

funding to upgrade facilities and on-going management and monitoring of stock 

composition on the spawning grounds and in the hatchery broodstock. A plan needs to be 
56 Progress Report to Congress – April 2005 Regional Implementation 

developed to establish protocols for hatchery broodstock for Skookumchuck Hatchery 

after renovation is complete. WDFW has made good use of available funds, including 

hatchery reform funding, but permanent funding is needed to ensure that the benefits of 

proper integration and segregation will continue into the future. In particular, resources 

needed to safely collect and transport natural origin spawners for incorporation in 

hatchery broodstock must be a high priority. 

b) Have steps been taken to size programs consistent with goals for all hatchery 

and naturally-spawning stocks? Have specific questions raised in the regional 

review been adequately addressed? 

WDFW reports that some hatchery program sizes, such as Satsop River coho and Satsop 

River late coho, are being reviewed and may be changed. The Wishkah River chum 

program has been discontinued, as recommended by the HSRG. No information has been 

provided regarding whether the co-managers have resized or will resize other hatchery 

programs in this region, including the Wynoochee River fall Chinook program, which the 

HSRG recommended be suspended. While progress has been made, the managers in this 

region have generally not developed goals for harvest contribution of hatchery programs 

explicit enough to specifically size the programs to meet these needs. 

c) Have steps been taken to better meet hatchery operational guidelines, from 

broodstock collection through release? Have specific questions raised in the 

regional review been adequately addressed? 

The co-managers are committed to implementing HSRG operational guidelines. All 

programs in this region now employ single-pair mating protocols, to maximize effective 

population size. The spawning protocol of using ten percent jacks for coho will commence 

in 2005. Stable funding for facilities and operations to sustain hatchery reform over time 

must be a high priority. For example, funds are needed to improve the handling and 

sorting of coho and Chinook broodstock at all facilities, in order to allow those programs 

to operate as properly integrated. Skookumchuck Hatchery is being renovated to meet 

HSRG recommendations for the upper Chehalis basin programs. A plan for broodstock 

acquisition needs to be developed for the hatchery upon completion. 

3. Steps taken to track progress toward expected outcomes 

Please see general HSRG comments about managing for success. The co-managers in this 

region are working on developing a comprehensive monitoring plan to ensure continued 

success of their hatchery programs through adaptive management. 

a) Will status of major stock goals (e.g. harvest and escapement) be monitored 

over time? 

The co-managers need to agree on and implement a strategy for distinguishing all 

hatchery- and natural-origin fish in the region. 
Regional Implementation Progress Report to Congress – April 2005 57 

b) Will contributions of each hatchery program towards its purpose be 

monitored over time (e.g. contributions toward harvest and escapement)? 

The co-managers have made the most of their available resources in this region, however 

the potential need to expand spawning ground surveys and stock identification sampling 

programs, in particular, should be reviewed as a part of the development of a 

comprehensive monitoring plan for the region. Stable funding is needed for long-term 

monitoring of stock composition on the spawning grounds. The monitoring of hatchery 

contributions to harvest and natural spawning escapement is critical for tracking the 

success of both integrated and segregated programs. 

c) Will contributions of hatchery-origin fish to broodstock and natural 

escapement be estimated with sufficient accuracy and precision over time? 

It is likely that additional spawning surveys and biosampling will be needed in this region, 

as in others, in order for adequate accuracy and precision to be achieved. 

Project Coordination Progress Report to Congress – April 2005 59 

Project Coordination 

FACILITATION 

Throughout 2004, the facilitation team of Long Live the Kings (LLTK) and Gordon Thomas 

Honeywell coordinated and facilitated regular meetings among and between the project’s scientific, 

technical, policy-making and stakeholder groups. This included monthly HSRG meetings, quarterly 

Coordinating Committee and Hatchery Reform Coalition meetings, and biweekly technical 

discussions during the spring and regional workshops during the summer. The team also facilitated 

numerous small group meetings and interactions between and among project participants and 

stakeholders. Each of these involved significant preparation and follow-through activities, as well as 

ensuring the conversation at the meetings remained productive and consistent with the project’s goals. 

Beginning in August 2004 and continuing into 2005, the facilitation team has been helping the comanagers conduct regional decision-making meetings intended to reach consensus on changes to 

recovery plans, resource management plans (RMPs), Hatchery and Genetic Management Plans 

(HGMPs), and other salmon management documents and processes through which the managers can 

implement hatchery reform. These meetings have focused on addressing issues that need to be 

resolved to complete implementation. The facilitation team’s participation in these meetings has 

varied by region, depending on the needs of the regional co-managers. Some regions are comfortable 

operating without much facilitation and coordination, while others request more active assistance. 

COMMUNICATIONS/OUTREACH 

Throughout 2004, LLTK implemented a strategy for communicating Hatchery Reform Project 

background, activities and progress to federal, state, tribal, regional and local stakeholders. The 

strategy ensures that stakeholders, decision-makers and the public are informed about the project’s 

scientific findings and the co-managers’ progress in implementing the resulting recommendations. It 

helps ensure that the co-managers continue to make progress and have external support for 

implementing reform. 

In 2004, this included providing briefings for legislators, agency managers and their staffs; making 

presentations at a wide range of venues (such as a West Coast Steelhead Meeting in Port Townsend, 

Salmon and Steelhead Alliance in Bellevue, World Fisheries Congress in Vancouver, Skagit 

Watershed Council in Mount Vernon, Steelhead and Cutthroat Policy Advisory Group in Lacey, 

Northwest Fish Culture Conference in Victoria and many others); authoring or being interviewed for 

articles on the project for mainstream and stakeholder media publications; keeping project 

communication materials updated; and many other activities. Thirty-one presentations were made and 

11 publications produced in 2004 (see Appendix B, 2004 Hatchery Reform Project Communications). 

The Hatchery Reform Project has received extensive local, regional, national and international media 

coverage. The April 2004 press conference alone generated more than 45 stories in 40 outlets and 1.6 
60 Progress Report to Congress – April 2005 Project Coordination 

million audience impressions (including stories on two of the Seattle market’s top TV news stations, 

12 western Washington radio stations, and a three minute feature on ten NPR radio affiliates). Media 

coverage of hatchery reform has been both consistent and supportive throughout the project. For 

example, The Seattle Times has run two editorials on the project, calling it “a blueprint for making 

Puget Sound and coastal hatcheries a smarter, more efficient piece of salmon recovery.” 

In spring 2004, the hatchery reform web site (www.hatcheryreform.org) was completely updated. The 

web site has a detailed description of the Hatchery Reform Project and makes available hatchery 

reform publications including the HSRG’s report, technical papers and other publications; five years 

of monthly HSRG meeting summaries; and press releases and other public materials. The web site also 

includes a password-protected page where project participants can access specific tools and documents 

tailored for their use. Since its re-release, the site has averaged more than 500 visits a month, with 

more than half coming from repeat visitors. To date, nearly four gigabytes of information has been 

downloaded, confirming that the site is performing well as a tool for disseminating information. The 

HSRG’s report alone has been downloaded by nearly 400 visitors. 

HATCHERY REFORM COALITION 

In 2004, LLTK pursued its mandate from Congress to help ensure implementation of hatchery reform 

by reactivating a coalition of organizations that came together to support the Hatchery Reform Project 

in 2002. That coalition now features 18 regional and national conservation, recreation and sport 

fishing organizations and advocates with a combined membership base of over 300,000 (see Appendix 

H, Hatchery Reform Coalition Members). The Coalition includes organizations that are not always on 

the same side on all issues, but all have agreed that the HSRG’s principles and recommendations 

represent the right way to proceed with managing the hatchery system. Now, Coalition members are 

working together to build a constituency for hatchery reform, and to ensure that the co-managers’ 

reform efforts are consistent with the findings of the HSRG. The coalition has full meetings six times 

per year. 
Initial Investments Progress Report to Congress – April 2005 61 

Initial Investments Made/Needed at 

State, Tribal and Federal Facilities 

WDFW INVESTMENTS 

Information below provided by the Washington State Department of Fish and Wildlife 

The State of Washington provides legislative appropriations to WDFW to implement hatchery reform. 

For budget period 2003–05, WDFW received one million dollars in operations funds and $6.5 million 

in capital funds to implement hatchery reform (WDFW received an additional $300,000 in capital 

funds for planning a proposed new Deschutes Hatchery). Capital projects included retrofits, fish 

passage, pollution abatement, water quality, hatchery infrastructure, critical salmon recovery actions 

(like a new acclimation pond on the Nooksack), etc. WDFW has spent current capital funds on facility 

improvements at Whitehorse and Samish hatcheries, along with planning and permitting activities for 

a slate of other capital projects. These projects are ranked according to a set of approximately six 

criteria, including compliance with legal standards, whether a listed stock is involved, whether they 

implement HSRG recommendations, and geographic distribution. 

For budget period 2005–07, WDFW is requesting $1.1 million in operations funds for implementation 

of the Hatcheries 2020: A Clear Vision for the Future strategic plan for hatchery reform in 

Washington. Building upon emerging work to improve hatchery practices including Hatchery and 

Genetic Management Plans (HGMPs), Artificial Production Review and Evaluation (APRE), HSRG 

recommendations, recovery planning, etc., Hatcheries 2020 provides a prioritized and scheduled series 

of actions that transform hatcheries from an “all-H risk factor” to a productive tool for restoring 

salmon and enhancing fishing opportunities. These actions include: 1) collection of natural-origin 

broodstock and rearing programs that emulate natural conditions; 2) supplementation programs to 

accelerate the restoration of critically depressed stocks; and 3) adaptive management of programs to 

maximize survival rates, meet ESA permitting requirements, and minimize the likelihood of third 

party lawsuits. In addition, WDFW is requesting $16.55 million in capital funds for renovations and 

upgrades to existing hatchery complexes in the areas of water quality and fish health, along with the 

removal of barriers that currently restrict natural stocks from reaching their spawning areas. 

The HSRG recommendations associated with operating funds can be divided into three broad 

categories related to the time span of funding required: 1) one-time costs (e.g., equipment purchases, 

baseline assessment of pathogens); 2) short-term projects of two to six years (e.g., collection of a new 

broodstock, assessment of survival rates and catch distribution); and 3) long-term costs associated with 

the ongoing, improved operation of hatchery programs. To date, WDFW has addressed approximately 

35% of the HSRG recommendations that fall into the first two categories. Prioritized actions targeted 

for implementation in 2005–07 are summarized below. 
62 Progress Report to Congress – April 2005 Initial Investments 

Science Foundation 

The development of scientifically defensible hatchery programs is critically dependent on 

monitoring the incidence of hatchery-origin adults in natural spawning areas. WDFW hatchery 

performance measures, HSRG guidelines and NMFS best management practices all are reliant on 

monitoring this statistic. Funding of this program provides staffing to collect, analyze and report 

the incidence of hatchery-origin adults in the following areas: 1) Chinook in the Nooksack, 

Stillaguamish, Snohomish, Lake Washington, Green, Puyallup, mid-Hood Canal, and Dungeness 

rivers; and 2) coho in the Naselle and Willapa rivers. 

Immediate Risk Reduction Measures 

Priority program modifications emphasize reducing risks through improved broodstock 

management and initiating an artificial production program to accelerate the restoration of a 

critically depressed stock. Funding of this program provides staffing and services to: 1) integrate 

natural-origin fish into hatchery broodstocks for listed Chinook at the Wallace River and Voights 

Creek hatcheries; 2) integrate natural-origin coho into the broodstock for the Willapa River and 

Naselle River hatcheries; and 3) initiate restoration programs for the critically depressed and listed 

Cedar River and South Fork Nooksack Chinook populations. 

Performance-Based Management 

Continued review, evaluation and modification of hatchery programs is essential to assure that 

fishing-related economic benefits are maximized, while ensuring risks to natural populations are at 

or below acceptable levels. WDFW is identifying goals and performance measures for each 

program which, when paired with the monitoring associated with the science foundation, will 

provide a powerful force for continued enhancement of hatchery programs. WDFW proposes to 

collaborate with Mobrand Biometrics, Inc. to develop and implement a readily accessible, 

computerized and unified performance-based management system driven by a set of questions, 

linked to performance measures, which will evaluate the success of hatchery programs. 

In addition, the engineering assessment of hatchery facilities identified the need for $34 million to 

comply with intake/passage and abatement regulations, $67 million to implement HSRG 

recommendations, and $52 million to continue to operate facilities at existing production levels, a 

total of $152 million. Additional funding is badly needed, since current funding of three to four 

million dollars per year puts hatchery renovations on a 50 year cycle. Since concrete at hatcheries 

has a 30 year life expectancy, most facilities are falling into extreme disrepair and/or becoming out 

of compliance with federal and state regulations long before they can be renovated. 

NWIFC INVESTMENTS 

Information below provided by the Northwest Indian Fisheries Commission 

The majority of the hatchery reform funds received by member tribes and their Northwest Indian 

Fisheries Commission (NWIFC) from FY 2000–04 have been used to implement 68 projects at tribal 

facilities that cost a total of $2,889,372. Tribes developed a science-based, competitive project 
Initial Investments Progress Report to Congress – April 2005 63 

application and ranking process for awarding contracts to individual tribes to implement hatchery 

reform activities. A list of projects funded in FY 2004 is included as Appendix C. 

Federal appropriations are the only avenue available to the tribes for hatchery management and reform 

funding. Hatchery reform is an ongoing process, and consistent federal funding is critical to enable 

tribes to conduct hatchery-specific studies that provide information leading to progressive 

modifications of hatchery programs and facilities. Tribes are continually re-evaluating their programs 

to address the most pressing salmon related issues. Significant portions of tribal programs and 

resources have been refocused to address salmon recovery issues such as ESA and hatchery reform. 

The member tribes of the NWIFC continue to contribute to the technical expertise regarding changes 

needed in hatchery programs. They have jointly completed resource management plans for Puget 

Sound hatcheries. They will also continue to contribute technical expertise in genetics and hatchery 

management and, to the degree feasible, use extremely limited hatchery maintenance funds provided 

through the Bureau of Indian Affairs (BIA) to assist in implementation of hatchery reform. 

For FY 2006, the tribes are requesting that $400,000 be added to existing BIA 638 contracts to support 

existing scientific staff positions necessary for ongoing hatchery reform implementation. The tribes 

also are requesting that Congress place five million dollars per year, for ten years, in the BIA Hatchery 

Rehabilitation and Cyclical Maintenance line item, to fund implementation of hatchery reform projects 

at tribal facilities. 

USFWS INVESTMENTS 

Information below provided by US Fish and Wildlife Service 

The following needed facilities improvements have been identified at National Fish Hatcheries (NFH) 

in western Washington, in order to implement hatchery reform strategies: 

• Add water chilling capability at Makah NFH ($75,000) 

• Fish pumps at Quinault NFH ($20,000) 

• Water pre-settling chambers at Quinault NFH ($1,500,000) 

• Improve adult handling facilities at Quinault NFH ($1,500,000) 

• Expand hatchery building at Quinault NFH ($1,000,000) 

• Add water chilling capability at Quinault NFH ($75,000) 

• Rehabilitate electric weir and improve upstream passage at Quilcene NFH ($750,000) 

In order to meet these identified needs, USFWS is seeking funding through Department of the Interior 

maintenance and construction appropriations in 2007 and beyond. 

Work in Progress Progress Report to Congress – April 2005 65 

Work in Progress 

The HSRG’s work for 2005 will be to ensure that the set of scientific evaluation, management and 

monitoring tools developed during the Hatchery Reform Project are refined, completed and published 

in the scientific literature. The co-managers’ work will be to incorporate the ecological and genetic 

principles outlined by the HSRG, refine the recommendations based on more comprehensive analyses, 

and implement them into salmon and steelhead management, strategic planning, and organizations to 

operate more effectively. The facilitation team’s work will be to educate stakeholders and the general 

public on the scientific and conceptual frameworks that underlie this new approach to managing 

salmon and steelhead and the existing management frameworks of United States v. Washington, the 

Puget Sound Salmon Management Plan, and Hoh v. Baldridge; build support among these 

stakeholders for implementation; and assist the co-managers, as requested, in their efforts to resolve 

outstanding management issues. 2005 budgets and work plans are attached as Appendices D and E. 

HSRG WORK IN PROGRESS 

Now that the regional review phase of the project has been completed and the HSRG has delivered a 

report detailing its principles and recommendations, the HSRG has turned its attention to completing 

the set of scientific tools it has assembled for the managers’ use into the future. Through full HSRG 

meetings, task team meetings and individual work, the HSRG intends to accomplish a series of tasks 

in 2005 that will wrap up its work on behalf of the Hatchery Reform Project. 

The first of these will be publishing key findings in the peer-reviewed, scientific literature. The 

HSRG’s work includes a great deal of new thinking about how hatchery management can be altered to 

increase benefits and reduce risks associated with hatchery programs for anadromous salmonids. It is 

vital to the cause of reform that these new ideas and concepts be subjected to the rigors of the peer 

review process and disseminated widely throughout the scientific community. 

HSRG members will support these publications with presentations at symposia and conversations with 

influential thinkers. The HSRG will also conduct its annual research review and continue to fund a 

subset of its research grant projects. Another research-related task will be the development of an 

agenda to guide hatchery-related research in the future. 

Another area of focus will be continuing technical discussions with key state and tribal scientists. Last 

year, these discussions resulted in a refining of the integrated/segregated concept (which led to the 

AHA management tool), furthered the conversation on when to start a conservation hatchery program, 

and created momentum for the effort to provide “managing for success and accountability” criteria. 

This year’s discussions will be expanded to include a larger group of co-manager scientists and 

technical staff. Topics will include refining AHA, moving forward on “managing for success,” and 

beginning a dialogue on steelhead management and/or wild salmonid management zones. 

Perhaps the most important of these tasks to the future of salmon and steelhead management is the 

“managing for success and accountability” criteria. The HSRG sees monitoring and evaluation as 
66 Progress Report to Congress – April 2005 Work in Progress 

critical to determining if the reform process is achieving its intended results, citing accountability and 

adaptive management as two of the cornerstones of hatchery reform. These require collecting and 

using information that reveal: 1) if hatchery programs are meeting stock goals; and 2) if they are not, 

how they should change. The HSRG recommends monitoring and evaluation be perceived as a 

continuous effort, since the variety of components that require monitoring and evaluation do not all 

adhere well to a set timescale. Results will be reported through vehicles established by the managing 

tribe and/or agency. 

Based on the scientific framework it developed in the project’s first year, the HSRG created a set of 

draft monitoring and evaluation criteria to guide the managers in measuring the success and/or failure 

of hatchery programs. The HSRG is currently turning these criteria into a set of practical tools the comanagers can use to manage for success and accountability at hatcheries. Completing these tools and 

working with the managers to put them into use will be a major focus of the project in 2005. 

The above deliverables will complete the “toolbox” the HSRG has created for managing hatcheries in 

the context of the watersheds in which they operate and the status of wild stocks. That toolbox will 

then be presented to state/tribal/federal staff, other scientists, legislators, stakeholders and the public at 

a workshop in the fall. The workshop will also provide the managers with the opportunity to discuss 

the challenges involved in implementing this new approach. 

CO-MANAGERS WORK IN PROGRESS 

Information below provided by the Washington State Department of Fish and Wildlife 

WDFW has embarked on a multiyear effort to implement hatchery reform and transform hatcheries 

from an “all-H risk factor” to a productive tool for restoring salmon and enhancing fishing 

opportunities. The expected benefits are substantial—enhanced fishing opportunities, improved stock 

status, economic stimulation of rural communities, and a reduced risk of third party litigation. 

Building upon the broad consensus emerging from the independent reviews of hatchery programs 

conducted by the HSRG (Puget Sound and Washington coast) and Artificial Production Review and 

Evaluation (Columbia Basin) teams, WDFW has developed a strategic approach to implement 

hatchery reform. The approach, described in Hatcheries 2020: A Clear Vision for the Future, 

recognizes that a staged, prioritized, incremental approach to hatchery reform is necessitated by 

funding, logistical and environmental constraints. The objective remains, however, to build the 

foundation for scientifically defensible programs, implement priority actions to improve hatchery 

programs, and assure continued program modifications through results-oriented, performance-based 

management. 

AHA is being used to develop precise integration and production rates for each hatchery program. 

Hatchery modifications are currently underway to implement integrated brood stock management at 

two facilities. In addition, a computerized data system for hatchery information is being developed that 

will integrate and provide ready access for all aspects of hatchery fish. Ongoing major hatchery 

renovations, as per HSRG recommendations, include Whitehorse Rearing Ponds and Samish and 

Skookumchuck hatcheries. 
Work in Progress Progress Report to Congress – April 2005 67 

Information below provided by the Northwest Indian Fisheries Commission 

The tribes’ objective in the multiyear effort to implement hatchery reform is to build the foundation 

for scientifically defensible programs, implement priority actions to improve hatchery programs, and 

assure continued program modifications through results-oriented, performance-based management. To 

this end, the Tribes will continue to focus on scientific and policy approaches for using hatcheries to 

maintain fisheries, fishing communities and their cultures, and to restore natural runs of salmon to 

western Washington in the face of increasing loss of salmon habitat to development and the expected 

consequences of global warming. 

Refitting existing hatchery facilities to be able to implement ecological and genetic principles of 

hatchery reform is critically important. Identifying and securing funding opportunities to do this needs 

to be a major focus of hatchery reform. The tribes will also continue to pursue program-specific 

research and monitoring to help resolve key uncertainties identified by scientific review and 

recommendations, such as how and when to begin new hatchery programs. New programs for 

Chinook and other species are expected to add an important safety net for existing populations. 

Tribal scientists will also continue to develop the innovative adaptive management framework 

described in the Puget Sound Chinook Salmon Resource Management Plan (RMP), which combines 

passive adaptive management and evolutionary problem-solving strategies to guide decision making. 

As part of this, the tribes will continue to refine their tools for tracking hatchery reform 

implementation. Tribal scientists will also continue to develop quantitative risk/benefit tools, to aid 

decision-making assessment as part of the Risk Assessment Modeling Project (RAMP). In addition, 

the tribes will continue to develop better ways of disseminating information about what they have 

learned in managing hatchery programs for success. 

USFWS WORK IN PROGRESS 

Information below provided by US Fish and Wildlife Service 

USFWS is committed to effectively incorporating individual hatchery programs into regional fish 

management strategies, in order to protect and restore native fish species, as well as to develop and 

maintain sustainable fisheries. USFWS is an active participant in the Hatchery Reform Project and 

will continue its role on the HSRG and in providing administrative support to the project. USFWS also 

intends to implement the following management, accountability, demonstration and science support 

projects in 2005: 

• Water filtration, formalin delivery and flow metering improvements at Quinault National Fish 

Hatchery (NFH) 

• Isolation/quarantine facility operational support at Makah NFH 

• Summer chum monitoring project support by western Washington (Lacey) field office 

• Volitional release study by Abernathy Fish Technology Center 

• Fish feed analysis, quality assistance/quality control at Olympic Peninsula hatcheries 
68 Progress Report to Congress – April 2005 Work in Progress 

USFWS believes that the review process developed and demonstrated in the Hatchery Reform Project 

has the potential for wide application outside of the western Washington area. The Service is now 

developing a similar review process for implementation at NFHs through the Northwest states. 

USFWS expect to begin implementing such reviews later this year. The Service is also advocating that 

other fishery managers engage in a similar cooperative review process. 

FACILITATION TEAM WORK IN PROGRESS 

As mentioned above, the Hatchery Reform Project facilitation team’s challenge for 2005 is to educate 

stakeholders and the general public on the scientific and conceptual frameworks that underlie the new 

approach to managing salmon and steelhead; build support among these stakeholders for its 

implementation; and assist the co-managers, as requested, in their efforts to resolve outstanding 

management issues. One portion of this work involves using the team’s facilitation, communications 

and project coordination skills to help the scientists and managers successfully complete the project in 

2005. This will involve facilitating co-manager decision-making meetings and discussions (as 

requested); assisting the HSRG in completing a series of scientific publications; facilitating technical 

discussions between HSRG and co-manager scientists to refine AHA and develop a monitoring and 

evaluation/adaptive management system; helping the HSRG complete a hatchery research agenda; 

communicating project accomplishments and challenges; and helping the HSRG host a workshop to 

examine the latest science and address the challenges of institutionalizing hatchery reform. 

A second portion of this work is to take advantage of the team’s experience, independent perspective, 

imagination and communications skills to begin a discussion about what happens next for hatchery 

and salmonid management in and beyond Puget Sound and the coast. The Hatchery Reform Project 

has led to the development of innovative tools, knowledge bases and recommendations that could have 

significant application to and relevance for related natural resource challenges and processes. As the 

project’s non-governmental participants, the facilitation team can tell the story, make the connections, 

and foster offshoots and outcomes that take full advantage of the investment to date in this new way of 

thinking about the role of hatcheries in meeting harvest and conservation goals for salmon and 

steelhead. 
Looking Ahead Progress Report to Congress – April 2005 69 

Looking Ahead 

When the HSRG began reaching conclusions about how hatcheries can be better used to meet the twin 

goals of helping conserve wild salmon and supporting sustainable fisheries, it became apparent that 

hatcheries can no longer be designed, operated and evaluated in isolation. In order to properly evaluate 

the benefits and risks from a hatchery program, it is necessary to examine the program in the context 

of the watershed in which it resides and the goals for all stocks in the watershed. This means first 

understanding the current and expected future status of all hatchery and natural stocks in the watershed 

and the habitat on which they rely. Only when these factors are understood can managers determine if 

their conservation and harvest goals for the watershed are appropriate, whether a hatchery program is 

the right tool for helping reach those goals, and, if so, what type and size of program will maximize 

benefits and minimize the risks. 

This watershed-based approach goes beyond hatchery management, representing a new model for 

holistic management of salmon and other natural resources, one that takes into account all the factors 

that affect a species and the habitat in which it resides. The HSRG’s principles, recommendations and 

tools provide a pathway for moving toward this new management model. For this reason, the work is 

attracting attention from the federal agencies charged with implementing the Endangered Species Act. 

NOAA Fisheries is planning to use the HSRG’s tools to aid its evaluation of the salmon recovery 

plans it will be receiving in 2005. USFWS is forming a task team to apply the HSRG’s principles, 

recommendations and tools to all of its hatchery programs in the Northwest region. 

The Washington State Governor’s Office, the Shared Strategy for Salmon Recovery in Puget Sound, 

and others are relying on the Hatchery Reform Project for direction on how hatchery reform can be 

integrated with habitat recovery and harvest management for the recovery plans those parties have 

committed to provide NOAA Fisheries. NOAA Administrator Conrad Lautenbacher has pledged that 

his agency will ensure the HSRG’s approach to hatchery reform is implemented. The Northwest 

Power and Conservation Council retained the HSRG chair and co-chair in 2003 in a separate project, 

to conduct a review of all artificial production facilities in the Columbia River Basin (called the 

Artificial Production Review and Evaluation or APRE) using the HSRG’s scientific framework and 

review tools. WDFW has indicated that it intends to use the HSRG’s principles, framework and tools 

on all its hatchery programs. The project has also attracted attention from the Oregon Department of 

Fish and Wildlife, Alaska Department of Fish and Game, and Department of Fisheries and OceansCanada. 

Appendices 

Appendices Progress Report to Congress – April 2005 73 

A: 2004 Project Expenditures 

Puget Sound and Coastal Washington Hatchery Reform Project Expenditures FY 2004 

Hatchery Scientific Review Group 

HSRG Members, Travel, Meeting Expenses $297,095 

Research Grants $335,010 

SUBTOTAL $632,105 

Washington State Department of Fish and Wildlife 

Agency Staffing 

HSRG member; HSRG support staff; hatchery biologist 

$100,000 

Deschutes Chinook and Steelhead Studies 

Fish counting; adult by-pass; spawning surveys; downstream enumeration; predation studies; 

radio-telemetry 

$200,000 

Hatchery Engineering Assessments 

For screening/passage, capital costs to implement HSRG recommendations, structural 

improvements, predator control 

$377,000 

Coded Wire Tagging Chinook and Coho $143,000 

Hatchery New Technology Equipment $250,000 

Hatchery Research, Monitoring and Evaluation 

Diet modulation; diet supplementation; electronic tag detection; natural rearing; sorting and 

growth acceleration; new marking methods, disease research, etc. 

$31,057 

SUBTOTAL $1,101,057 

Northwest Indian Fisheries Commission 

HSRG Member and Support Staff $281,237 

Improve, Monitor and Evaluate Hatchery Practices 

Type I projects at Tulalip, Stillaguamish, Lower Elwha, Makah, Puyallup, Nisqually, Squaxin 

Island and Lummi 

$243,567 

Improve Hatchery Facilities 

Type II projects at Tulalip, Stillaguamish, Makah, Nisqually and Upper Skagit 

$187,041 

SUBTOTAL $711,845 

US Fish and Wildlife Service 

Science Team 

HSRG member, fish feed analysis, QA/QC for Olympic Peninsula hatcheries 

$85,900 

Management, Accountability and Demonstration Projects 

Quinault NFH formalin delivery system/flow meters, Quilcene NFH adult fish handling device, 

Makah NFH I/Q facility operational support, WWFWO Fisheries Division Staff support (Quilcene 

coho stock issue, Makah production reductions, Hoh steelhead program, HSRG 

communications) 

$52,500 

SUBTOTAL $138,400 

NOAA Fisheries 

Science Team $42,950 

Long Live the Kings

Project Coordination, Facilitation, Communications 

Staffing; materials; office expenses; travel; subcontracts

$292,060 

Budget Administration 

Interagency Commission for Outdoor Recreation $32,926 

US Fish and Wildlife Service $25,000 

FY 2004 TOTAL $2,976,343 

Appendices Progress Report to Congress – April 2005 75 

B: 2004 Project Communications 

OUTREACH 

Congressman Norm Dicks 

January 23, 2004

LLTK Executive Director Barbara Cairns, NWIFC Executive Director Jim 

Anderson, WDFW Director Jeff Koenings, HSRG Chair Lars Mobrand, 

HSRG Vice Chair John Barr, and Hatchery Reform Project Lead 

Facilitator Jim Waldo met with Congressman Dicks in Tacoma, to provide 

a briefing on the project and implementation progress. 

West Coast Steelhead Meeting 

March 11, 2004

HSRG member Don Campton and LLTK Director of Facilities Kathleen 

Hopper participated in a session on integrated/segregated steelhead 

management at this annual meeting in Port Townsend of steelhead 

managers from across the west coast. Don’s presentation focused on the 

HSRG’s integrated/segregated hatchery programs concept. Kathy’s 

presentation related to some of the unique challenges in operating 

steelhead programs as properly integrated or segregated. 

Letter to WDFW/NWIFC on 

Key Regional Reform Issues 

March 4, 2004

Responding to a request from the co-managers, LLTK helped the HSRG 

write and transmit a letter from HSRG Chair Lars Mobrand to WDFW and 

NWIFC containing key regional issues identified by the HSRG as being 

central to achieving hatchery reform. 

Hatchery Reform Coalition 

March 31, 2004

HSRG Vice Chair Lee Blankenship and LLTK Project Manager for 

Hatchery Reform Michael Kern presented an overview of the Hatchery 

Reform Project at this Coalition meeting in Olympia. 

Dungeness River 

Management Team 

April 14, 2004

John Barr presented in Sequim to this regional watershed group on the 

Hatchery Reform Project, the HSRG’s principles and system-wide 

recommendations, and program-specific recommendations for the 

Dungeness River and independent tributaries in the Eastern Straits. 

Hatchery Reform Project 

Press Conference

April 23, 2004

LLTK coordinated a press conference at the Seattle REI to mark the 

release of Hatchery Reform: Principles and Recommendations of the 

Hatchery Scientific Review Group. WDFW Director Jeff Koenings and 

NWIFC Chair Billy Frank, Jr. pledged to implement the recommendations. 

Washington Governor Gary Locke pledged to include funding for hatchery 

reform in his proposed 2005–07 biennial budget. Congressman Norm 

Dicks, D-WA, applauded the progress achieved. Barbara Cairns emceed. 

Hatchery Reform Coalition 

Letter of Support 

April 23, 2004

Coalition representatives signed a letter to the co-managers indicating 

their support for the Hatchery Reform Project and implementation of the 

HSRG’s recommendations. 

World Fisheries Congress 

May 5, 2004

Lee Blankenship presented a poster on the Hatchery Reform Project at 

this international conference in Vancouver, BC. 

Northwest Indian Fisheries 

Commission 

May 11, 2004

Lars Mobrand and John Barr attended this NWIFC annual meeting in 

Olympia, at which the commissioners discussed hatchery reform 

implementation. Lars and John also held several informal meetings with 

tribal technical and policy staff members. 

Hatchery Reform Coalition 

May 12, 2004

Don Campton presented the HSRG’s integrated/segregated concept and 

John Barr presented NWIFC’s request to Congress for Tribal Hatchery 

Rehabilitation funding through the Bureau of Indian Affairs at this Olympia 

meeting. 
76 Progress Report to Congress – April 2005 Appendices 

Steelhead Summit Alliance 

May 15, 2004

Lee Blankenship gave a presentation in Bellevue on the HSRG’s 

principles and recommendations to this informal network of west coast 

wild steelhead groups. Barbara Cairns and Lee Blankenship both 

participated in a panel discussion on hatchery reform implementation. 

Tri-County Salmon 

Conservation Coalition 

May 20, 2004

Barbara Cairns made a presentation to the Coalition’s Executive 

Committee on the role of hatcheries in responding to endangered species 

listings. 

Shared Strategy for Salmon 

Recovery in Puget Sound 

May 20, 2004

Barbara Cairns made a presentation to the Shared Strategy Development 

Committee on the release of recommendations for hatchery reform. 

Workshops on the Role of 

Hatcheries in Sustainable 

Fisheries 

May 25 & 27, 2004

Lee Blankenship, HSRG member Connie Mahnken, Jim Waldo and 

Michael Kern presented an overview of the Hatchery Reform Project and 

Don Campton presented the integrated/segregated concept at these 

workshops held in Juneau and Anchorage to introduce the work of the 

HSRG and facilitate an exchange of information on hatchery-related 

issues with Alaskan researchers, managers and policy makers. HSRG 

members Lisa Seeb, Bill Smoker, John Barr, Trevor Evelyn, Paul Seidel 

and facilitation team member Bj Mirk also participated in these briefings. 

NOAA Fisheries Hatchery 

Policy Release 

May 28, 2004

Lars Mobrand and Barbara Cairns participated in a briefing for NOAA 

Administrator Admiral Conrad Lautenbacher, Jr. on the Hatchery Reform 

Project and the work of the HSRG. NOAA Fisheries Regional 

Administrator Bob Lohn and Rob Walton (Assistant Regional 

Administrator for Salmon Recovery) were also present. 

Hatchery Reform Coalition 

Letter of Support 

June 1, 2004

Coalition members signed onto a letter of support to the House 

Appropriations Subcommittee on Interior and Related Agencies for 

NWIFC’s request to Congress for Tribal Hatchery Rehabilitation funding 

through the Bureau of Indian Affairs. 

Puget Sound Co-Managers’ 

Annual Meeting 

June 8, 2004

Jim Waldo, Jim Anderson and WDFW Deputy Director Larry Peck made 

presentations on the 2004 work plan for implementing hatchery reform at 

this annual co-management meeting in SeaTac. 

Washington State House 

Fisheries, Ecology and Parks 

Committee 

June 9, 2004

Don Campton, HSRG member Paul Seidel, Barbara Cairns, and NWIFC 

staffer Terry Wright made a presentation on the HSRG’s work and comanager implementation of hatchery reform at a Committee work session 

and public hearing. 

HSRG/Co-Manager Technical 

“Kick-Off” Meeting 

June 10, 2004

Lars Mobrand, Terry Wright and Larry Peck introduced the regional 

workshops and co-management meetings to be held in the summer and 

fall of 2004 at this meeting in Seattle. Connie Mahnken reviewed the 

HSRG’s principles and system-wide recommendations. WDFW’s Craig 

Busack and Andy Appleby presented different aspects of the 

integrated/segregated concept. Michael Kern introduced speakers and 

facilitated a Q&A session. 

Northwest Power and 

Conservation Council 

June 18, 2004

Lars Mobrand and Connie Mahnken met with the Washington state 

representatives to the NPCC to explain the HSRG’s recommendations 

and their applicability to Columbia River hatchery issues. 

Hatchery Reform Coalition 

July 7, 2004

Paul Seidel and Terry Wright provided WDFW and NWIFC updates on 

hatchery reform implementation at this Coalition meeting in Olympia. 
Appendices Progress Report to Congress – April 2005 77 

Recreational Fishing Alliance 

July 13, 2004 

Barbara Cairns and Michael Kern met in Seattle with RFA Executive 

Director Jim Donofrio, along with RFA Washington State Representative 

and Hatchery Reform Coalition member Mike Gilchrist. Jim was visiting 

from RFA’s New Jersey headquarters. He pledged RFA’s full support for 

the Hatchery Reform Project. 

The Mountaineers 

August 12, 2004 

Barbara Cairns and Michael Kern met in Seattle with Mountaineers 

Conservation Director Norm Winn and Public Policy Assistant Fatima 

Oswald, to introduce the Hatchery Reform Project and the Hatchery 

Reform Coalition. Norm pledged the Mountaineers’ support for the Project 

and accepted an invitation to join the Coalition. 

Skagit Watershed Council 

September 8, 2004 

Lee Blankenship, Barbara Cairns, and Michael Kern presented to the 

Council in Mount Vernon on the Hatchery Reform Project and the HSRG’s 

recommendations for the Skagit region. 

Hatchery Reform Coalition 

September 22, 2004

Lars Mobrand introduced the Coalition to the AHA tool and provided an 

overview of the technical workshop series at this meeting in Seattle. Larry 

Peck and Paul Seidel discussed WDFW’s biennial budget proposal and 

how it will implement hatchery reform. 

Steelhead and Cutthroat 

Policy Advisory Group 

September 30, 2004 

Lee Blankenship and Michael Kern presented to this WDFW advisory 

committee in Lacey, WA on the Hatchery Reform Project, the HSRG’s 

principles, integrated/segregated hatchery programs and the system-wide 

recommendations for steelhead. The group asked for a follow-up 

presentation on the technical workshop series and the AHA tool. 

Washington Agriculture and 

Forestry Education 

Foundation Leadership 

Program 

October 7, 2004

Kathleen Hopper made a presentation in Vancouver, WA on the Hatchery 

Reform Project to this organization that trains natural resource industry 

leaders. 

National Fish and Wildlife 

Foundation Salmon Recovery 

Symposium 

October 22, 2004 

Barbara Cairns provided a briefing on hatchery reform for this exchange 

of information between Northwest Pacific salmon recovery leaders and a 

delegation of Maine Atlantic Salmon recovery leaders in Seattle, 

sponsored by the National Fish and Wildlife Foundation. 

LLTK’s Chairman’s Council 

October 25, 2004 

Lars Mobrand and Jim Lichatowich made presentations at the LLTK 

Chairman’s Council luncheon in Seattle. Lichatowich endorsed the 

Hatchery Reform Project. Lars Mobrand introduced the AHA tool. 

NOAA Fisheries Salmon 

Conservation Division 

November 8, 2004 

Lars Mobrand, Don Campton, Connie Mahnken and WDFW staffer Andy 

Appleby presented in Portland to Rob Walton, Rob Jones and other 

NOAA Fisheries regional leaders on the integrated/segregated concept 

and the AHA tool. John Barr, Paul Seidel and Michael Kern also 

participated. 

Tribal Strategies Meeting 

November 10, 2004 

Barbara Cairns and Jim Waldo made presentations on the Hatchery 

Reform Project’s progress over 2004–05, and how it fits with other tribal 

salmon recovery efforts and responsibilities at this meeting of tribal 

leaders in SeaTac. Bj Mirk and Betsy Daniels also attended. 

The Mountaineers 

November 30, 2004 

Don Campton, Barbara Cairns and Michael Kern made a presentation in 

Seattle on the Hatchery Reform Project to the Northwest’s oldest, and one 

of its largest, conservation organizations. 

Hatchery Reform Coalition 

December 6, 2004

Larry Peck and Paul Seidel provided an update in Olympia on WDFW’s 

budget proposal and how it will implement hatchery reform. 
78 Progress Report to Congress – April 2005 Appendices 

Northwest Fish Culture 

Conference 

December 8, 2004

Paul Seidel made a presentation on the principles, recommendations and 

tools of the HSRG at this gathering in Victoria, BC of hatchery personnel 

from across the Northwest. 

PUBLICATIONS 

Report to Congress

March 11, 2004

The 2004 Hatchery Reform Project Report to Congress was sent to 20 

members of Congress, Congressional staffers, and others involved in the 

appropriations process. It contained a summary of 2003 activities, a 2004 

work plan and budget, and a 2005 request. 

Shared Salmon Strategy for 

Puget Sound Bulletin 

March 15, 2004

This email bulletin included a preview of the April 2004 release of the 

HSRG’s recommendations. 

Seattle Post-Intelligencer 

March 30, 2004

Headline: “Hatchery Study To Offer Different Way of Thinking.” This 

article previewed the April release of the HSRG’s recommendations. 

Hatchery Reform Project 

Press Conference

April 23, 2004

The release of the HSRG’s report led to extensive coverage in the print, 

radio and television media (at least 44 stories and 1.6 million audience 

impressions). 

Skagit Valley Herald 

September 9, 2004 

Headline: “Scientists Hatching New Hatchery Plan.” This article on the 

Hatchery Reform Project was based on the September 8 presentation to 

the Skagit Watershed Council (see above). 

Fisheries Magazine Essay 

November 2004 

The HSRG submitted an overview paper on the Hatchery Reform Project 

and the findings of the HSRG for this American Fisheries Society peerreviewed journal. It will be published in June 2005. 

Northwest Fish Culture 

Conference 

December 8, 2004

Paul Seidel and Michael Kern authored a manuscript entitled “A New 

Model for Hatchery Management: Principles, Recommendations and 

Tools of the Hatchery Scientific Review Group,” for inclusion in the 

proceedings of the 55th annual Northwest Fish Culture Conference. 

Recreational Fishing Alliance 

Newsletter 

Fall 2004 

Headline: “Hatchery Reform: Bringing Hatchery Management into the 21st 

Century.” 

Hatchery Reform Project Web 

Site www.hatcheryreform.org 

The web site was completely redesigned as part of the preparation for the 

April 2004 release of the HSRG’s Principles and Recommendations

report. Throughout the year, LLTK kept the site up to date, providing 

electronic access to information about hatchery reform projects and 

publications including reports, meeting summaries and background 

information. 

Hatchery Reform PowerPoint 

Throughout the year, LLTK kept the project’s PowerPoint presentation up 

to date and tailored it for the various audiences to whom HSRG members 

and LLTK staff have made presentations.

Hatchery Reform Project 

Overview 

A revised, six-page overview of the Hatchery Reform Project was printed 

for use at and beyond the April 23 Briefing.
Appendices Progress Report to Congress – April 2005 79 

C: 2004 Tribal Hatchery Reform Projects 

TYPE I PROJECTS TO IMPROVE, EVALUATE OR 

MONITOR HATCHERY PRACTICES 

• Tulalip Tribes: Contribution of Tulalip hatchery Chinook to Terminal Fisheries and Local 

Naturally Spawning Populations Using Otoliths (ear bones). 

• Stillaguamish Tribe: Accurate Monitoring of North Fork Stillaguamish Chinook Out-migration 

Numbers. 

• Makah Tribe: Upgrade Incubation Equipment at Stony Creek Remote Rearing Site. 

• Makah Tribe: Umbrella Creek Sockeye Broodstock Capture and Adult Escapement Monitoring. 

• Nisqually Tribe: Weir Feasibility Study for Adult trap on the Main Stem Nisqually River. 

• Lower Elwha Klallam Tribe: Lower Elwha Enriched Rearing Environment Study. 

• Stillaguamish Tribe: Stillaguamish Chinook Smolt Production Estimation – Hatchery and Wild 

Contributions. 

• Makah Tribe: Lake Ozette Sockeye Salmon Out-migration Monitoring Project. 

• Tulalip Tribes: Survival Rate Comparison of Summer and Fall Chinook Broodstock at Tulalip 

Hatchery. 

• Stillaguamish Tribe: Stillaguamish River Fish Wheel Pilot Project. 

• Squaxin Island Tribe: Acoustic Tagging and Tracking of Minter Creek Hatchery and Peale 

Passage Net Pen Coho. 

• Lummi Nation: Skookum Hatchery Coho Release and Transfer Improvements (Fish Counter and 

Pumps). 

TYPE II PROJECTS TO RETROFIT, MODIFY OR 

BUILD FACILITIES 

• Tulalip Tribes: Purchase and Install Bird Netting and Fencing at Upper Tulalip Creek Pond. 

• Upper Skagit Tribe: Upper Skagit Hatchery Water Supply Modification/Retrofit. 

• Makah: Hoko Falls Hatchery Adult Ladder Feasibility Study. 

• Stillaguamish Tribe: Electrical Panel Relocation. 

• Nisqually Tribe: Adult Pond Retrofit Phase III. 

Appendices Progress Report to Congress – April 2005 81 

D: 2005 Project Budget 

Puget Sound and Coastal Washington Hatchery Reform Project Budget FY 2005

Hatchery Scientific Review Group

HSRG Members $166,000

Research Grants $278,050

Hatchery Reform Workshop $166,000

SUBTOTAL $610,050 

Washington Department of Fish and Wildlife

Science Team, Management, Accountability and Demonstration Projects $850,750

Northwest Indian Fisheries Commission

Science Team, Management, Accountability and Demonstration Projects $510,450

Nisqually Support for HSRG Member $41,500

SUBTOTAL $551,950 

US Fish and Wildlife Service

Science Team $70,550

Management, Accountability and Demonstration Projects $41,500

SUBTOTAL $112,050 

NOAA Fisheries

Science Team $70,550

Long Live the Kings

Project Management, Facilitation and Communications $244,850

Budget Administration 

IAC $35,000 

USFWS $25,000 

SUBTOTAL $60,000

TOTAL $2,500,200

Appendices Progress Report to Congress – April 2005 83 

E: 2005 HSRG Work Plan 

Focus: publications, tools and ongoing training to support 

scientifically defensible hatchery programs 

1st Quarter: January-March 2005 

Monthly HSRG meetings scheduled for: 

• January 12-14, Tukwila 

• February 22-24, Seattle 

• March 14-16, Tukwila 

Scientific Publications and Technical Papers 

o Fisheries essay revisions 

o Integrated/Segregated Paper 

o Applying Integrated/Segregated to Management including AHA 

o When to Start a Conservation Hatchery Program 

o Wild Fish Template 

o Outplanting/Net Pens 

Progress Report to Congress 

o Develop responses and recommendations to co-manager implementation actions at February and 

March meetings 

o Send to co-managers for review 

Technical Discussions 

o AHA Tool Discussions (HSRG/WDFW/NWIFC/tribes) 

o Managing for Success and Accountability (M&E/adaptive management, analytic tools; data 

collection/management, feed back loop; ways to document decisions and success over time). 

 HSRG Task Team - focus on completing draft 

 Form Technical Discussion Group (determine skill sets required, involve decision-makers, 

data managers, operators/information gatherers) 

 Institute secure website review process to garner feedback, both scientific and operational 

 Option for workshop with facilities operators if necessary 

 Finalize system/tools (mock-up)/how-to 

o Steelhead Management Plan - Follow up on WDFW request for assistance 

o Review DFO Canada Technical Paper Applying HSRG Principles/System-Wide Recommendations

Communications within Scientific Community 

o Key meetings and presentations at symposia 

o Meetings with key individuals 

Research - HSRG Research Review to be held/research grants awarded in Feb/March 

Hatchery Reform Workshop - Preparation and planning
84 Progress Report to Congress – April 2005 Appendices 

2nd Quarter: April-June 2005 

Monthly HSRG meetings to be scheduled for: 

• April 12–14, Tukwila 

• May 17–19, Tukwila 

• June 14–16, Tukwila 

Scientific Publications and Technical Papers 

o Integrated/Segregated Paper 

o Applying Integrated/Segregated to Management including AHA 

o When to Start a Conservation Hatchery Program 

o Wild Fish Template 

o Outplanting/Net Pens 

Progress Report to Congress - Complete report by April 

Technical Discussions 

o Wild Salmonid Management Zones- Determine need for HSRG task group/publication 

o AHA tool discussions 

o Managing toward Success and Accountability 

 HSRG Task Team - focus on completing draft 

 Technical Discussion Group meetings 

 Continue review process with managers 

 Option for workshop with facilities operators if necessary 

o Steelhead Management Plan – continue follow up on WDFW request for assistance if needed 

Communications within Scientific Community 

o Key meetings and presentations at symposia 

o Meetings with key individuals 

Research 

o Begin development of recommended research agenda for hatcheries 

o Review new research/receive presentations, revisit principles and recommendations 

o Provide HSRG research grant final reports on web site. 

Hatchery Reform Workshop – Continue Preparation and Planning 
Appendices Progress Report to Congress – April 2005 85 

3rd Quarter: July-September 2005 

Determine HSRG and task group meetings for: 

• July 

• August 

• September 

Scientific Publications and Technical Papers 

o Integrated/Segregated Paper 

o Applying Integrated/Segregated to Management including AHA 

o When to Start a Conservation Hatchery Program 

o Wild Fish Template 

o Outplanting/Net Pens 

Technical Discussions

o Wild Salmonid Management Zones? 

o AHA tool discussions? 

o Managing toward Success and Accountability (M&E/adaptive management, including analytic tools; 

data collection/management equipment, facilities; feedback loops; and ways to document decisions 

and success over time). 

 HSRG Task Team - focus on completing draft 

 Technical Discussion Group (determine skill sets required, involve decision-makers, data 

managers, operators/information gatherers) 

 Institute secure website review process to garner feedback, both scientific and operational 

 Option for workshop with facilities operators if necessary 

 Finalize system/tools (mock-up)/how-to 

o Steelhead Management Plan – continue follow up on WDFW request for assistance if needed 

Communications within Scientific Community 

o Key meetings and presentations at symposia 

o Meetings with key individuals 

Research 

o Continue development of recommended research agenda for hatcheries 

o Review new research/receive presentations, revisit principles and recommendations 

Hatchery Reform Workshop – Conference planning continues, to be held late in the quarter 
86 Progress Report to Congress – April 2005 Appendices 

4th Quarter : October-December 2005 

Determine HSRG and task group meetings for: 

• October 

• November 

• December 

FY2005 Report to Congress 

Scientific Publications and Technical Papers 

o Complete remaining publications 

Technical Discussions 

o Wild Salmonid Management Zones? 

o AHA tool discussions? 

o Finalize Managing toward Success and Accountability 

o Steelhead Management Plan – continue follow up on WDFW request for assistance if needed 

Communications within Scientific Community 

o Key meetings and presentations at symposia 

o Meetings with key individuals 

Research – Complete Recommended Research Agenda for Hatcheries

Hatchery Reform Workshop – Proceedings completed and distributed 
Appendices Progress Report to Congress – April 2005 87 

F: Technical Discussions Papers on 

Integrated and Segregated Hatchery 

Programs 

HSRG/WDFW/NWIFC Technical Discussion Paper #1: 

Integrated Hatchery Programs 

June 21, 2004 

Genetic and ecological interactions have been at the center of the debate over benefits and 

risks of hatchery programs (e.g., NRC 1993; HSRG 2004; Williams et al. 2003). The two 

options for managing these risks are either to minimize interaction through segregation 

(isolation) of the hatchery population from the natural population or to manage the hatchery 

population as an integral, benign component of a composite hatchery-natural population. All 

salmon and steelhead hatchery programs must be classified either as integrated or segregated 

by intent. These classifications lead directly to a series of genetic and ecological management 

guidelines for each of the two types of programs. How well programs meet this intent will 

vary; this variation provides an important measure for evaluating the biological risks posed by 

hatchery programs on natural populations. 

The purpose of this summary is to provide a definition of an integrated hatchery program, 

describe operational guidelines for implementation, and identify some of the implications and 

constraints imposed by the guidelines. 

Definition of an Integrated Hatchery Program 

The terms integrated and segregated describe the intended reproductive relationship of 

hatchery populations to naturally spawning populations. An integrated hatchery program is 

associated with a specified natural population from which gene flow occurs. The goal of an 

integrated program is to demographically increase the abundance of fish representing a 

natural population (two environments, one gene pool). 

Formal Definition: A hatchery program is an Integrated Type if the intent is for the natural 

environment to drive the adaptation and fitness of a composite population of fish that spawns 

both in a hatchery and in the wild. 

Theoretical Premise for Integrated Programs 

For a natural/hatchery composite population at equilibrium (Ford 2002), the influence of the 

hatchery and natural environments on the adaptation of the composite population is 
88 Progress Report to Congress – April 2005 Appendices 

determined by the proportion of natural-origin broodstock in the hatchery (pNOB3) and the 

proportion of hatchery-origin fish in the natural spawning escapement (pHOS). The larger the 

ratio pNOB/(pHOS+pNOB), the greater the strength of selection in the natural environment 

relative to that of the hatchery environment (Figure 1). In order for the natural environment to 

dominate selection, this ratio must exceed 0.5 (Campton, Busack and Currens, personal 

communication). Furthermore, the greater the difference between the hatchery and natural 

stock components (e.g., in run timing) and the “less natural” the hatchery environment (e.g., 

longer hatchery rearing), the larger the ratio must be to reduce the effects of hatchery 

selection. 

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

Proportion natural origin fish in hatchery broodstock (pNOB)

Proportion hatchery fish on spawning 

grounds (pHOS)

1

9

4

2.33

1.5

Stronger Natural

Selective Forces

Figure 1. Proportionate effects of natural selective forces in integrated hatchery programs at equilibrium; 

values to the right indicate the ratio pNOB/(pHOS+pNOB); pNOB must be >0.1 to account for genetic 

drift. 

Operational Guidelines for Integrated Programs 

1. The targeted value of pNOB/(pHOS+pNOB) should be based upon the current status of 

the stock, the goals for the stock, and involves a benefit versus risk judgment. For any 

fixed pNOB, the smaller the pHOS, the stronger the selective forces for the natural 

environment (see Figure 1). 

 

3

 Terminology: NOR = Natural Origin Return, HOR = Hatchery Origin Return, NOB = Natural Origin fish 

included in hatchery Broodstock, and HOS = Hatchery Origin fish in the natural Spawning escapement. 

0.50

0.60

0.70

0.80

0.90
Appendices Progress Report to Congress – April 2005 89 

2. The proportion of natural-origin fish in the broodstock must exceed the proportion of 

hatchery-origin fish on the spawning grounds (pNOB>pHOS) for the natural environment 

to drive adaptation, which is equivalent to pNOB/(pHOS+pNOB)>0.50. 

3. pNOB/(pHOS+pNOB) for integrated programs with stocks of moderate or high biological 

significance and viability (or goals to maintain or improve the biological significance and 

viability of the stock) should be greater than 0.7 (see Figure 1) to ensure high levels of 

natural dominance. 

4. pNOB should be a minimum of 10% to avoid divergence of the hatchery population from 

the natural component, even when pHOS is zero. 

5. A general rule of thumb is that the total number of adults (hatchery- and natural-origin) 

used for broodstock cannot exceed the total number of natural-origin escapement. 

6. Hatchery fish should be reared under conditions that deviate as little as possible from 

those experienced by the natural population component, to minimize the effects of 

selective forces in the hatchery: 

a) Rear in a hatchery environment that allows synchronization of adult maturation, 

incubation and emergence, and out-migration with natural populations. 

b) Use rearing protocols that produce juvenile fish similar to natural populations in 

growth rate and size, to reduce competition with and predation on natural stocks, and 

to maintain the age structure of the natural population. 

c) Rear fish at reduced densities in enriched environments, to produce a fish with cryptic 

coloration, territorial fidelity and behavior similar to naturally-produced fish. 

d) Release fish volitionally during the out-migration timing of the natural stock. 

7. The size of the program should take into account the quantity and quality of habitat 

available for juveniles and adult spawners, and the effect of the hatchery program on 

natural stocks. 

8. Use marks, tags or other methods to distinguish natural- and hatchery-origin fish among 

natural spawners, in hatchery broodstocks and in harvests. 

9. Take into consideration the potential selective impacts of harvest (for example, size 

selectivity) on the long-term viability of integrated programs. 
90 Progress Report to Congress – April 2005 Appendices 

Implications/Constraints of Broodstock Management Guidelines for Integrated 

Hatchery Programs 

Broodstock management guidelines for an integrated 

hatchery program impose limitations on the size of that 

program. These limitations depend on the ability to control 

the mix of hatchery- and natural-origin fish both on the 

spawning grounds and in the hatchery. They also depend 

on factors affecting the number of natural spawners 

available for hatchery broodstock (i.e., the productivity of 

the natural environment and the harvest rate on natural 

fish). Identification of the options available to implement 

integrated programs (i.e., changing the ratio of pNOB to 

pHOS, and/or the size of the hatchery program) requires 

case-by-case analyses. 

Implementing an Integrated Hatchery Program 

Currently, few hatchery programs are meeting the 

broodstock guidelines recently developed for programs 

where integration is a goal. Assuming that it has been determined that an integrated program 

is appropriate to meet resource goals, how should the transition occur? The answer depends in 

large part on the genetic make-up of the current hatchery and natural population components. 

It also depends on a tolerance to risk that varies depending on the viability of, and goals for, 

the natural population. For example, in a recovery program, it may be necessary to rely on 

hatchery propagation to secure genetic resources, until the habitat is capable of supporting a 

fully integrated program. Initially, this type of program may have to be developed from one 

where the composite population is highly influenced by the hatchery environment, but where 

a detailed management plan has been developed to eventually have the natural environment 

dominate. Similarly, integrated harvest programs with goals to maintain or improve the 

biological significance of the stock should be operated to ensure that selective forces in the 

natural environment dominate. 

The tables below are intended to provide guidance in developing an action plan to implement 

an integrated program based on the initial condition (Scenarios 1-3). There may be 

circumstances where one or more elements of these approaches are not applicable.

Supplementation is a term frequently 

used when referring to hatchery 

programs where the intent is for 

hatchery origin fish to spawn in the 

wild and make a contribution to 

harvest and/or conservation (e.g., 

RASP, 1991). The key question for 

supplementation programs is whether 

the hatchery fish spawning in the wild 

indeed confer a net benefit. The 

HSRG has concluded that this may be 

possible in some circumstances and 

that such programs should always be 

accompanied by comprehensive 

monitoring and evaluation efforts. 

Supplementation programs may be 

either integrated or segregated.
Appendices Progress Report to Congress – April 2005 91 

Scenario 1: New Integrated Program

No hatchery program exists 

 Natural population has had little influence from hatchery fish

Recommended approach for initiating a new integrated 

program 

Considerations 

Initiate hatchery program by collecting representative sample of 

natural fish.

Collect a number of brood that allows for an effective 

population size of the composite population (natural plus 

hatchery) in excess of 500 fish. 

If a long-term goal of the hatchery program is to provide a 

conservation benefit, or if the natural spawning of 

hatchery-origin fish will be difficult to control, then the 

effective population size of the hatchery component should 

also be greater than 500 fish.

Incorporate a minimum of 10% NORs into hatchery broodstock 

each year. 

Ensure that gene flow from the natural to the hatchery 

population is greater than gene flow from the hatchery to 

the natural population (pNOB > pHOS). 

For stocks of moderate or high biological significance and 

viability (or goals to maintain or improve the biological 

significance and viability of the stock), 

pNOB/(pHOS+pNOB) should be greater than 0.7 . 

Size program consistent with goals, the ability of the natural 

population to support hatchery broodstock requirements, 

and gene flow limitations to the natural population.

Likelihood of achieving natural adaptation: High 

likelihood of attaining stock goals (developing a 

program where the natural environment drives the 

adaptation of the composite hatchery and natural 

population), as long as broodstock collection is 

feasible and gene flow is maintained within 

recommended guidelines for the goals of the stock. 

Cost: Additional program cost compared to 

segregated programs, primarily for natural 

broodstock collection. 

Effect on Harvest: Changes in harvest contribution 

are dependent on productivity of the natural 

component of the population, as well as 

productivity of the hatchery component.
92 Progress Report to Congress – April 2005 Appendices 

Scenario 2: Transition from a segregated program to an integrated program

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had little influence from hatchery fish

Approach #1 - Not recommended because of 

low likelihood of attaining stock goals Considerations 

Incorporate a minimum of 10% NORs into 

hatchery broodstock each year.

Ensure that gene flow from the natural to the 

hatchery population is greater than gene flow 

from the hatchery to the natural population 

(pNOB > pHOS).

Size program consistent with goals, the ability of 

the natural population to support hatchery 

broodstock requirements, and gene flow 

limitations to the natural population.

Likelihood of achieving natural adaptation: Low likelihood of attaining stock 

goals in the immediate future. Likelihood increases as additional NORs are 

incorporated into the hatchery population through time, or as the proportion of 

NORs in the hatchery broodstock is increased. Composite population is likely to 

have low to intermediate fitness in the natural environment. 

Cost: Increase in cost incurred for broodstock collection appears similar for all 

approaches. 

Effect on Harvest: Effect on harvest appears similar under all approaches other 

than Approach #2 in this and the next scenario, where the segregated harvest 

program is terminated or suspended to allow some level of adaptation of the 

hatchery stock. 

Approach #2 - Recommended approach if 

attaining harvest goal can be interrupted 

during transition to integrated program 

Considerations 

Initiate a new hatchery program by collecting a 

representative sample of natural fish. 

Collect a number of brood that allows for an 

effective population size of the composite 

population (natural plus hatchery) in excess 

of 500 fish. 

If a long-term goal of the hatchery program is to 

provide a conservation benefit, or if the 

natural spawning of hatchery-origin fish will 

be difficult to control, then the effective 

population size of the hatchery component 

should also be greater than 500 fish. 

Incorporate a minimum of 10% NORs into 

hatchery broodstock each year. 

Ensure that gene flow from the natural population 

to the hatchery population is greater than 

gene flow from the hatchery to the natural 

population (pNOB > pHOS). 

For stocks of moderate or high biological 

significance and viability (or goals to 

maintain or improve the biological 

significance and viability of the stock), 

pNOB/(pHOS+pNOB) should be greater 

than 0.70. 

Size program consistent with goals and the ability 

of the natural population to support hatchery 

broodstock requirements and gene flow 

limitations to the natural population. 

 Terminate segregated harvest program.

Likelihood of achieving natural adaptation: High likelihood of attaining stock 

goals as long as broodstock collection is feasible and gene flow is maintained 

within recommended guidelines. 

Cost: Increase in cost incurred for broodstock collection appears similar for all 

approaches. 

Effect on Harvest: A loss of contribution to harvest would be expected between 

termination of the segregated program and achieving the final size of the new 

integrated program. 
Appendices Progress Report to Congress – April 2005 93 

Scenario 2 (continued): Transition from a segregated program to an integrated program

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had little influence from hatchery fish

Approach #3 - Recommended approach if attaining harvest goal 

cannot be interrupted during transition to integrated program Considerations 

Initiate new hatchery program by collecting representative sample of 

natural fish.

Collect a number of brood that allows for an effective population size of 

the composite population (natural plus hatchery) to be in excess of 

500 fish.

If a long-term goal of the hatchery program is to provide a conservation 

benefit, or if the natural spawning of hatchery-origin fish will be 

difficult to control, then the effective population size of the hatchery 

component should also be greater than 500 fish. 

Differentially mark and release offspring of old/new broodstock. 

Preferentially use returns that represent the NOS broodstock. Phase 

out use of old broodstock as new broodstock returns.

Incorporate a minimum of 10% NORs into hatchery broodstock each 

year once new broodstock returns.

Ensure that gene flow from the natural population to the hatchery 

population is greater than gene flow from the hatchery to the 

natural population (pNOB > pHOS).

For stocks of moderate or high biological significance and viability (or 

goals to maintain or improve the biological significance and 

viability of the stock) pNOB/(pHOS+pNOB) should be greater than 

0.70 . 

Size program consistent with goals and the ability of the natural 

population to support hatchery broodstock requirements and gene 

flow limitations to the natural population.

Likelihood of achieving natural adaptation: High 

likelihood of attaining stock goals, as long as 

broodstock collection is feasible and gene flow is 

maintained within recommended guidelines. 

Cost: Increase in cost incurred for broodstock 

collection appears similar for all approaches. An 

additional cost for differentially marking the two 

hatchery broodstocks would be incurred. Cost in terms 

of operational complexity is higher than all other 

approaches except the final approach, but should be 

no greater than rearing an additional species. 

Effect on Harvest: The loss of contribution to harvest 

in Scenario 2, Approach #2, above, could be avoided 

during transition with additional marking cost. 
94 Progress Report to Congress – April 2005 Appendices 

Scenario 3: Transition from an incompletely segregated program to an integrated program. (Most common scenario).

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had significant influence from hatchery fish

Approach #1 - Not recommended because of low 

likelihood of attaining stock goals Considerations 

Incorporate a minimum of 10% NORs into hatchery 

broodstock each year.

Ensure that gene flow from the natural population to 

the hatchery population is greater than gene flow 

from the hatchery to the natural population 

(pNOB > pHOS).

Size program consistent with goals and the ability of 

the natural population to support hatchery 

broodstock requirements and gene flow 

limitations to the natural population

Restrict natural spawning by HORs.

Likelihood of achieving natural adaptation: Lowest likelihood of all options 

in attaining stock goals in the immediate future since NORs incorporated into 

hatchery broodstock may themselves have suffered loss of productivity as a 

result of past hatchery influence. Likelihood of reaching stock goals increases 

as additional NORs are incorporated into the hatchery population through 

time or as proportion of NORs in hatchery broodstock is increased. 

Composite population is likely to have the lowest fitness in the natural 

environment of all the approaches. 

Cost: Increase in cost incurred for broodstock collection appears similar for 

all approaches. 

Effect on Harvest: Effect on harvest appears similar under all approaches 

other than Approach #2 in Scenarios 2 and 3. 

Approach #2 - Recommended approach if attaining harvest goal can be 

interrupted during transition to integrated program. Considerations: 

Take steps to reduce the number of hatchery fish in the natural population to less 

than five percent of the natural population. (Reduce hatchery program, 

selective harvest to limit strays, weir, other measures to control straying)

 Allow a minimum of three to four generations to promote adaptation to the 

natural environment.

 Initiate a new hatchery program by collecting representative sample of natural 

fish.

 Collect a number of brood that allows for an effective population size of the 

composite population (natural plus hatchery) to be in excess of 500 fish.

If a long-term goal of the hatchery program is to provide a conservation benefit, or 

if the natural spawning of hatchery-origin fish will be difficult to control, then 

the effective population size of the hatchery component should also be 

greater than 500 fish. 

 Incorporate a minimum of 10% NORs into hatchery broodstock each year.

Ensure that gene flow from the natural population to the hatchery population is 

greater than gene flow from the hatchery to the natural population (pNOB > 

pHOS).

For stocks of moderate or high biological significance and viability (or goals to 

maintain or improve the biological significance and viability of the stock) 

pNOB/(pHOS+pNOB) should be greater than 0.70.

Size program consistent with goals and the ability of the natural population to 

support hatchery broodstock requirements and gene flow limitations to the 

natural population.

Terminate segregated harvest program.

Likelihood of achieving natural adaptation: 

Intermediate likelihood of attaining stock goals 

because of the uncertainly of adaptation to the 

natural environment after three to four 

generations. The likelihood of meeting stock 

goals increases with the amount of time allowed 

before initiating new program and lower 

contribution of hatchery fish in the natural 

population. 

Cost: Increase in cost incurred for broodstock 

collection appears similar for all approaches. 

Effect on Harvest: Highest likelihood of loss of 

contribution to harvest of all the approaches since 

the segregated program would likely be reduced 

to allow adaptation of the natural stock and the 

segregated program would be terminated to 

initiate a new integrated program. 
Appendices Progress Report to Congress – April 2005 95 

Scenario 3 (continued): Transition from an incompletely segregated program to an integrated program. (Most common 

scenario).

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had significant influence from hatchery fish

Approach # 2 Plus Differential Marking - Recommended approach if attaining 

harvest goal cannot be interrupted during transition to integrated program Considerations 

Take steps to reduce the number of hatchery fish in the natural population to less than 

five percent of the natural population (reduce hatchery program, selectively harvest 

to limit strays, use a weir or other measures to control straying).

Allow a minimum of three to four generations to promote adaptation to the natural 

environment.

Initiate a new hatchery program by collecting representative sample of natural fish.

Collect a number of brood that allows for an effective population size of the composite 

population (natural plus hatchery) in excess of 500 fish.

If a long-term goal of the hatchery program is to provide a conservation benefit, or if the 

natural spawning of hatchery-origin fish will be difficult to control, then the 

effective population size of the hatchery component should also be greater than 500 

fish.

Differentially mark and release offspring of old/new broodstock. Preferentially use 

returns that represent the NOS broodstock. Phase out use of old broodstock as new 

broodstock returns.

Incorporate a minimum of 10% NORs into hatchery broodstock each year once new 

broodstock returns.

Ensure that gene flow from the natural to the hatchery population is greater than gene 

flow from the hatchery to the natural population (pNOB > pHOS).

For stocks of moderate or high biological significance and viability (or goals to maintain 

or improve the biological significance and viability of the stock), 

pNOB/(pHOS+pNOB) should be greater than 0.70.

Size program consistent with goals and the ability of the natural population to support 

hatchery broodstock requirements and gene flow limitations to the natural 

population.

Likelihood of achieving natural 

adaptation: Intermediate likelihood of 

attaining stock goals because of the 

uncertainly of adaptation to the natural 

environment after three to four generations. 

The likelihood of meeting stock goals 

increases with the amount of time allowed 

before initiating a new program and a 

lower contribution of hatchery fish in the 

natural population. 

Cost: Increase in cost incurred for 

broodstock collection appears similar for all 

approaches. An additional cost for 

differentially marking the two hatchery 

broodstocks would be incurred. Cost in 

terms of operational complexity is higher 

than all other approaches except Approach 

#4, but should be no greater than rearing an 

additional species. 

Effect on Harvest: Reduces loss of 

contribution to harvest during transition 

from the previous approach. 

References: 

Ford, M.J. 2002. Selection in captivity during supportive breeding may reduce fitness in the wild. 

Conservation Biology 16: 815-825. 

HSRG (Hatchery Scientific Review Group)–Lars Mobrand (chair), John Barr, Lee Blankenship, 

Don Campton, Trevor Evelyn, Tom Flagg, Conrad Mahnken, Robert Piper, Paul Seidel, Lisa 

Seeb and Bill Smoker. April 2004. Hatchery Reform: Principles and Recommendations of the 

HSRG. Long Live the Kings, 1305 Fourth Avenue, Suite 810, Seattle, WA 98101 (available 

from www.hatcheryreform.org). 

Mobrand, Lars. 1991. Regional Assessment of Supplementation Program (RASP). Project #1985-

06200 (BPA Report DOE/BP-01830-11). Bonneville Power Administration, PO Box 3621, 

Portland, OR 97208. 

National Research Council Committee on Protection and Management of Pacific Northwest 

Anadromous Salmonids (NRC). 1996. Upstream: Salmon and Society in the Pacific 

Northwest, National Academy Press, Washington, DC. 

Williams, R. N., J. A. Lichatowich, P. R. Mundy, and M. Powell. 2003. Integrating artificial 

production with salmonid life history, genetic, and ecosystem diversity: a landscape 

perspective. Issue Paper for Trout Unlimited, West Coast Conservation Office, Portland.

Appendices Progress Report to Congress – April 2005 97 

HSRG/WDFW/NWIFC Technical Discussion Paper #2: 

Segregated Hatchery Programs 

June 21, 2004 

Genetic and ecological interactions have been at the center of the debate over benefits and 

risks of hatchery programs (e.g., NRC 1995; HSRG 2004). The two options for managing 

these risks are either to minimize interaction through segregation (isolation) of the hatchery 

population from the natural population or to manage the hatchery population as an integral, 

benign component of a composite hatchery-natural population. All salmon and steelhead 

hatchery programs must be classified either as integrated or segregated by intent. These 

classifications lead directly to a series of genetic and ecological management guidelines for 

each of the two types of programs. How well programs meet this intent will vary; this 

variation provides an important measure for evaluating the biological risks posed by hatchery 

programs on natural populations. 

The purpose of this paper is to provide a definition of a segregated hatchery program, describe 

operational guidelines for implementation, and identify some of the implications and 

constraints imposed by the guidelines. 

Definition of a Segregated Hatchery Program 

The terms integrated and segregated describe the intended reproductive relationship of 

hatchery populations to naturally spawning populations. 

Formal Definition: A hatchery program is a Segregated Type if the intent is for the hatchery 

population to represent a distinct population that is reproductively isolated from naturallyspawning populations.

Theoretical Premise for Segregated Programs 

Hatchery programs are classified as segregated if the hatchery population is propagated as a 

genetically discrete or segregated population relative to naturally spawning populations. The 

principal intent of a segregated program is to create a new, hatchery-adapted population to 

meet goals for harvest or other purposes (research, education, etc.). Hatchery broodstocks 

(and programs) are considered genetically segregated if the broodstock is maintained 

primarily or exclusively from adults returning back to the hatchery. As a consequence, little or 

no gene flow from a natural population to the hatchery broodstock is intended to occur in a 

segregated program. 

Natural spawning of fish from segregated programs may pose genetic and ecological risks to 

natural-spawning populations. The risks that segregated hatchery programs pose to natural 
98 Progress Report to Congress – April 2005 Appendices 

populations depend on the status and goals for the natural populations, the extent to which 

hatchery-origin fish interact genetically and ecologically with natural-origin fish, and on the 

amount of genetic and phenotypic divergence between the hatchery and natural populations. 

Operating Guidelines for Segregated Programs 

1. Each hatchery program should include a detailed genetic management plan for 

broodstock that outlines protocols, etc. 

2. Rear fish in a manner and/or at a location that minimizes potential straying and 

opportunities for natural spawning. 

3. Release fish in areas where opportunities to capture non-harvested adults are 

maximized, thus minimizing genetic risks to natural populations. 

4. Ensure adult production from segregated programs is commensurate with harvest 

opportunities. 

5. Take into consideration the potential selective impacts of harvest (for example, size 

selectivity) on the long-term viability of segregated programs. 

6. Ensure hatchery-origin adults constitute no more than five percent of the naturallyspawning population. 

7. Use marks, tags or other methods to distinguish natural- and hatchery-origin fish 

among natural spawners, in hatchery broodstocks and in harvests. 

8. Avoid unintentional inclusion of natural-origin adults in segregated broodstocks. 

9. Minimize the effects of predation and competition on naturally-spawning stocks when 

designing hatchery programs. 

Operational Considerations for Segregated Hatchery Programs 

Segregated programs, particularly those with only harvest goals, typically have few operational 

constraints. Segregated hatchery broodstocks may be bred selectively for particular traits (e.g., 

early run-timing), to facilitate ease of culture and/or to help achieve desired benefits (e.g., 

harvest). In general, segregated programs are managed in a way that maximizes productivity (i.e., 

recruits per spawner) or efficiency, irrespective of the ability of returning adults to reproduce 

naturally or confer any benefits to naturally spawning populations. Indeed, hatchery-origin fish 

from a genetically segregated program can impose unacceptable genetic and ecological risks to 

natural populations (Busack and Currens 1995). As a result, segregated programs often represent 

major trade-offs between minimizing biological risks to naturally spawning populations and 

maximizing efficiency and harvest benefits of the hatchery program. 

Many segregated hatchery programs in Puget Sound and coastal Washington have selectively bred 

adults, either purposefully or inadvertently, for “early” spawn or run timing, primarily by 
Appendices Progress Report to Congress – April 2005 99 

excluding late-returning adults from broodstocks. Many hatchery stocks of salmon and steelhead 

now return and spawn several weeks earlier than their natural-origin counterparts. Differences in 

return timing between natural- and hatchery-origin adults can be used as a management tool to 

focus fisheries on early-returning hatchery fish, while protecting late-returning natural fish. This 

approach can facilitate fisheries management from an agency perspective. 

Segregated programs can impose significant genetic risks to naturally spawning populations if 

non-harvested fish spawn naturally. Indeed, any natural spawning by fish from these broodstocks 

may be considered unacceptable, because of the potential genetic impacts on natural populations. 

Proponents of such “segregated” programs often argue that early-returning hatchery fish are mistimed biologically to stream flows and water temperatures and, thus, fail to reproduce successfully 

even if they do spawn in nature. However, empirical and experimental evidence indicates that such 

early-returning hatchery fish do indeed reproduce successfully, albeit at a reduced rate relative to 

natural-origin fish (Chilcote et al. 1986; Campton et al. 1991; Mackey et al. 2001). Although these 

hatchery-origin fish have a lower reproductive success relative to their natural-origin counterparts, 

their overall genetic and ecological risks can be substantial if hatchery-origin fish constitute a 

significant number of natural-origin spawners (Chilcote et al. 1986; Leider et al. 1990; Kostow et 

al., 2003). 

Clearly, the degree to which segregated hatchery programs are successful depends significantly on 

the degree to which genetic and ecological risks to natural populations can be minimized. Many 

segregated hatchery broodstocks also represent the genetic products of historical stock transfers 

among facilities or regions, thus further compounding the genetic and ecological risks that those 

programs may impose on naturally spawning populations. To minimize these risks, segregated 

hatchery programs need to be located in areas where virtually all returning adults can be harvested 

or recaptured, or where natural spawning or ecological interactions with natural-origin fish are 

considered minimal or inconsequential. Outplanting fish from segregated programs where 

effective adult recapture does not exist should be discontinued (see HSRG emerging issue paper 

on this topic).
100 Progress Report to Congress – April 2005 Appendices 

Implementing a Segregated Hatchery Program: 

Scenario 1: New Segregated Program 

No hatchery program exists 

Status of natural population in terms of past hatchery influence is not important

• Initiate the program with enough fish to provide a minimum effective population size of 500 fish. 

• Identify HORs and NORs; avoid unintentional inclusion of NORs in the broodstock

• Operate the program so that it does not create significant genetic or ecological interactions with natural populations 

(e.g., proper sizing, selective removal to limit strays, adult collection facilities or weir, long–term acclimation at point of

release, other measures to control straying).. 

• Ensure that the contribution of hatchery-origin fish spawning naturally does not exceed five percent of the natural 

spawning population. 

Scenario 2: Transition from a incompletely segregated or integrated program to a properly segregated program (Most 

common scenario for both incompletely segregated and incompletely integrated programs) 

Hatchery broodstock has had no systematic gene flow from the natural population 

Natural spawning population has had significant influence from hatchery fish 

• Identify HORs and NORs; avoid unintentional inclusion of NORs in the broodstock.

• Operate the program so that it does not create significant genetic or ecological interactions with natural populations 

(e.g., proper sizing, selective removal to limit strays, adult collection facilities or weir, long–term acclimation at point of

release, other measures to control straying).. 

• Ensure that the contribution of hatchery-origin fish spawning naturally does not exceed five percent of the natural 

spawning population.

Scenario 3: Transition from a well integrated program to a segregated program 

Hatchery broodstock has had systematic gene flow from the natural population 

Gene flow from the natural population to the hatchery population has been greater than gene flow from the 

hatchery to the natural population 

• Identify HORs and NORs; avoid unintentional inclusion of NORs in the broodstock. 

• Operate the program so that it does not create significant genetic or ecological interactions with natural populations 

(e.g., proper sizing, selective removal to limit strays, adult collection facilities or weir, long–term acclimation at point of

release, other measures to control straying).. 

• Ensure that the contribution of hatchery-origin fish spawning naturally does not exceed five percent of the natural 

spawning population 

References: 

Busack, C. A., and K. P. Currens. 1995. Genetic risks and hazards in hatchery 

operations: Fundamental concepts and issues. Pages 71-80 in H. L. Schramm , Jr. 

and R. G. Piper, editors. Uses and effects of cultured fishes in aquatic ecosystems. 

American Fisheries Society Symposium 15, Bethesda, MD. 

Campton, D. E., Allendorf, F. W., Behnke, R. J., Utter, F. M., Chilcote, M. W., Leider, S. 

A., and Loch, J. J. 1991. Reproductive success of hatchery and wild steelhead. 

Transactions of the American Fisheries Society 120: 816-827. 
Appendices Progress Report to Congress – April 2005 101 

Chilcote, M. W., S. A. Leider, and J. J. Loch. 1986. Differential reproductive success of 

hatchery and wild summer-run steelhead under natural conditions. Transactions of 

the American Fisheries Society 115: 726-735. 

HSRG (Hatchery Scientific Review Group)–Lars Mobrand (chair), John Barr, Lee 

Blankenship, Don Campton, Trevor Evelyn, Tom Flagg, Conrad Mahnken, Robert 

Piper, Paul Seidel, Lisa Seeb and Bill Smoker. April 2004. Hatchery Reform: 

Principles and Recommendations of the HSRG. Long Live the Kings, 1305 Fourth 

Avenue, Suite 810, Seattle, WA 98101 (available from www.hatcheryreform.org). 

Kostow, K. E., A. R. Marshall, and S. R. Phelps. 2003. Naturally spawning hatchery 

steelhead contribute to smolt production but experience low reproductive success. 

Transactions of the American Society 132:780-790. 

Leider, S. A., P. L. Hulett, J. J. Loch, and M. W. Chilcote. 1990. Electrophoretic 

comparison of the reproductive success of naturally spawning transplanted and wild 

steelhead trout through the returning adult stage. Aquaculture 88: 239-252.Mackey et 

al. 2001 

Mackey, G., J.E. McLean, T.P. Quinn. 2001. Comparisons of run timing, spatial 

distribution and length of wild and newly established hatchery populations of 

steelhead in Forks Creek, Washington. N. Am. J. Fish. Mgmt. 21:717-724. 

National Research Council Committee on Protection and Management of Pacific 

Northwest Anadromous Salmonids (NRC). 1996. Upstream: Salmon and Society in 

the Pacific Northwest, National Academy Press, Washington, DC. 

Appendices Progress Report to Congress – April 2005 103 

G: Example Application of the All-H Analyzer 

(AHA) Management Tool 

See graphic, next page. 

Appendices Progress Report to Congress – April 2005 105 

H: Hatchery Reform Coalition Members 

April 2005 

Gestin Suttle, Friends of Issaquah Salmon Hatchery 

Gary Loomis, G. Loomis Rods/Fish First 

Buzz Ramsey, Luhr Jensen 

Norm Winn, The Mountaineers 

Jeff Curtis and Kaitlin Lovell, National Trout Unlimited 

Liz Hamilton and Karl Burke, NW Sportsfishing Industry Association 

Peter Bergman and Frank Haw, Northwest Marine Technology 

Tony Floor, Northwest Marine Trade Association 

Clint Muns, Puget Sound Anglers 

Jim Martin, Berkeley Conservation Institute 

Mike Gilchrist and Corey Freeman, Recreational Fishing Alliance 

Scott Weedman, Three Rivers Marine 

Dick Burge and Nate Mantua, Wild Steelhead Coalition 

Terry Turner, Washington Council of Trout Unlimited 

Bill Wilkerson and Heather Rowton, Washington Forest Protection 

Association 

Mark Cedergreen, Westport Charterboat Association 

Bill Robinson, Fish Advocate 

Frank Urabeck, Fish Advocate 
Embedded Secure Document

The file http://www.lltk.org/pdf/HR_Report_to_Congress_Applying_Science_Apr05.pdf is a secure 

document that has been embedded in this document. Double click the pushpin to view. 
THE NEED

ABOUT THE PROJECT

HSRG

REFORM PRINCIPLES

REGIONAL REVIEWS

IMPLEMENTATION

PUBLICATIONS

CONTACT US

HSRG 

RECOMMENDATIONS 

HATCHERY REFORM: PRINCIPLES AND RECOMMENDATIONS OF THE HATCHERY SCIENTIFIC 

REVIEW GROUP

In April 2004, the Hatchery Scientific Review Group published Hatchery Reform: Principles and 

Recommendations of the Hatchery Scientific Review Group. This document includes the principles, tools and 

recommendations that resulted from the HSRG's three-year review of over 200 hatchery programs at over 100 

hatcheries. 

Read Selected Coverage of the HSRG Report Release

HSRG REPORT PRESS PACKET, APRIL 23, 2004

Press Release

Press Conference Agenda

Hatchery Reform Project Update

Hatchery Reform Support Letter

HSRG Member List

Quote Sheet

FULL REPORT

Hatchery Reform: Principles and Recommendations of the Hatchery Scientific Review Group, April 

2004 (2.7 MB) 

FULL REPORT - By Individual Section

Introduction 

Foundation for Hatchery Reform

Scientific Framework 

Emerging Issues in Hatchery Reform 

Research Grants Program 

Applied Hatchery Reform

Regional Review Process 

Principles and System-Wide Recommendations

Program-Specific Regional Recommendations 

Conclusions

The Future of Hatcheries 

Examples of Successful Hatchery Programs 

Appendices

Scientific Framework for the Artificial Propogation of Salmon and Steelhead

Emerging Issues in Hatchery Reform:

1. Management Goals for Hatchery Broodstocks: Genetic Integration versus Segregation

2. Using Hatchery Salmon Carcasses for Nutrification of Freshwater Ecosystems While Reducing 

Associated Fish Health Risks

3. Hatchery Smolt Quality and Achieving the Wild Salmon Template

4. Benefits of Hatchery Fish as a Source of Food

5. Marine Carrying Capacity

6. Outplanting and Net Pen Release of Hatchery-Origin Fish

7. Assessing the Potential for Predation on Wild Salmonid Fry by Hatchery-Reared Salmonids in 

Washington
8. Using Acclimation Ponds in the Rearing of Salmon

Operational Guidelines 

Monitoring and Evaluation Criteria 

Regional Information Key Questions Form 

Regional Information Instruction Form

Benefit/Risk Tool

Research Grants 

PROGRAM-SPECIFIC RECOMMENDATIONS BY REGION:

February 2002 (Full Report, 1.9 MB)

Components of this Report:

1. Eastern Strait of Juan de Fuca

2. South Puget Sound

3. Stillaguamish/Snohomish Rivers

4. Appendices

March 2003 (Full Report, 4.8 MB) 

Components of this Report:

1. Skagit River Basin

2. Nooksack/Samish Rivers

3. Central Puget Sound

4. Appendices

March 2004 (Full Report, 2.6 MB): 

Components of this Report:

1. Hood Canal

2. Willapa Bay

3. North Coast

4. Grays Harbor

5. Appendices

CONTACT US | 

HOME
HATCHERY REFORM 

Principles and Recommendations 

of the 

Hatchery Scientific Review Group

April 2004 
Please cite as: 

Hatchery Scientific Review Group (HSRG)–Lars Mobrand (chair), John Barr, Lee Blankenship, 

Don Campton, Trevor Evelyn, Tom Flagg, Conrad Mahnken, Robert Piper, Paul Seidel, 

Lisa Seeb and Bill Smoker. April 2004. Hatchery Reform: Principles and 

Recommendations of the HSRG. Long Live the Kings, 1305 Fourth Avenue, Suite 810,

Seattle, WA 98101 (available from www.hatcheryreform.org). Cite in text as HSRG 2004. 

All Hatchery Reform Project publications are available from the project’s web site 

(www.hatcheryreform.org) or by contacting Long Live the Kings at (206) 382-9555 ext. 21 
Table of Contents 

INTRODUCTION ....................................................................................................................3

BACKGROUND ............................................................................................................................................3

THE NEED FOR REFORM.............................................................................................................................4

PROJECT OVERVIEW ..................................................................................................................................5

REPORT OVERVIEW....................................................................................................................................8

NEXT STEPS..............................................................................................................................................12

FOUNDATION FOR HATCHERY REFORM ..................................................................15

SCIENTIFIC FRAMEWORK.........................................................................................................................15

EMERGING ISSUES IN HATCHERY REFORM.............................................................................................19

RESEARCH GRANTS PROGRAM................................................................................................................20

APPLIED HATCHERY REFORM......................................................................................25

REGIONAL REVIEW PROCESS...................................................................................................................25

PRINCIPLES AND SYSTEM-WIDE RECOMMENDATIONS...........................................................................31

PROGRAM-SPECIFIC REGIONAL RECOMMENDATIONS ...........................................................................46

CONCLUSIONS.....................................................................................................................55

THE FUTURE OF HATCHERIES..................................................................................................................55

EXAMPLES OF SUCCESSFUL HATCHERY PROGRAMS .............................................................................57

APPENDICES.........................................................................................................................63

A. SCIENTIFIC FRAMEWORK FOR THE ARTIFICIAL PROPAGATION OF SALMON AND STEELHEAD.... A-1

B. EMERGING ISSUES IN HATCHERY REFORM......................................................................................B-1

C. OPERATIONAL GUIDELINES..............................................................................................................C-1

D. MONITORING AND EVALUATION CRITERIA.................................................................................... D-1

E. REGIONAL INFORMATION KEY QUESTIONS FORM..........................................................................E-1

F. REGIONAL INFORMATION INSTRUCTION FORM...............................................................................F-1

G. BENEFIT/RISK TOOL ........................................................................................................................ G-1

H. RESEARCH GRANTS......................................................................................................................... H-1

I. PROGRAM-SPECIFIC RECOMMENDATIONS BY REGION.......................................................................*

2001: EASTERN STRAIT OF JUAN DE FUCA, SOUTH PUGET SOUND,

 STILLAGUAMISH/ SNOHOMISH RIVERS

2002: SKAGIT RIVER BASIN, NOOKSACK/ SAMISH RIVERS, CENTRAL PUGET SOUND

2003: HOOD CANAL, WILLAPA BAY, NORTH COAST, GRAYS HARBOR

*The three volumes that constitute Appendix I are available online at www.hatcheryreform.org or by contacting Long 

Live the Kings at lltk@lltk.org or 206-382-9555 ext 21.

Table of Contents i 

Introduction - Background 3 

Introduction 

BACKGROUND 

In 1999, in response to a request from Washington state’s Congressional representatives, a group of 

leading scientists presented its recommendations to the US Congress in a report entitled The Reform 

of Salmon and Steelhead Hatcheries in Puget Sound and Coastal Washington to Recover Natural 

Stocks While Providing Fisheries. The report determined that the potential exists for hatcheries to 

provide benefits to the recovery of naturally spawning salmon. The report called for a comprehensive 

hatchery reform effort to conserve indigenous genetic resources; assist with the recovery of naturally 

spawning populations; provide for sustainable fisheries; conduct scientific research; and improve the 

quality and cost-effectiveness of hatchery programs. The effort was to be led by an independent panel 

of scientists called the Hatchery Scientific Review Group (HSRG). 

Congress adopted and funded these recommendations in fiscal year 2000, launching the Puget Sound 

and Coastal Washington Hatchery Reform Project, also known simply as the “Hatchery Reform 

Project.” This project has taken a systematic, science-driven approach to evaluating hatcheries and 

providing recommendations for how hatcheries can be used to help: 

1. conserve naturally spawning salmon and steelhead populations; and 

2. support sustainable fisheries. 

The appropriations language provided funding to: 

• Establish an independent scientific panel to ensure a scientific foundation for hatchery 

reform; 

• Provide a competitive grant program for needed research on hatchery impacts; 

• Support state and tribal efforts to implement new hatchery reforms; and 

• Provide for the facilitation of a reform strategy by an independent third party. 

The role of independent science in the Hatchery Reform Project is to advise fishery managers, agency 

scientists, legislators, and the public about the benefits and risks of alternative actions that could be 

undertaken to meet goals for salmonid resources, including the consequences of inaction. This report 

results from the HSRG’s four-year evaluation of the Puget Sound and coastal Washington hatchery 

system, from 2000-03 and documents their products, processes, recommendations and conclusions. 
4 Introduction - The Need for Reform 

 

THE NEED FOR REFORM 

There are approximately 100 hatchery facilities in Puget Sound and coastal Washington operated by 

the Washington State Department of Fish and Wildlife (WDFW), Puget Sound and coastal Indian 

tribes and nations, and the US Fish and Wildlife Service (USFWS). Some of these hatcheries have 

been operating for nearly 100 years. Most hatcheries were built to produce fish for harvest, 

compensating for declines in naturally spawning salmon populations. Funding for these hatchery 

programs comes from a variety of sources, including federal, state, tribal, local and private sources. 

Hatcheries now provide over 80% of Washington’s resident trout, over 90% of the inland catch of 

resident salmonids, 70% of the salmon harvested in Puget Sound, approximately 75% of all coho and 

Chinook harvested, and 96% of all steelhead harvested state-wide. In 1995, 157 million salmon and 

8.9 million steelhead were released into Washington’s waters. In the Hood Canal and Puget Sound 

areas, more than 88 million Chinook, chum, coho, sockeye and pink salmon and steelhead trout were 

released. Washington gets an annual direct benefit of over $850 million from recreational fishing 

(which ranks eighth nationally).1

Hatcheries also play an important role in meeting tribal treaty harvest obligations. Federal court 

rulings have affirmed tribal treaty harvest rights and established the tribes as co-managers of the 

salmon resource. State and federal governments must ensure that there are salmon available for the 

tribes to harvest. As naturally-spawning salmon stocks declined over the years, the tribal, state and 

federal governments became dependent on hatcheries to provide a meaningful level of harvest for 

Indian and non-Indian fishers. 

Although hatcheries have generally been successful at providing fish for harvest, societal goals, 

priorities and circumstances have changed during the 100 years in which hatcheries have been in 

operation, particularly in the past 30 years. For example:

1

Washington State Hatcheries (brochure); Washington Department of Fish and Wildlife September 1997 Final Environmental Impact 

Statement for the Wild Salmonid Policy; John Kerwin; Washington Department of Fish and Wildlife, 600 Capitol Way North, Olympia, WA 

98501. 

1. Artificial production programs must be consistent with the sometimes conflicting objectives of 

various legal mandates relating to fish production and protection throughout Puget Sound and 

coastal Washington. Resolving these potential conflicts requires legal, policy, and biological 

judgment. These legal mandates include: 

• Treaty fishing rights of Indian tribes under US v. Washington and Hoh v. Baldridge 

and the development of a co-management relationship between the state and the 

tribes; 

• The US/Canada Salmon Treaty; 

• The responsibility of the State of Washington to preserve, protect and enhance fish 

populations; 
Introduction - Project Overview 5 

• The U.S. Endangered Species Act (ESA); Numerous mitigation obligations in law and 

agreement. 

2. As better and more complete scientific information has become available, a more complex 

picture has emerged about the interdependency of natural ecosystems and their respective 

components. Hatchery production and facilities, including the harvest of hatchery-propagated 

fish, have been identified as one of the factors contributing to the overall decline of naturallyspawning populations. 

3. Population growth and resulting human land use activities have resulted in a continued loss of 

habitat and a decline of naturally spawning salmon. This has led to different management 

goals and objectives, including conservation goals. 

4. Three Puget Sound stocks are currently listed under the ESA. As part of a larger recovery 

process, state, tribal and federal managers of Washington’s salmon and steelhead must ensure 

that their hatcheries do not present a risk to listed species. 

5. A major change is currently taking place in the economics of fisheries. Aquaculture, including 

salmon farming, is growing rapidly and competing with commercial fishing in many markets. 

Within this context, the Hatchery Reform Project was developed as a cooperative effort to reform a 

decades-old hatchery system, to meet new purposes. The intent was to let science direct the process of 

ensuring today’s hatchery system matches current circumstances and goals. 

PROJECT OVERVIEW 

The elements of the Hatchery Reform Project include a unique combination of independent science, 

coordination by managers, political support, and third-party facilitation. These components are 

described below. 

Independent Science: The Hatchery Scientific Review 

Group

The Hatchery Scientific Review Group is the scientific panel established and funded by Congress 

to independently review hatchery programs in Puget Sound and coastal Washington. The objective 

of the HSRG is to assemble, organize and apply the best available scientific information available 

to provide guidance and recommendations to the policy makers and technical staff who are 

responsible for implementing hatchery reforms. 

The HSRG is composed of five independent scientists (selected from a pool of candidates 

nominated by the American Fisheries Society) and four agency scientists designated by WDFW, 

the Northwest Indian Fisheries Commission (NWIFC), National Oceanic and Atmospheric 

Administration Fisheries/National Marine Fisheries Service (NOAA Fisheries) and USFWS. Like 
6 Introduction - Project Overview 

the independent scientists, the agency scientists are responsible for evaluating scientific merits and 

are not to represent agency policies. The nine scientists serving on the HSRG have a broad range 

of experience and expertise, including salmon biology, genetics, ecology, fisheries, fish culture, 

fish pathology and biometrics. Members have included: 

• John Barr, NWIFC (Vice Chair) 

• Lee Blankenship, Northwest Marine Technology (Vice Chair) 

• Donald Campton, PhD, USFWS 

• Trevor Evelyn, PhD, retired, Department of Fisheries and Oceans Canada 

• Tom Flagg, NOAA Fisheries Manchester 

• Conrad Mahnken, PhD, retired, NOAA Fisheries Manchester 

• Lars Mobrand, PhD, Mobrand Biometrics (Chair) 

• Robert Piper, retired, USFWS 

• Lisa Seeb, PhD, Alaska Department of Fish and Game 

• Paul Seidel, WDFW 

• William Smoker, PhD, University of Alaska 

Policy-Level Involvement: The Hatchery Reform 

Coordinating Committee

The managers have established a Hatchery Reform Coordinating Committee (Coordinating 

Committee) as a vehicle for cooperative management and implementation of this reform effort. 

The purpose of the committee is to ensure a successful working relationship between the HSRG, 

the managers’ decision-makers and their own hatchery reform science teams, and other staff. The 

Coordinating Committee’s immediate adoption of the project’s twin goals was an important early 

sign of leadership, their commitment to the process, and the role of the HSRG. The establishment 

of the Coordinating Committee also served to recognize the co-manager relationship and the 

responsibility of the managers to develop policy and ultimately implement hatchery reform. 

Committee members include: 

• Billy Frank Jr., Chairman/Spokesman, NWIFC 

• Jim Anderson, Executive Director, NWIFC 

• David Troutt, Natural Resources Director, Nisqually Tribe 

• Terry Williams, Commissioner of Fisheries and Natural Resources, The Tulalip Tribes 

• Jeff Koenings, Director, WDFW 
Introduction - Project Overview 7 

• Larry Peck, Deputy Director, WDFW 

• Dan Diggs, Assistant Regional Fisheries Director, USFWS 

• Chuck Dunn, USFWS 

• David Stout, Manager for Fisheries and Watershed Assessment, USFWS Division 

• Bob Lohn, Regional Administrator, NOAA Fisheries 

• Rob Jones, Hatchery and Inland Programs Branch Chief, NOAA Fisheries 

• Pete Bergman, former member of the Congressional Hatchery Science Advisory Team 

• Frank Haw, former member of the Congressional Hatchery Science Advisory Team 

• Terry Wright, NWIFC and former member of the Congressional Hatchery Science 

Advisory Team 

• Barbara Cairns, Executive Director, Long Live the Kings 

Support from Elected and Appointed Officials 

Many factors have come together to create this opportunity to reform hatchery practices and 

improve the contribution from hatcheries to salmon conservation and sustainable fisheries. As 

mentioned above, an important factor has been the support of strong and creative leaders at the 

fisheries management agencies. Just as important has been the backing of federal, state, tribal and 

local elected officials. The project has received bipartisan support from many regional leaders, 

including: 

• US Representative Norm Dicks (D-WA) 

• Washington Governor Gary Locke (D) 

• US Senator Patty Murray (D-WA) 

• Former US Senator Slade Gorton (R-WA) 

• US Representative Jennifer Dunn (R-WA) 

• Billy Frank, Jr., Chair, NWIFC 

• Jeff Koenings, Director, WDFW 

• William Ruckelshaus, Chair, Washington State Salmon Recovery Funding Board 

Agency Science Teams

A portion of the Congressional funding dedicated to supporting state and tribal efforts to 

implement new hatchery reforms has been used to establish agency science teams. These teams 

have undertaken a variety of activities that support the hatchery reform process. One of these has 
8 Introduction - Report Overview 

been helping the facilitation team (see below) acquire, assemble and make available to the HSRG 

regional briefing information about the hatcheries, individual hatchery programs and the 

ecosystems in which they operate. This ensured that the HSRG made its evaluations and 

recommendations based on the same data the co-managers use to establish their goals and operate 

programs. 

Other valuable functions being provided by the agency science teams include conducting risk 

analyses on hatchery programs to meet hatchery ESA requirements; conducting and overseeing 

agency research on hatchery effects and practices that complements the HSRG’s research grant 

program (see below); coordinating the implementation of early reforms; reporting agency 

activities for Congressional reports; acting as points of contacts for the project within the agencies; 

interpreting technical literature for hatchery managers; and otherwise providing technical support 

to the HSRG, the Coordinating Committee, and the regional staff that are participating in the 

review process. 

Project Management, Facilitation and Communications

The third party facilitator for the project, specified by Congress, is Long Live the Kings (LLTK), a 

private, non-profit organization whose mission is to restore wild salmon to the waters of the 

Pacific Northwest. LLTK’s role includes providing facilitation and project management to the 

HSRG and the Coordinating Committee; and helping the managers communicate hatchery reform 

progress to Congress, state legislators, stakeholder groups and the public. LLTK retained Gordon, 

Thomas, Honeywell to serve with LLTK staff on the facilitation team. The HSRG and LLTK are 

responsible for annual reporting to Congress on progress made in implementing hatchery reforms. 

The Regional Hatchery Review chapter describes the role of the facilitation team’s project 

management, facilitation and communications efforts in more detail. 

REPORT OVERVIEW 

This report provides a detailed description of the HSRG’s scientific framework, tools and resources 

developed for evaluating hatchery programs, the processes used to apply these tools, and the resulting, 

principles, system-wide recommendations, and program-specific recommendation for reform. It also 

includes conclusions about the future of hatcheries and a summary of successful hatchery programs. 

Foundation for Hatchery Reform

At the beginning of the project, the HSRG recognized that their review process would set a new 

standard for considering under what circumstances hatcheries can help achieve salmon and 

steelhead resource goals. Under this new model, productive, available habitat is essential to an 

effective hatchery program. In addition, managers have to consider whether a hatchery program is 

the best means to help achieve the stated resource goal, once the risks and benefits from the 

program are considered. To accomplish this level of evaluation, the HSRG recognized the need for 
Introduction - Report Overview 9 

 

a scientific foundation for its work and tools and resources to conduct an evaluation of the Puget 

Sound and coastal hatchery system. 

Scientific Framework 

That scientific foundation was developed in the project’s first year from a collation and review 

of the scientific literature, and by reviewing current analytical tools and operational protocols, 

and decision making processes used by the state, tribal and federal fisheries managers and 

scientists. The resulting Scientific Framework for the Artificial Propagation of Salmon and 

Steelhead 2

 underlies and informs all of the HSRG’s tools, processes and recommendations. 

The scientific framework organizes the current state of knowledge, about how actions 

associated with hatcheries affect the environment and fishery resources, around six key topics: 

1. Hatchery Programs: Definitions of Purpose and Type 

2. Hatcheries in the Ecosystem Context: The Regional Approach; 

3. Hatcheries in the Populations/Species Context; 

4. Effects of Hatchery Operations on Harvest and Conservation of the Target Stock; and 

5. Effects of Hatchery Fish on Harvest and Conservation of Other Stocks and Species. 

6. Monitoring and Evaluation: Managing Hatchery Programs for Accountability and 

Success 

Emerging Issues in Hatchery Reform 

These papers are authored by individual HSRG members, task teams or the HSRG as a whole. 

They are as simple as a few paragraphs or as detailed as an article for a peer-reviewed journal. 

They represent some of the emerging topics concerning the role and operations of hatcheries 

in conserving natural populations and supporting fisheries and are intended to serve as an 

extension of the scientific framework and encourage new thinking and actions in applied 

science for hatchery management.3

 

Research Grant Program 

The HSRG’s competitive grant program has funded over two million dollars in projects. These 

projects are helping to answer questions such as how to reduce the impact of harvest on 

naturally-spawning fish, avoid adverse genetic effects of hatchery fish on naturally-spawning 

stocks, avoid adverse ecological interactions, improve hatchery practices, and monitor and 

measure success. The need for answers to these questions became apparent in the first year of 

the project as the HSRG drafted a scientific framework to guide the region-by-region review 

2

 See summary in the Foundation of Hatchery Reform chapter and the full framework in Appendix A. 

3

 See summary in Foundation of Hatchery Reform chapter and Appendix B. 
10 Introduction - Report Overview 

process (discussed below). Grantees have reported their findings to the HSRG and other 

scientists at annual research review meetings, and the results have often answered questions 

and further identified or validated a wide range of research needs for hatcheries. This section 

of the report provides a description of the research program and a table summarizing each 

funded research project.4

Applied Hatchery Reform

From 2001–03, the HSRG used the tools described previously to systematically review all 

hatchery programs in Puget Sound and the Washington coast. As a result of this experience, the 

HSRG produced 3 principles, 18 system-wide recommendations, and over 1000 program-specific 

recommendations. Success of the hatchery reform effort, will ultimately be measured by effective 

and on-going implementation of these principles and recommendations by the state, tribal and 

federal managers in there effort to reform hatcheries toward the twin goals. 

Regional Review Process 

Early in the process, the HSRG and Coordinating Committee agreed that hatchery programs 

must be evaluated in the context of (a) the watersheds in which they operate and (b) the goals 

set for them by the managers for each stock in the watershed. To accomplish this level of 

evaluation, the scientists and managers worked together to divide Puget Sound and the coast 

into ten regions. This approach provided an opportunity to make region-by-region 

recommendations based on: 1) regional management goals for conservation, harvest and other 

purposes; 2) the status of each stock within a region (biological significance and population 

viability); 3) the status of the habitat that supports each stock (current and future); and 4) the 

operational details of each hatchery program. 

The HSRG used the scientific framework to develop a series of tools for use in the regional 

review process and for the managers to use into the future. These included operational 

guidelines, a benefit/risk tool, and monitoring and evaluation criteria. 

For each regional review, the HSRG toured the hatchery facilities, conducted interviews with 

operators and managers, considered stock and habitat information provided by the managers, 

applied this information to the benefit/risk tool, met with the managers to discuss the findings, 

and then produced specific recommendations for reducing the risks and maximizing benefits 

from each program. This chapter summarizes the review process and the role of the facilitation 

team. 

 

4

 See Appendix H for details of each grant by year. 
Introduction - Report Overview 11 

Principles and System-Wide Recommendations

In order to provide a complete picture of what was needed to achieve hatchery reform, the 

HSRG concluded that both program-specific recommendations within the context of the goals 

set by the managers and system-wide recommendations for hatcheries generally that allowed 

for regional differences were needed. The 18 system-wide recommendations were developed 

as a direct result of the HSRG’s experience in the applying the tools in a regional context. The 

HSRG has organized these system-wide recommendations under three basic principles of 

good natural resource management. These principles in the context of hatcheries are: welldefined goals, scientifically defensible programs, and informed decision making. 

In order to achieve reform, whereby the hatchery system is a functioning part of an integrated 

strategy to achieve recovery of naturally spawning populations and provide sustainable 

fisheries, the HSRG has concluded that these principles and system-wide recommendations 

must set the standard for successful implementation of hatchery reform. This chapter outlines 

each principle and system-wide recommendation. 

Program-Specific Recommendations by Region 

In each of the regions reviewed, the HSRG found significant differences in the quality of the 

habitat, stock status, the goals the managers have prescribed for each region’s salmon and 

steelhead stocks, and the purposes of each region’s hatchery programs. The HSRG’s regional 

review process produced roughly 1,000 program-specific recommendations addressing these 

specific circumstances. Recommendations ranged from changes in broodstock management, 

to addressing water quality concerns, to removal of fish passage impediments, and many 

others. Some program-specific recommendations referenced system-wide recommendations; 

others were unique to the program. 

After each year of reviews, a report was published containing recommendations for each 

hatchery program reviewed that year. The results of this three year regional review process are 

summarized in Chapter 3. The program-specific recommendations for each region are 

available as appendices to this document in three companion volumes.5

 

Conclusions

Because of its Congressional mandate, the Hatchery Scientific Review Group (HSRG) has had a 

unique opportunity over the last four years to intensively study all aspects of salmon and steelhead 

hatchery management in Puget Sound and coastal Washington. As a result, the HSRG has 

formulated a number of conclusions about hatcheries and how they should be operated. This 

chapter outlines these conclusions and gives examples of successful hatchery programs. 

 

5

 See Appendix I, Program-Specific Recommendations by Region. 
12 Introduction – Next Steps 

NEXT STEPS 

Through four years of creating a scientific framework, tools and recommendations under the Hatchery 

Reform Project, the HSRG has outlined new ways to apply science to hatchery management. 

Recognizing this, the managers of Washington’s fish resources have asked the HSRG to stay 

empanelled beyond the recommendations phase, as the manager’s design mechanisms for 

implementation, monitoring and evaluation, and feedback loops that ensure that new information leads 

to continuing improvements in decision making, policy and operations. 

The HSRG and the managers have agreed that achieving the implementation of hatchery reform must 

be viewed in the long-term. This approach is necessary because hatchery reform should be an ongoing process that continues to change as new information is gained. Additionally, it will take time to 

secure funding to implement all of the elements of hatchery reform. There is also agreement that 

implementation of many important elements of hatchery reform can take place in the short-term as 

well. The manager’s efforts to develop an implementation database to track longer term trends and 

results is critical to successful hatchery reform. 

For 2004, the HSRG, the managers, and the facilitation team have developed a work plan to: 

• ensure an exchange of knowledge, information and ideas between the HSRG and state, 

tribal, and federal managers in the hatchery, harvest and science divisions; 

• track and communicate implementation progress and significant scientific findings from 

the project. 

• develop a long-term monitoring and evaluation strategy; 

• provide facilitated co-manager discussions that address unresolved regional 

implementation issues; 

• hold follow-up workshops in all 10 regions with case studies for how the regional 

hatchery managers can use the principles, recommendations and tools to continue 

reviewing hatchery programs in the context of regional goals into the future; and 

• encourage further research that addresses significant uncertainties about the uses of 

hatcheries. 

The result of this work plan are intended not only ensure successful implementation of the HSRG’s 

recommendations for Puget Sound and the coast, but should also provide a working model that can be 

replicated elsewhere in the Pacific Northwest. 

Additionally, the Washington state Governor’s Office, the Shared Strategy for Salmon Recovery in 

Puget Sound, and others are relying on the Hatchery Reform Project’s results for direction on how 

hatchery reform can be integrated with habitat recovery at the watershed level. This watershed 

approach is an essential piece of the recovery plans that those parties have pledged to provide NOAA 

Fisheries for Puget Sound Chinook salmon, listed as threatened under the ESA in 1999. 
Introduction - Next Steps 13 

 

It is important to note that the tools and recommendations contained in this document are based upon 

current goals and the best scientific information available at the time the reviews were conducted. In 

keeping with the tenets of adaptive management,6

 it will be necessary to review and adapt these tools 

and recommendations as new scientific information arises and/or goals change. 

This and all other Hatchery Reform Project-related publications are available from the project’s web 

site (www.hatcheryreform.org) or by contacting Long Live the Kings at (206) 382-9555. 

6

 

See HSRG System-Wide Recommendation on adaptive management.

Foundation for Hatchery Reform – Scientific Framework 15 

Foundation for Hatchery Reform 

Early in the project’s first year (2000), the Hatchery Scientific Review Group (HSRG) agreed that 

hatchery programs should no longer be seen as surrogates for lost habitat. Instead, hatchery programs 

must be viewed as tools that can be managed as part of an integrated strategy to meet watershed or 

regional resource goals, in concert with actions affecting habitat, harvest rates, water allocation and 

other factors. Using the best available science, and having considered the benefits and risks to all 

stocks that will result, a hatchery program should be conducted only if it is deemed the best available 

tool for achieving those goals. 

To scientifically evaluate the hatcheries in Puget Sound and the coast in this new context, the scientists 

recognized the need for a scientific foundation for their work, a method for updating this foundation, 

and tools and resources for conducting and evaluation of the Puget Sound and coastal hatchery system. 

This chapter summarizes the Scientific Framework for the Artificial Propagation of Salmon and 

Steelhead, the emerging issues papers, and the HSRG’s research program. The complete framework, 

all the emerging issues papers, details of funded grants, and the tools used in the regional review 

process are found in the appendices. 

SCIENTIFIC FRAMEWORK 

The scientific framework was first published in December 2000, after review by over 200 scientists 

and stakeholders, and before the rest of the review tools were developed and the regional review 

process began. The framework was periodically updated throughout the review process to include new 

information as it became available. Over the last year, this framework was reorganized in order to 

better serve as a blueprint for achieving scientifically defensible hatchery programs (Principle 2).7

 

The scientific framework forms the basis for all of the HSRG’s tools, processes and recommendations 

and organizes the current state of knowledge, about how actions associated with hatcheries affect the 

environment and fishery resources, around six key topics: 

1. Hatchery Programs: Definitions of Purpose and Type; 

2. Hatcheries in the Ecosystem Context: The Regional Approach; 

3. Hatcheries in the Populations/Species Context; 

4. Effects of Hatchery Operations on Harvest and Conservation of the Target Stock; 

5. Effects of Hatchery Fish on Harvest and Conservation of Other Stocks and Species; and 

6. Monitoring and Evaluation: Managing Hatchery Programs for Accountability and 

Success. 

 

7

 See Applied Hatchery Reform chapter, Principles and System-wide Recommendations section. 
16 Foundation for Hatchery Reform – Scientific Framework 

1. Purpose and Type

The HSRG has concluded that each hatchery program must explicitly define its strategies in terms 

of: a) the purpose or desired benefits to be derived from the program; and b) the type of program 

desired, relative to the genetic management goals for the broodstock and naturally spawning 

populations. These purposes and types provide the starting point for evaluating the benefits and 

risks of a specific hatchery program. Each hatchery program must first define its goals in terms of 

purpose and type before subsequent program components can be developed or evaluated. 

The HSRG recognizes two primary purposes or potential benefits of hatchery programs: 1) help 

conserve naturally spawning populations, and 2) provide fish for harvest. Many hatchery programs 

are designed to provide both harvest and conservation benefits. Other purposes of hatchery 

programs include scientific research, education, and providing cultural benefits, particularly for 

American Indian tribes. 

Hatchery programs for Pacific salmon and steelhead can be classified as either “integrated” or 

“segregated” based on the genetic management goals and protocols for propagating a hatchery 

broodstock. Hatchery programs are classified as genetically integrated if a principal goal is to 

minimize potential genetic divergence between the hatchery broodstock and a naturally-spawning 

population such that natural-origin fish are systematically included in the broodstock each year or 

generation. Hatchery programs are classified as genetically segregated if the broodstock is 

propagated as a reproductively distinct population primarily, if not exclusively, from adult returns 

back to the hatchery. In segregated programs, little or no gene flow should occur from a naturally 

spawning population to the hatchery broodstock. 

In the context of managing salmon and steelhead hatcheries, all programs need to identify their 

broodstocks goal as either genetically integrated or segregated relative to naturally spawning 

populations. The choice of broodstock goal defines operational guidelines by which each hatchery 

programs can be evaluated. Successful hatchery programs must conform closely to the guidelines 

specified by a properly integrated or properly segregated program; no individual hatchery program 

can be both or intermediate without imposing significant genetic risks to naturally spawning 

populations. 

2. Hatchery Programs in the Ecosystem Context: The 

Regional Approach

Hatcheries can no longer be regarded as surrogates for lost habitat. In operating hatcheries, 

consideration must be given not only to the receiving habitat in which they operate but also to the 

naturally-spawning and hatchery-propagated fish that depend on the existing habitat. In addition, 

hatcheries must take into account the programs of other hatcheries occurring in the same 

watershed or region. Only in this way will adverse interactions between salmonid stocks in the 

watershed or region be minimized. 

This chapter outlines how to review hatchery programs in Puget Sound and coastal Washington 

using a regional approach, taking into account the nature of the watersheds in which the programs 
Foundation for Hatchery Reform – Scientific Framework 17 

occur and the goals for naturally spawning populations and the individual programs set by the 

regional managers. Each watershed or region differs significantly in the quality and quantity of 

habitat, the status of its salmonid stocks, the goals set for each stock by the managers, and the 

purposes of the region’s hatchery programs. 

3. Hatchery Programs in the Species/Population 

Context

Hatchery populations of salmonids are subject to many of the same biological processes as their 

naturally-spawning counterparts. This chapter outlines how these biological processes shape the 

biological significance and viability of both hatchery and naturally-spawning populations. 

Assessment of the biological significance and viability of salmonid populations provides an 

important benchmark for developing both long- and short-term goals and management strategies 

for a particular population or stock. In the case of integrated hatchery programs, where the 

management strategy is to maintain hatchery broodstocks as similar as possible genetically to 

naturally-spawning populations, the combined population (hatchery + wild) shares similar 

characteristics for biological significance and viability. In the case of segregated hatchery 

programs, the biological significance is based solely on the composition of the hatchery 

population, and the viability is linked to the performance of a “hatchery stock” in both the 

hatchery and natural environments. 

4. Effects of Hatchery Operations on Harvest and 

Conservation of the Propagated Stock

Hatchery operations including broodstock choice and collection, spawning, incubation and rearing 

protocols as well as the hatchery environment in which fish are reared can affect the short and 

long-term survival and behavior of the stock that is the target of hatchery propagation. These 

operations can affect the achievement of harvest goals as well as the goals for biological 

significance and viability of the target stock. This is true whether the target stock represents only 

the hatchery stock as in segregated programs or represents a component of the natural stock, as in 

integrated programs. This chapter describes how hatchery operations can have both long-term 

genetic effects and short-term, non-genetic effects on the target population. 

5. Effects of Hatchery Fish on Harvest and 

Conservation of Other Stocks and Species

Depending on the number, size, location and other release factors, hatchery fish may directly or 

indirectly affect other stocks and species through genetic or ecological interactions. The presence 

of hatchery fish may also alter fishing patterns and thereby affect harvest rates on naturally 

produced stocks. This chapter describes these potential effects and identifies management actions 

that can help alleviate adverse impacts. 
18 Foundation for Hatchery Reform – Scientific Framework 

6. Monitoring and Evaluation: Managing Hatchery 

Programs for Accountability and Success

Today’s salmon and steelhead hatcheries are called upon to help meet conservation, harvest, 

and/or other goals (e.g., education, research, cultural and ceremonial needs, and indicator stocks), 

while minimizing adverse impacts on natural-origin salmonids within the watersheds or regions in 

which they operate. To be successful at meeting these goals, accountability for decisions and 

actions is required at all levels within the agencies responsible for management and operation of 

hatcheries. Success will also require an accurate and timely management information system that 

can measure benefits, evaluate actions, and provide information for hatchery management and 

operations. This chapter outlines a monitoring and evaluation approach to help ensure 

accountability and success of hatchery programs. 
Foundation for Hatchery Reform – Emerging Issues in Hatchery Reform 19 

 

EMERGING ISSUES IN HATCHERY REFORM 

The HSRG—recognizing that the scientific framework needs to be a “living document” that is 

regularly updated to include new information and issues not identified in its original drafting—decided 

that significant revisions to the scientific framework should be derived – not just from new published 

scientific literature – but also from “emerging issue” papers authored by the HSRG or its individuals 

members. These papers can be as simple as a few paragraphs or as detailed as an essay for a peerreviewed journal. They are presented collectively in Appendix B under the title Emerging Issues in 

Hatchery Reform. The HSRG welcomes feedback on these “emerging issues.” They are incorporated 

into the framework once they have been reviewed and refined. Several that have been incorporated to 

date remain in this chapter as well, to highlight their importance. 

These emerging issues papers also relate to two other key elements of the Hatchery Reform Project. 

They are tied to the hatchery reform research program8

 because they discuss topics that reflect recently 

available scientific information or an emerging principle derived from the collation of old and new 

information. In addition, they are tied to the three principles of hatchery reform9

 because developing 

scientific knowledge in these areas will support hatchery operation and management in the context of 

well-defined goals, scientifically defensible programs, and informed decision making. 

In keeping with their status as “emerging issues,” it is important to keep in mind that all of these 

papers are “works in progress,” to be revised as new information comes to light on the issues at hand. 

They are not to be considered definitive, exhaustive and/or final statements on their respective topics, 

although some of them may form the basis for publications in the scientific literature if they so 

warrant. 

The current list of emerging issues papers includes: 

MANAGEMENT GOALS FOR HATCHERY BROODSTOCKS: GENETIC INTEGRATION VERSUS 

SEGREGATION ........................................................................................................................................B-3

USING HATCHERY SALMON CARCASSES FOR NUTRIFICATION OF FRESHWATER ECOSYSTEMS WHILE 

REDUCING ASSOCIATED FISH HEALTH RISKS. ...................................................................................B-28

HATCHERY SMOLT QUALITY AND ACHIEVING THE WILD SALMON TEMPLATE ..............................B-30

BENEFITS OF HATCHERY FISH AS A SOURCE OF FOOD.......................................................................B-39

MARINE CARRYING CAPACITY ...........................................................................................................B-41

OUTPLANTING AND NET PEN RELEASE OF HATCHERY-ORIGIN FISH................................................B-44

ASSESSING THE POTENTIAL FOR PREDATION ON WILD SALMONID FRY BY HATCHERY-REARED 

SALMONIDS IN WASHINGTON..............................................................................................................B-51

USING ACCLIMATION PONDS IN THE REARING OF SALMON..............................................................B-68

8

 See Research Program in Applied Hatchery Reform chapter. 

9

 See Principles and System-Wide Recommendations in Applied Hatchery Reform chapter. 
20 Foundation for Hatchery Reform – Research Grants Program 

RESEARCH GRANTS PROGRAM 

The ability to fully achieve hatchery reform goals is compromised by lack of scientific certainty on 

many subjects. To reduce this uncertainty, the HSRG developed a competitive grant program to fund 

scientific research projects that could provide new scientific information in support of the goals of 

hatchery reform in Puget Sound and coastal Washington. This chapter provides a description of the 

research grant program. A summary of each research project funded by the HSRG can be found in 

Appendix H. 

The HSRG established the following procedures for administering this grant program: 

1. The Washington State Interagency Commission for Outdoor Recreation (IAC) shall be the 

administrative agency for the grant program. 

2. The steps involved in the grant program each fiscal year could include: 

a. The HSRG will issue a Request for Pre-Proposals. 

b. Pre-Proposals received will be reviewed and evaluated by the HSRG. Applicants with preproposals selected for further consideration will be asked to prepare full proposals. 

c. Full proposals will be reviewed and evaluated by the HSRG. External ad hoc reviewers 

with scientific expertise complementary to the HSRG may be solicited to assist the HSRG 

with their reviews of specific proposals. 

d. The HSRG will inform applicants whether their proposal was accepted. 

e. Funds will be disbursed by IAC to accepted research proposals. 

f. Progress reports and final reports will be provided to the HSRG by funded researchers. 

3. The HSRG will use its Scientific Framework for Artificial Propagation of Salmon and 

Steelhead (Scientific Framework) to identify research needs. Innovative research in other 

areas of Hatchery Reform will also be considered. 

4. Proposals will be judged—using a standardized evaluation system— based on scientific merit, 

the qualifications of the investigators, ability to provide quantifiable results and the potential 

to achieve results applicable to hatchery reform goals. Preference will also be given to projects 

that show collaboration among researchers and agencies. 

5. To avoid conflicts of interest, agency members of the HSRG will participate in discussion of 

proposals sponsored by their respective agencies but will excuse themselves from final voting 

to avoid potential conflicts of interest. 

6. Written progress and annual/final reports are required of all funded projects. In addition, an 

oral presentation describing the project and its progress is required each year. The 

presentations are given each year (January/February) and open to the public. 
Foundation for Hatchery Reform – Research Grants Program 21 

7. Multiple-year projects are encouraged, but funds will only be awarded on a year-to-year basis. 

Successful grants from the previous year must submit pre-proposals to be considered for a 

second year of funding. 

8. Although the HSRG respects and understands the need for protecting the intellectual property 

contained in research proposals, Washington state law requires that materials submitted in 

response to this grant announcement shall become the property of the IAC and shall be 

deemed public records. 

9. Applications approved for funding will be required to sign a Project Agreement that 

incorporates the full proposal, negotiated parameters and any required federal terms and 

conditions as appropriate. 

The HSRG has awarded over two million dollars in research funds to help answer questions such as 

how to reduce harvest on natural-origin fish, how to avoid adverse genetic effects of hatchery fish on 

natural-origin stocks, how to avoid adverse ecological interactions, how to improve hatchery practices, 

and how to monitor and measure success. Grantees have reported back to the HSRG at annual research 

review meetings and they are making good progress. But there are many questions left to answer and a 

number of projects that will take several years to provide useful findings. 

During HSRG meetings in the early part of each year, research proposals have been evaluated by the 

group, with projects receiving funding being divided into four general categories for prioritized 

research: A) Sustainable Fisheries; B) Recovery and Conservation of Naturally Spawning Populations; 

C) Improvement in Quality and Cost-effectiveness of Hatchery Programs; and D) Protection of 

Genetic Resources. A list of funded projects is included as Table 1 with details provided in Appendix 

H. 

TABLE 1: Summary of Research Grants 

Year 

Funded Project Description10 Principal Investigators11

Category A: Sustainable Fisheries 

2000, 

2001 

1. Development of Field Methods to 

Determine the Effects of Hatchery 

Release Methods on Residualism and 

Interactions Between Hatchery and Wild 

Juvenile Salmonids in Relation to Stream 

Carrying Capacity 

Howard Fuss, WDFW; Stephen Riley, 

NOAA Fisheries 

 

10 Multiple year projects list the most recent title. 

11 Multiple year projects list the most recent Principle Investigator(s). 
22 Foundation for Hatchery Reform – Research Grants Program 

2000, 

2001 

2. Test Commercial Selective Harvest 

Gears Geraldine VanderHaegen, WDFW 

2000 

3. Impacts of Size Selective Gillnet 

Fisheries on Puget Sound Coho Salmon 

Populations 

Curtis Knudsen, 

Craig Busack, WDFW 

2001, 

2002, 

2003 

4. Salmon Marine Trophic DemandDistribution David Beauchamp, UW 

Category B: Recover and Conserve Natural Spawning Populations 

2000 1. Genetic Characterization of Lake 

Ozette Sockeye Salmon 

Ken Currens, NWIFC; Jim Shaklee, WDFW; 

Michael Crewson, Makah Tribe 

2000 2. White River Acclimation Pond 

Evaluation 

Chuck Baranski,WDFW; Blake Smith, 

Puyallup Tribe; Richard Johnson, 

Muckleshoot Tribe 

2000, 

2001, 

2002, 

2003 

3. Differences in Natural Production 

between Hatchery and Wild Coho 

Salmon 

Howard Fuss, WDFW; Michael Ford, NMFS

2000, 

2001, 

2002, 

2003 

4. Snow Creek Coho Recovery Program Steve Schroder, WDFW 

2000, 

2001, 

2002, 

2003 

5. Hamma Hamma River Steelhead 

Supplementation Evaluation Barry Berejikian, NOAA Fisheries 

Category C: Improve Quality and Cost-Effectiveness of Hatchery Programs 

2000, 

2001, 

2002, 

2003 

1. Development of Engineered Streams 

for Salmon Production Ernest Brannon, UI 

2000, 

2001, 

2002, 

2003 

2. Increase Post-Release Survival by 

Rearing Coho with NATURES SemiNatural Raceway Habitat 

Desmond Maynard, NOAA Fisheries 

2000 

3. Using Semi-Natural Rearing Habitat to 

Improve Smolt-Adult Survival of Chinook 

Salmon 

Geraldine VanderHaegen, WDFW; Bill St. 

Jean, Nisqually Tribe 
Foundation for Hatchery Reform – Research Grants Program 23 

2001 4. Development of BKD Vaccine Jed Varney, WDFW 

2001 5. Nature vs. Nurture: Do Hatchery 

Practices Impair Brain Development? Penny Swanson, NOAA Fisheries 

Category D: Protect Genetic Resources 

2000, 

2001 

1. Interactions between Wild and 

Hatchery Steelhead: Evaluating Key 

Assumptions 

Thomas Quinn, UW 

2001 2. Residualism in Wild Broodstock 

Steelhead Cameron Sharpe, WDFW 

2001 3. Olfactory Imprinting in Hatchery 

Salmon Andrew Dittman, NOAA Fisheries 

Hatchery Research Agenda

After three years of administering this program and working to develop program-specific 

recommendations for 10 regions and over 200 hatchery programs throughout Puget Sound and the 

Washington coast, the HSRG has concluded that a research agenda must be established to guide 

funding for applied hatchery research in the Pacific Northwest. Hatchery research answering specific 

unknowns and that can be directly applied to better, more informed decision making will be essential 

to the long-term success of hatchery reform. 

Hatchery programs must be operated to adapt to changes in the status of naturally spawning stocks, 

carrying capacity of the receiving waters, ocean productivity and harvest demands. Hatchery research 

is needed to reduce uncertainty and better evaluate the risks and benefits from hatchery practices. 

Additionally, new information is required to further understand the impacts of hatchery programs on 

natural-origin salmonids and on the environment within the watersheds or regions in which they 

operate. 

The development of this agenda will require collaboration among states, institutions and disciplines. 

The HSRG is developing a proposal for an Applied Hatchery Research Agenda that builds on the 

outcomes of the HSRG Research Grant Program, uncertainties identified in the development of the 

HSRG’s scientific framework and operational guidelines, and the findings from the three-year regional 

review process. 

Applied Hatchery Reform – Regional Review Process 25 

Applied Hatchery Reform 

The Puget Sound and Coastal Washington Hatchery Reform Project has provided an unprecedented 

opportunity to review current hatchery practices at over 100 hatcheries. At the close of 2003, the nine 

members of the Hatchery Scientific Review Group (HSRG) had spent four years together participating 

in monthly, three-day work sessions and devoting at least as much time—often more—to the project 

between meetings. They have discussed and debated the latest scientific thinking on hatcheries; 

digested 500-plus page briefing books in each of ten regions that detail stock status, habitat conditions, 

and harvest goals; spoken face-to-face with the people in charge of the day-to-day management of 

hatchery programs in these regions; weighed the benefits and risks of over 200 stock-specific 

programs; and come to consensus on 3 principles, 18 system-wide recommendations, and over 1,000 

program-specific recommendations for reform. This chapter provides an overview of the HSRG’s 

regional review process and tools; and the resulting principles and recommendations. 

REGIONAL REVIEW PROCESS 

Early in the project, the HSRG and the Hatchery Reform Coordinating Committee agreed that it is 

important to evaluate hatchery programs in the context of the watersheds in which they operate and the 

goals set for them by the managers. For this reason, they divided Puget Sound and coastal Washington 

into ten regions (see Figure 1 on next page for locations). These ten regions include: 

• Eastern Strait of Juan de Fuca 

• South Puget Sound 

• Stillaguamish/Snohomish Rivers 

• Skagit River Basin 

• Nooksack/Samish Rivers 

• Central Puget Sound 

• Hood Canal 

• Willapa Bay 

• North Coast 

• Grays Harbor 
26 Applied Hatchery Reform – Regional Review Process 

FIGURE 1: Hatchery Reform Region Map 
Applied Hatchery Reform – Regional Review Process 27 

The HSRG used the scientific framework to develop a series of tools for use in the regional review 

process and for use by the managers. These included operational guidelines, a benefit/risk tool, and 

monitoring and evaluation criteria. The complete tools and example forms are included in the 

appendices noted. 

• Operational Guidelines: The HSRG developed a set of operational procedures consistent with 

the scientific framework, to address ecological effects, genetic integrity and fish health 

concerns, and to provide new guidelines for fish rearing and accountability for success. These 

guidelines inform the questions contained within the part of the benefit/risk tool that examines 

hatchery operations (see Appendix C). 

• Monitoring and Evaluation Criteria: These criteria were developed from the scientific 

framework, operational guidelines and benefit/risk tool to help the managers determine the 

success of a hatchery program. These criteria suggest which information to collect and 

evaluate relating to the health of out-migrating smolts, stray rates of returning adults, 

whether or not hatchery rearing has affected fish size and run timing, and other factors 

(see Appendix D). 

• Benefit/Risk Tool: The HSRG developed the benefit/risk tool for evaluating the benefits and 

risks specifically derived from each hatchery program. This tool was adapted and simplified 

from a tool developed by the co-managers.12 It allowed the HSRG to evaluate the relative 

benefits and risks associated with specific actions and choices in hatchery management—in a 

scientifically sound, methodical manner. This tool was central to the regional review effort in 

that it allowed for a systematic evaluation of all aspects of hatchery and program operations in 

the context of the harvest, conservation or other goal for the resource set by the managers (see 

Appendix G).

The HSRG applied the hatchery review tools to all hatchery programs in ten regions over three full 

years between 2001 and 2003. This approach provided an opportunity to make region-by-region 

recommendations based on: 

A. regional management goals for conservation, harvest and other purposes; 

B. stock status (biological significance and population viability); 

C. habitat status (current and future); and 

D. the operational details of each hatchery program.13

For each hatchery program the HSRG addressed three questions: 

1. Are the current hatchery practices consistent with the short- and long-term goals for the 

target stock? 

 

12 Draft Benefit-Risk Assessment Procedure (BRAP) for Washington State Department of Fish and Wildlife Artificial Propagation 

Programs, November 17, 2000.

13

 See the Benefit/Risk Tool section of the Appendices for detail on how these categories of information are defined. 
28 Applied Hatchery Reform – Regional Review Process 

 

2. Is the program likely to attain those goals? 

3. Are the current hatchery practices consistent with the goals for other salmonid stocks in 

the region? 

The regional reviews normally took place over two three-day meetings, held in the region over 

consecutive months. Following an introductory meeting between the HSRG and the regional 

participants held three months prior to the review meetings, the facilitation team worked with the 

regional managers and state and tribal agency science teams to assemble a briefing book containing 

the four key categories of background information for the region, arranged by sub-region and stock 

(for example, Dungeness Chinook was a sub-regional stock examined in the Eastern Straits region). 

This briefing book was provided to the HSRG one month prior to the first meeting. 

Regional participants from the state, tribal and federal management agencies were provided a detailed 

regional information instruction form to guide them in assembling information for the briefing book. 

Other regional participants were provided a regional information key questions form. 14

For the reviews, the HSRG developed a standardized approach for expressing harvest and 

conservation goals for the stocks and the environment potentially affected by a hatchery program. 

Within each region, the current stock status, and short term and long term goals for stock conservation 

were provided by the co-managers in terms of: a) the biological significance of the stock (i.e., its 

importance to the Evolutionarily Significant Unit, or ESU, to which it belongs), b) the viability (or 

genetic fitness) of the stock. Conservation goals in these categories were rated qualitatively as high, 

medium or low. The current status and short term and long term goals for the suitability of the habitat 

available to each stock was also provided, also in qualitative terms. Similarly, harvest goals were 

expressed in terms of the frequency of harvest opportunity (annually, most years, some years, or 

never). 

Day 1: The first day of a regional review meeting (and often the evening before) consisted of field 

tours arranged by the facilitation team and regional managers, to complement the briefing book 

information and provide the HSRG with a better understanding of the region and its hatchery 

facilities. 

Day 2: On the second day, the HSRG worked with the regional participants to apply the 

Benefit/Risk Tool’s Part One worksheet Summary of Goals for Affected Stocks and Habitat; 

Objectives for Current Hatchery Programs.15 This process ensured that the scientists understood 

the management goals under which the co-managers are operating their hatchery programs, and 

the purpose and type of each program being conducted to meet those goals. 

Day 3: On the third day (the final day of the first meeting), the HSRG completed its Benefit/Risk 

Tool Part Two worksheet How Current Operations Compare to HSRG Guidelines. Categories 

include: 1) accountability and education; 2) genetics and conservation; 3) physiology, morphology 

and ecology; and 4) culture methods. Regional hatchery managers joined the HSRG during this 

14 See Appendices E and F, Regional Information Instruction Forms. 

15 See Appendix G, Benefit/Risk Tool for a description of these worksheets. 
Applied Hatchery Reform – Regional Review Process 29 

process to fill in any operations information not provided in the briefing book, tour or previous 

discussions. 

Day 4: On the fourth day (the first day of the second meeting), the HSRG reviewed the 

information provided by the managers between meetings, to fill in any remaining information 

gaps. The HSRG then began using in the Benefit/Risk Tool Part Three worksheet Benefit/Risk 

Analysis; Recommendations and Alternatives. This involved identifying the risks and benefits 

from each hatchery program to all hatchery and naturally spawning stocks in the region, then 

making preliminary recommendations for improving the region’s hatchery programs. 

Day 5: On the fifth day, the HSRG completed the Part Three worksheet. The group then decided 

how best to present the results to the regional managers at an informal review session. 

Day 6: On the sixth and final day, the HSRG provided the regional participants with an informal 

review of the region. The session involved only oral presentations. No written report was provided 

at that time. The regional managers had the opportunity to take notes, ask questions and engage in 

discussion. 

In all the regions reviewed, the regional participants chose to hold a follow-up meeting amongst 

themselves, where they discussed what they heard at the informal review session and prepared 

feedback to provide to the HSRG for their report writing process. HSRG and facilitation team 

members did not attend this meeting, in order to promote a free exchange of reactions and opinions. 

At the end of the calendar year, the HSRG drafted a written report on the regions reviewed during that 

year.

16 This report took into consideration any actions taken and information provided by the 

managers after the informal review session. The HSRG provided the draft report to the managers to 

check for factual errors or omissions, and to allow the managers to draft concise responses that 

indicate where they agree or disagree with the recommendations, and describe implementation plans. 

Project Management/Facilitation

In general, the role of the Hatchery Reform Project facilitation team has been to manage the 

project; facilitate interactions between the scientists and the managers; provide internal and 

external project communications; ensure that all parties involved in the project know their 

responsibilities, roles, tasks and deadlines; and ensure that these deadlines are met, with a quality 

product resulting. During the review process, the facilitation team coordinated the agenda, and 

produced meeting materials for each meeting (including detailed briefing books before each 

regional review session), and communicated with regional participants (inviting them to 

introductory and regional review meetings, informing them of assignments and deadlines). 

During the meeting, the facilitation team helped keep the group on time and on agenda, helped to 

resolve problems and impasses, and suggested solutions and alternatives. After each meeting, the 

facilitation team provided the group with a list of decisions/action items/assignments and 

 

16 See Appendix I, Program-Specific Recommendations by Region. 
30 Applied Hatchery Reform – Regional Review Process 

developed a meeting summary for public distribution. The team also maintains the project’s files 

and archives. 

Communications activities by the facilitation team include drafting, sending and tracking project 

correspondence; fielding inquiries from stakeholders and the public; keeping the project’s written 

materials, web site and PowerPoint presentations updated; providing articles, interviews, editorials 

and news conferences for local, regional and national media outlets; making briefings and 

presentations to a wide range of organizations and conferences; and editing and publishing project 

publications and reports. The HSRG and LLTK are also responsible for annual reporting to 

Congress on progress made in implementing hatchery reforms. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 31 

PRINCIPLES AND SYSTEM-WIDE 

RECOMMENDATIONS 

Over the period of this project, the HSRG has developed a thorough understanding about applying 

existing science to hatchery management. After three years of regional reviews, the HSRG concluded 

that while any individual program may be successful in broodstock collection, rearing or other 

operational considerations, it may still be operating in a manner that does not, for example, adequately 

take into account risks to other stocks or to the environment, maximize benefits to the target stock, or 

consider whether adequate habitat will be available over time for the fish it produces. 

In each region, the HSRG found: 

• If the goals for each stock (conservation, harvest, research, education, etc) were clearly 

understood by the hatchery operator, the ability to evaluate the benefits and risks of a hatchery 

program was greatly improved; 

• A clearly articulated, scientific rationale for a hatchery program can provide the managers 

with a science-based foundation for decision making and a range of scientific tools and 

strategies for achieving goals; and 

• Hatchery managers who were able to measure the contribution of a hatchery program toward a 

particular resource goal had a greater chance of achieving that goal. 

Based on these observations, the HSRG developed three principles, based on principles of good 

natural resource management, to guide the use of hatcheries. These principles include: 1) WellDefined Goals, 2) Scientific Defensibility, and 3) Informed Decision Making. The HSRG also 

assembled system-wide recommendations (applicable to programs across the Puget Sound and coastal 

Washington hatchery system) that serve as hatchery based strategies for achieving these principles. 

Just as the program-specific recommendations were developed for each hatchery program, systemwide recommendations were developed for hatcheries collectively. 

These principles and recommendations are presented here to help guide the managers as they 

implement hatchery reform, and to help answer how hatcheries can serve as tools for recovering 

naturally-spawning salmonid populations and providing sustainable fisheries. 

Principle 1: Well-Defined Goals 

Goals for all affected stocks must be well-defined. These goals should be quantified, where possible 

and expressed in terms of values to the community (harvest, conservation, education, research, 

employment, recreation, etc.). Hatcheries can then be managed as tools to help meet those goals. The 
32 Applied Hatchery Reform – Principles and System-Wide Recommendations 

 

HSRG’s scientific framework17 outlines the issues involved with, and conditions required for, 

hatcheries to be an appropriate contributor to meeting harvest, conservation or other goals. 

Harvest and conservation were the most common stock goals encountered by the HSRG. They can be 

defined as follows: 

• Harvest goals promote commercial, subsistence, ceremonial, and recreational fishing 

• Conservation goals promote the conservation of indigenous salmonid resources. They 

include endangered species protection and recovery, gene banking, maintaining native 

stocks for which natural spawning habitat is lost, and restoring stocks to streams where 

they have been extirpated. 

The HSRG observed that goals for the fish resource were not always explicitly communicated and/or 

fully understood by the managers and operators of hatchery programs. To be successful, hatcheries 

should be used as part of an integrated strategy where habitat, hatchery management and harvest are 

coordinated to best meet resource management goals defined for each stock in the watershed. 

Hatcheries are by their very nature a compromise, a balancing of benefits and risks to the target stock, 

other stocks and the environment affected by the hatchery program. The use of a hatchery program is 

appropriate when benefits significantly outweigh the risks, and when the use of a hatchery program is 

more favorable than the benefits and risks associated with non-hatchery strategies for meeting the 

same goals. 

The HSRG has developed the following system-wide recommendations to help ensure a 

comprehensive goal setting process. 

Set Goals for all Stocks and Manage Hatchery Programs on a 

Regional Scale 

Early in the project, the HSRG and the managers agreed that hatchery programs must be evaluated 

in the context of the regions and watersheds in which they operate and the goals set by the 

managers. In designing the review process, the HSRG determined that a review of Puget Sound 

and coastal hatcheries and their programs as a whole would have led to broad generalities not 

suited to regional differences in stock and habitat status. Similarly, a hatchery-by-hatchery review 

would not have allowed for evaluation in the context of each region’s current and future habitat, 

harvest goals, the status of all regional, anadromous salmonid stocks, and the cumulative effects of 

all regional hatchery programs. The HSRG recommends that the managers continue this regional 

approach to reviewing and setting goals, managing hatchery programs, and implementing the 

principles and recommendations. The HSRG further recommends that implementation of hatchery 

reform recommendations be coordinated by regional technical groups, to ensure that goals for the 

resource and the role of each hatchery program in achieving those goals are tracked. These 

regional bodies may currently be in existence or may be patterned after the regional participant 

lists generated for the HSRG’s regional review process. 

17 See Appendix A, Scientific Framework. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 33 

Measure Success in Terms of Contribution to Harvest, 

Conservation and Other Goals 

The HSRG recommends that the managers measure hatchery contributions to harvest opportunity, 

the conservation of genetic resources, and other goals for salmon and steelhead populations. It is 

not uncommon for the direct hatchery output (i.e., numbers or pounds of juveniles released) to be 

cited as the goal by which a program’s success is measured. More appropriate measures of success 

include: 

• The scale and availability of harvest provided. 

• The number of returning adults and their ability to reproduce and sustain the stock. 

• The relative risks and benefits of each hatchery program. 

• Alternative strategies for meeting similar goals. 

• Whether the program is part of a comprehensive strategy to meet a stated resource goal. 

Have Clear Goals for Educational Programs 

The HSRG strongly supports the many educational programs conducted at, or supported by, 

hatchery facilities across Puget Sound and coastal Washington. These programs are valuable for 

educating the public on the biology of salmon, the importance of maintaining healthy salmon 

habitat, and sustainable fisheries. 

A clear understanding of a program’s specific educational goals needs to be articulated, along with 

methods for determining if those goals are being met and for reporting educational benefits. It is 

incumbent upon the fisheries managers, as the professional partners of these often volunteerdriven programs, to ensure that such goal statements are developed for these programs and 

understood by participants. It is also essential that these programs be operated consistent with the 

conservation principles they are intended to promote. 

Principle 2: Scientifically Defensible Programs

Once the goals for the resource have been established (see above), the scientific rationale for a 

hatchery program – in terms of benefits and risks - must be spelled out to explain how the hatchery 

program expects to achieve its goals. The purpose, operation, and management of each hatchery 

program must be scientifically defensible. The strategy chosen must be consistent with current 

scientific knowledge. Where there is uncertainty, hypotheses and assumptions should be articulated. In 

general, scientific defensibility will occur at three stages: (1) during the deliberation stage to determine 

whether a hatchery should be built and/or a specific hatchery program initiated; (2) during the 

planning and design stage for a hatchery or hatchery program; and (3) during the operations stage. 

This approach ensures a scientific foundation for hatchery programs, a means for addressing 

uncertainty, and a method for demonstrating accountability. Documentation for each program should 

include citations from the scientific literature and models that take into account the various factors 
34 Applied Hatchery Reform – Principles and System-Wide Recommendations 

 

(e.g., predation assumptions, cumulative effects, etc.). The scientific framework, the Benefit/Risk Tool 

and the operational guidelines developed by the HSRG to guide the regional review process all 

provide resources for ensuring scientific defensibility for hatchery programs (see appendices). 

The HSRG has developed the following system-wide recommendations to help ensure a 

scientifically defensible hatchery program. 

Operate Hatchery Programs within the Context of Their 

Ecosystems 

The benefits and risks of hatchery programs can only be properly evaluated in the context of their 

ecosystems. Hatchery management requires understanding interactions between species and in 

particular, managing the risk of negative interactions. This requires knowing the status of the 

hatchery stocks and of other stocks, understanding the interactions between the stocks, and how 

well the habitat can support these stocks now and in the future. 

The release of hatchery fish into the environment will affect the ecosystem. While these effects are 

not fully predictable, information about, for example, competitive and predatory relationships 

among species is available to help avoid unwanted outcomes. 

Each ecosystem is unique, based on its history, natural events, (human) land use, and the strategies 

and goals developed by resource managers. The status and expectation for naturally-spawning 

stocks and the environment prescribe the potential for success and the limitations on any hatchery 

program. Therefore, in making decisions about current and future hatchery programs, decision 

makers should have current and future habitat assessments available to them in order to make 

informed decisions about goals for other stocks. 

Operate Hatchery Programs as either Genetically Integrated or 

Segregated Relative to Naturally-Spawning Populations18

Hatchery broodstocks should be managed as either genetically integrated or genetically 

segregated. Hatchery programs are classified as integrated if a principal goal is to manage the 

broodstock as an artificially propagated component of a naturally spawning population. In 

contrast, hatchery programs are classified as segregated if the management goal is to propagate 

the hatchery broodstock as a discrete or genetically segregated population, relative to naturally 

spawning populations. 

In this context, “intermediate” programs cannot exist without potentially posing significant risks to 

natural populations. The concepts of genetic integration and segregation, as they relate explicitly 

to hatchery programs, lead to well-defined operational guidelines and objectives for achieving the 

respective broodstock management goals while minimizing risks to naturally spawning 

populations. Each concept provides a template for broodstock management and operations. The 

18 See Appendix A, Scientific Framework, Applied Hatchery Reform-Regional Review Process, and, Emerging Issues paper on integrated 

and segregated programs. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 35 

greater the deviation from one of these templates, the greater are the risks to naturally spawning 

populations with increased likelihood that the benefits of a hatchery program will not outweigh the 

risks. Consequently, from the outset, each hatchery program must identify one of the two 

broodstock strategies and follow that strategy as closely as possible to acheive the desired purpose 

of the program. 

Integrated Program – A hatchery program is of an integrated type if the intent is for 

the natural environment to drive the adaptation of a composite population of fish that spawns 

both in a hatchery and in the wild. A fundamental goal of an integrated program is for the 

hatchery broodstock to be as similar genetically as possible to naturally spawning populations, 

in areas where fish are released and/or collected for broodstock. The long-term goal is to 

maintain genetic characteristics of a local, natural population among hatchery-origin fish, by 

minimizing genetic changes resulting from artificial propagation and potential domestication. 

In an idealized integrated program, natural-origin and hatchery-origin fish are genetically 

equal components of a common gene pool. 

A hatchery supporting an integrated program can be viewed conceptually as an artificial 

extension of the natural environment where the population as a whole (hatchery + wild) is 

sustained at a much higher level of abundance than would occur without the hatchery. A 

properly managed integrated broodstock can potentially serve as a genetic repository in the 

event of a major decline in the abundance of natural-origin fish. 

An integrated program does not imply that natural spawning of hatchery-origin fish is desired 

or even occurs. Natural spawning (a.k.a., supplementation) relates to the purpose, desired 

benefits and potential risks of a hatchery program and not to the genetic management goals for 

a hatchery broodstock, although the two sets of goals are usually correlated. Hatchery-origin 

fish spawning naturally does not make a hatchery broodstock genetically integrated—only if 

natural-origin fish are included in the broodstock in a systematic, prescribed manner can the 

broodstock be considered genetically “integrated.” In this context, the management goal of an 

integrated program is to maintain the genetic characteristics of naturally-spawning fish among 

hatchery-origin fish, not vice-versa. 

Specific recommendations for integrated programs include: 

• Develop a detailed, genetic management plan for the hatchery broodstock and the 

naturally spawning population in the watershed where adults are trapped for broodstock. 

• Ensure that an average of 10–20% of the hatchery broodstock is composed of naturalorigin adults each year. 

• Collect and spawn adults randomly with respect to time of return, time of spawning, age, 

size and other characteristics related to fitness. 

• Impose hatchery management practices that minimize the potential domestication effects 

of the hatchery environment. 
36 Applied Hatchery Reform – Principles and System-Wide Recommendations 

• Use marks, tags or other methods to distinguish natural- and hatchery-origin fish among 

natural spawners, in hatchery broodstocks, and in harvests. 

• Monitor and control natural spawning by hatchery-origin adults so that the percentage of 

natural spawners composed of hatchery-origin fish is significantly less than the percentage 

of the hatchery broodstock derived from natural-origin fish. This general rule may be 

violated in restoration supplementation programs where natural spawning by hatcheryorigin adults is an intended purpose of the hatchery program. 

• Adjust the size of integrated hatchery programs relative to the size of the naturally 

spawning population so that the number of natural-origin adults spawning naturally in a 

watershed is greater than the total number of adults required for broodstock. 

• In order to avoid broodstock mining, the natural component of the hatchery broodstock 

should not cause the number of natural spawners to fall below the escapement goal for 

natural spawners. 

Segregated Program - The fundamental goal of a segregated program is to propagate 

the hatchery broodstock as a discrete population or gene pool that is reproductively segregated 

from naturally spawning populations. Once established, segregated broodstocks are composed 

entirely of returning, hatchery-origin adults. As a consequence, genetically segregated 

hatchery populations can, and will, change genetically, relative to naturally spawning 

populations. Such changes may be intentional to maximize the desired benefits of the 

program, while minimizing risks to naturally spawning populations. However, in contrast to 

integrated programs, any natural spawning by hatchery-origin fish from a segregated program 

will impose potentially unacceptable risks to natural populations. 

Specific recommendations for segregated programs include: 

• Release and release fish in areas where opportunities to capture non-harvested adults are 

maximized, thus minimizing genetic risks to natural populations. 

• Rear fish in a manner and/or at a location that minimizes potential straying and 

opportunities for natural spawning. 

• Ensure harvest opportunities are commensurate with potential adult production from 

segregated programs and take into consideration the potential selective impacts of harvest 

on the long term viability of segregated programs. 

• Ensure hatchery-origin adults constitute no more than one to five percent of natural 

spawners. 

• Use marks, tags, or other methods to distinguish natural- and hatchery-origin fish among 

natural spawners, in hatchery broodstocks, and in harvests. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 37 

 

• Avoid trapping natural-origin adults, and exclude them from the broodstock. 

Size Hatchery Programs Consistent with Stock Goals 

Fisheries managers should determine the proper size (number of fish released) of a hatchery 

program based on clearly defined goals established for the stock. The size of hatchery program 

must consider two parameters: (1) the number of released fish to meet the purpose of the program 

and (2) the number of adult spawners necessary to meet both the purpose of the program and the 

genetic management goals for the broodstock. In general, the number of fish released should be 

the smallest number necessary to meet the management goal of the program. In addition, the 

number and composition (hatchery- or natural-origin) of adults used for broodstock must meet 

genetic guidelines and constraints consistent with maintaining a viable population. 

Hatchery programs that are sized incorrectly present ecological and economic risks. For example, 

large hatchery releases may interact through competition and predation with natural stocks and 

other ecological processes in a detrimental way. These “extra” fish may also impact the survival of 

other populations once they enter the ocean. Resources spent producing these fish may be wasted 

if returning adults cannot be harvested and/or overwhelm hatchery workers. 

Consider both Freshwater and Marine Carrying Capacity in 

Sizing Hatchery Programs 

Freshwater and marine trophic conditions and carrying capacity may limit the ability of a program 

to contribute to a resource goal.19

For example, stocks of coho and Chinook have shown a decrease in survival over the past decade 

in certain regions of Puget Sound and the coast, such as southern Puget Sound. The decrease may 

be related to the general decline in productivity of inland, marine waters. There has been a great 

deal of speculation as to additional cause(s) for the decline in these regions, (e.g., increased bird 

and marine mammal predation; a general lowering of water quality from urbanization in a body of 

water with low turnover; continuing loss of freshwater habitat, a shift in the forage base, etc). 

Whatever the cause, the trophic capacity of southern Puget Sound to support salmonid fishes 

appears to have diminished in recent years. 

Lowered survival may also be related to the total biomass of salmonids presently being released 

from hatcheries, despite recent reductions in the actual numbers of fish released. Closure of certain 

unproductive hatcheries and reduced production at other hatcheries may in fact benefit the quality 

and survival of both naturally spawning and hatchery fish. 

Factors that should be considered in sizing a hatchery program may include (but not be limited to) 

the following: 

1. the potential for ecological interactions with natural populations; 

19 See HSRG Scientific Framework and Hatchery Review Program, Emerging Issues chapter, section on marine carrying capacity. 
38 Applied Hatchery Reform – Principles and System-Wide Recommendations 

 

2. the physical capacity of the individual hatchery; 

3. the carrying capacity of receiving waters in terms of both juveniles and adults (see 

recommendations above); 

4. changes in ocean productivity; and 

5. the ability to control the contribution of hatchery-origin fish to the natural spawning 

escapement, (e.g., through selective harvest). 

Overall, the managers should maintain a repertoire of release strategies that can be adjusted in 

response to changing environmental or trophic conditions. There must be a defensible rationale for 

any given level of hatchery production, leading to sustainability and cost effectiveness. 

Ensure Productive Habitat for Hatchery Programs 

The HSRG has concluded that productive habitat, in which a salmon population conducts the 

various phases of its life cycle, is necessary to the success of any hatchery program. The fitness of 

the naturally-spawning population, its productivity, and the number of adult salmon (artificially or 

naturally produced) returning to the watershed ultimately depend on the natural habitat, not on the 

output of the hatchery. Silt free incubation gravels and cool, stable incubating water are necessary 

for the survival of salmon embryos. Flowing streams with complex structure, riparian vegetation, 

seasonal flow stability, and productive estuaries are necessary to the survival of juvenile salmon. 

Flowing streams are also necessary for the successful passage and spawning of returning adults. 

In particular, habitat is essential to the success of integrated hatchery programs because the 

hatchery broodstock is directly supported genetically and demographically by the naturally 

spawning component.20 Integrated hatchery programs will be limited in scope by the productivity 

of the natural habitat. Natural populations are expected to increase in fitness and productivity as 

habitats improve. In addition to the habitat described for all programs, silt free incubation gravels 

and cool reliably stable irrigating water are necessary for the survival of salmon embryos. 

Emphasize Quality, Not Quantity, in Fish Releases 

Release the lowest number of fish (consistent with goals for the resource) with the highest quality 

to maximize potential benefits while minimizing risks to naturally spawning populations. The 

HSRG’s working model is that the best a hatchery program can expect to do is to match a wild 

salmon template in terms of the physiological, morphological and behavioral traits that affect 

smolt-to-adult performance. Measures of quality can include affects on physiological, 

morphological and behavioral fitness, including competency of juvenile fish to migrate, establish 

territory, and displace other individuals, prey and forage. 21 These fitness characteristics clearly 

have both genetic and environmental components (nature vs. nurture). 

20 See HSRG System-wide Recommendation on Integrated and Segregated broodstock management 

21 See Emerging Issues paper “Hatchery Smolt Quality and Achieving the Wild Salmon Template”in Appendix B. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 39 

It is important that some measure of the quality, rather than simply the quantity, of fish released 

from hatcheries be measured and evaluated. In the past, performance has been measured by 

numbers of juvenile released. As discussed in the recommendation to “Size Hatchery Programs 

Consistent with Stock Goals,” releasing too many fish may have ecological risks and economic 

costs. In the future, performance should be measured by the level of post-release survival and the 

rate of adult returns, both of which depend on the quality of the fish released. 

Use In-Basin Rearing and Locally-Adapted Broodstocks 

Some hatchery programs, for lack of adequate facilities and/or proper escapement management, 

transfer eggs and/or juveniles between facilities and among watersheds/regions. The HSRG 

recommends that “backfilling” of broodstock shortages should be terminated. Managers should 

use in-basin rearing and locally adapted broodstocks to increase the productivity of hatchery 

programs and minimize risks. Failure to do so results in a loss of local genetic adaptability, 

increased potential for disease transfer, and lowered productivity of hatchery stocks. This practice 

of importation and movement of eggs and juveniles into and out of the region should thus be 

ended. 

Spawn Adults randomly throughout the Natural Period of Adult 

Return 

The HSRG recommends that the managers adopt and implement policies that conserve or recover 

natural life history traits of the various hatchery stocks to assure long-term sustainability. There 

can be loss of certain life history traits in hatchery stocks through the process of domestication. An 

example is the shift in spawn timing resulting from selective breeding for early adult return. 

Use Genetically-Benign Spawning Protocols that Maximize 

Effective Population Size 

The HSRG recommends that the mating of hatchery fish should be designed to achieve two 

principal objectives: 1) maximizing the genetic effective number of breeders; and 2) ensuring that 

every selected adult has an equal opportunity to produce progeny (i.e. avoid selective breeding and 

artificial selection in the hatchery environment). This is particularly critical in conservation 

programs, where populations are small or have experienced significant declines. 

To achieve these objectives, male and female hatchery fish can be mated following pairwise (one 

male to one female), nested (e.g., one male to three females), or factorial (e.g., three-by-three 

spawning matrix) designs. Mixed milt spawning where eggs are fertilized by the simultaneous or 

sequential addition of sperm should be avoided because of unequal genetic contributions among 

male spawners and consequential reductions in effective population size. 
40 Applied Hatchery Reform – Principles and System-Wide Recommendations 

 

During its review of hatchery programs, the HSRG has seen a variety of spawning protocols, 

including modified factorial mating,22 single family pairing, as well as protocols that pool gametes 

prior to fertilization. The approaches of single family mating and modified factorial mating have 

proven to be feasible and effective (up to 94% fertilization), even in some of the largest programs 

reviewed (up to five million eggs taken per year). Because these methods achieve the two 

principle objectives and can be implemented relatively easily, the HSRG recommends that all 

programs, up to the size noted, adopt one of these protocols. 

Hatchery spawning protocols prescribed by the managers typically incorporate gametes from all 

age classes, including jacks (early returning males), to maintain genetic continuity or gene flow 

among brood years within populations. A common approach by the co-managers is to use jacks 

for 2% of the adult male spawning population. This rate is probably lower than what occurs 

among natural spawning populations. The HSRG therefore recommends that jacks be spawned 

according to their occurrence among returning adults up to a maximum of 10%, with the exception 

of coho salmon where a minimum of 10% jacks among male spawners should be used. The 

inclusion of jacks to maintain genetic continuity among brood years of coho is especially 

important, because they mostly mature at three years of age. 23

Reduce Risks Associated with Outplanting and Net Pen Releases 

Releasing smolts in streams geographically removed from a hatchery or adult collection facility is 

commonly called outplanting. This practice may pose significant genetic risks by promoting stray 

rates, often exceeding natural levels, to freshwater areas where interbreeding with naturally 

spawning populations is undesirable. 

Steelhead programs in Puget Sound and coastal Washington have often used outplanting to 

support sport fisheries in a large number of small streams. Similarly, saltwater net pens are used to 

acclimate and release salmon smolts in marine areas where a targeted marine fishery on returning 

adults is desired. A common feature of these programs is that they release fish where no facilities 

exist to trap returning adults that escape target fisheries. Outplanting and net-pen releases from 

segregated hatchery programs24 are especially problematic, because of the potentially high level of 

genetic divergence between the hatchery stock and natural populations where straying and natural 

spawning may occur. 

The HSRG recommends reducing risks associated with outplanting and net-pen releases by 

reducing the number and/or size of such programs. Risks can also be reduced by: 

1) intense, selective harvest and/or the use of adult traps; 

2) implementing the HSRG’s system-wide recommendations for steelhead, to substantially 

reduce the geographic range of outplanting; 

22 Currens, K.P., J.M. Bertolini, C.A. Busack, and J. Barr. 1998. An Easier Way to Meet Genetic Spawning Guidelines. Pages 41-44 in 

Proceedings of the 49th Pacific Northwest Fish Culture Conference, Boise, ID 

23 Van Doornik, D.M., M.J. Ford, and D.J. Teel. 2002. Patterns of temporal genetic variation in coho salmon: estimates of the effective 

proportion of two year-olds in natural and hatchery populations. Transactions of the American Fisheries Society. 131: 1007-1019

24 See recommendation above on operating integrated and segregated hatchery programs. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 41 

 

3) restricting release to areas where adult collection facilities are available or can be easily 

developed; 

4) using locally-adapted and integrated stocks25 in net pens, so that strays have less of a 

deleterious effect on natural populations; 

5) evaluating the benefits and risks of each program every two or three years, and reducing 

or terminating programs that impose significant risks relative to benefits; 

6) monitoring and evaluating high risk programs to ensure that adverse effects to naturallyspawning populations are minimal, straying risks are appropriately managed, and offstation releases are appropriately located; and 

7) developing system-wide, risk management guidelines and protocols for outplanting and 

net-pen programs.26

Develop a System of Wild Steelhead Management Zones (a 

special case)

Segregated hatchery steelhead programs are used extensively throughout Puget Sound and coastal 

Washington to provide a harvest opportunity. These segregated steelhead programs often outplant 

non-native stock with no provision for the recapture of returning adults. This is unlike segregated 

Chinook and coho hatchery programs, which release fish directly from the hatchery where the 

returning adults can be recaptured. The HSRG understands it is the intention of the managers to 

continue segregated steelhead programs into the future. In general, the HSRG believes that the 

widespread stocking and outplanting of steelhead smolts poses unacceptable ecological and 

genetic risks to naturally spawning populations, particularly in small streams that receive such 

outplants or to which hatchery-origin fish stray. The biggest concern is the genetic risk posed by 

the spawning overlap between the hatchery (Chambers Creek origin), early-timed winter run stock 

and the native, late-timed winter run stock. 

The HSRG recommends that the managers develop a system of “wild steelhead management 

zones” where entire sub-regions or portions of watersheds for large rivers (e.g. Skagit River) are 

not planted with hatchery-origin fish but are managed for “wild” steelhead only. This approach 

will increase protection of native stocks in while still permitting harvest opportunities in areas 

where the genetic and ecological risks of hatchery releases are substantially less (e.g. where adult 

recapture facilities exist). 

The HSRG recommends that wild steelhead management zones be developed for each of the ten 

regions within Puget Sound and coastal Washington. Harvest for steelhead may be compatible 

with this approach, but no hatchery-propagated steelhead would be introduced into the wild 

steelhead management zones. Such areas would reduce the risk of naturally spawning fish 

interbreeding with non-native hatchery fish, and provide native stocks for future fisheries 

programs. The streams selected should represent a balance of large and small streams, habitat 

25 Ibid. 

26 See Emerging Issues, paper on out-planting and net pens. 
42 Applied Hatchery Reform – Principles and System-Wide Recommendations 

 

types, stock status, etc. Hatchery production may need to be increased in streams selected for 

hatchery harvest. 

The HSRG acknowledges the need to promote segregated hatchery steelhead programs that are 

self-sustaining. Existing programs are based largely on steelhead of Chambers Creek origin winter 

and Skamania origin summer steelhead. These stocks have been transplanted to many locations 

throughout Puget Sound and coastal Washington. Once these segregated stocks have been 

transplanted they should be maintained as separate broodstocks now maintained with returning 

adults at those locations so they can adapt to the local environment. 

When implementing a segregated steelhead program, it is important to minimize interaction with 

naturally spawning steelhead, through such tools as differential timing and a decision on benefits 

versus risks on outplanting in freshwater habitat. Adult collection procedures need to be 

incorporated to capture adults that are not harvested from the returning segregated population. 

The HSRG recognizes the role integrated hatchery programs can serve for conservation or harvest, 

using native broodstocks. It is important to recognize the differences between integrated stock 

management, incorporating native origin broodstock, and segregated stock management, using 

non-native origin broodstock.27

Monitoring and evaluation should be a basic component for streams managed for native stocks and 

those managed for hatchery harvest.

Use Hatchery Salmon Carcasses for Nutrification of Freshwater 

Ecosystems, while Reducing Associated Fish Health Risks28

Returning adult salmon are a unique vector for the delivery of marine nutrients into the freshwater 

ecosystem. The importance of these nutrients to consumers such as raccoons, bear, eagles and 

even man has been recognized for some time. Recent research also suggests that a significant 

portion of nitrogen in plants and animals in streams where adult salmon are abundant is derived 

from those returning adults. Marine-derived nutrients from returning adult salmon have been 

found to make a significant contribution to riparian vegetation and even old-growth forests. In 

streams in interior British Columbia up to 60% of the nitrogen in benthic insects was derived from 

the carcasses in streams where salmon were abundant. They also found that juvenile salmon show 

higher growth rates in streams where adult salmon spawn than in streams without spawning adults. 

Use of hatchery salmon carcasses as a source of these marine-derived nutrients was found to 

increase the density of age 0+ coho and age 0+ and 1+ steelhead in small, southwestern 

Washington streams. 

The deliberate distribution of hatchery salmon carcasses into watersheds for purposes of 

nutrification can have a positive ecological benefit to natural salmonid stocks. This practice may, 

however, also pose a fish health risk to these stocks if those carcasses carry live pathogens and are 

27 See System-wide Recommendation above on operating integrated and segregated hatchery programs. 

28 See Appendix B, Emerging Issue paper for references and more information on this topic. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 43 

not properly treated or managed prior to distribution. It is well recognized that disease organisms 

present in salmon carcasses can be transmitted to other salmonids following the release of these 

organisms into water or through their direct consumption unless appropriate disease risk-aversive 

measures such as pathogen-free certification are followed. 

Principle 3: Informed Decision Making

Assuming that goals for the resource have been established (see Principle 1), and the scientific 

rationale and defensibility for a particular hatchery program have been developed into a 

comprehensive management and operational plan, the HSRG further recommends that the managers’ 

decisions be informed and modified by continuous evaluations of existing programs and by new 

scientific information. Such an approach will require a substantial increase in scientific oversight of 

hatchery operations, particularly in the areas of genetic and ecological monitoring. 

With clear decision making processes in place that respond to new information, the HSRG believes 

that hatcheries can be managed in a more flexible and dynamic manner in response to changing 

environmental conditions, new scientific information, economic value of the resource, and other 

models where actions are evaluated and modified to determine the best use of limited resources. 

This model applied to hatcheries requires that performance standards and indicators be identified so 

that monitoring activities will focus on key uncertainties and effective evaluation of results can occur. 

Results of the monitoring and evaluation (M&E) must then be brought forward to a decision making 

process in a clear and concise way so needed changes can be implemented. This responsive process 

should be structured to allow for innovation and experimentation so hatchery programs may be 

responsive to new goals and concepts in culture practice. 

The HSRG has developed the following system-wide recommendations to help ensure the principle 

of informed decision making for hatchery programs is achieved. 

Adaptively Manage Hatchery Programs 

The HSRG recommends that adaptive management is particularly important in the context of 

hatchery reform. Adaptive management, as related to ecosystems, is defined as an “adaptive 

policy that is designed from the outset to test clearly formulated hypotheses about the behavior of 

the ecosystem being changed by human use.”29 There is a significant amount of scientific 

uncertainty about the effects and proper uses of hatcheries, and a great need for flexibility and 

adaptation to changing goals, new scientific knowledge, and new information about the condition 

of stocks and habitat. A structured adaptive management program will be a key component of a 

strategy for success in these circumstances. 

A critical implication is the notion of responsive change—rather than the status quo—as the 

normal operating procedure. Put simply, adaptive management is learning by doing, assuming 

 

29 Lee, K. N. 1993. Compass and gyroscope: integrating science and politics for the environment. Island Press, Washington, DC. 
44 Applied Hatchery Reform – Principles and System-Wide Recommendations 

 

your program and operations will change regularly to reflect new information and better meet 

goals, and taking action in the face of scientific uncertainty. However, the actions taken through 

adaptive management are not selected at random. Rather, action is prescribed through the 

thoughtful and disciplined application of the scientific method. 

The scientific method and adaptive management require a scientific framework for organizing and 

understanding information and identifying uncertainties. The HSRG has developed such a 

framework for the context of anadromous salmonid hatcheries30 and encourages the managers to 

use this framework and keep it up to date. Equally important is a structured process that assures 

the right information is collected, analyzed, reported and brought forward in the decision making 

processes at all levels of hatchery operation. The HSRG encourages the managers to adopt an 

adaptive management approach to implementing hatchery reform, and offers both the tools it has 

developed for the regional review process, and the experience it has acquired during the review 

process, to aid the managers in their creation of this approach. 

Incorporate Flexibility into Hatchery Design and Operation 

The HSRG recommends that facilities be designed and operated in such a way that they are able to 

respond relatively easily to changes in harvest and conservation goals and priorities, ocean 

carrying capacity, stock status, freshwater habitat conditions, and the myriad other factors that will 

alter current policies and programs. The goal of a hatchery or regional manager should not be to 

“fill the hatchery facility to its biological capacity,” but rather, to manage the facility to achieve 

programmatic goals. 

Programs must also be able to respond to uncertainty and risk. For example, an empty raceway 

today may be necessary to provide this type of flexibility in the future. The keys to flexibility are 

having sufficient supplies of land, water quality and quantity, and physical facilities; along with a 

planning mindset that takes the concepts of flexibility, managing change, and future needs into 

account. 

Evaluate Hatchery Programs Regularly to Ensure Accountability 

for Success 

Achieving successful hatchery programs (where benefits and risks are managed effectively) will 

require ongoing monitoring and evaluation (M&E), with some level of commonality and 

standardization across Puget Sound and coastal Washington. Each region of Puget Sound and the 

coast will need to develop its own M&E program consistent with the goals and programs of that 

region. 

Monitoring should include not only expanded efforts to distinguish hatchery- and natural-origin 

fish, but also determining the fate of migrants in fresh and saltwater environments following 

30 See Appendix A, Scientific Framework for the Artificial Propagation of Salmon and Steelhead. 
Applied Hatchery Reform – Principles and System-Wide Recommendations 45 

 

release. An integrated, region-wide hatchery M&E system needs to be developed that includes the 

systematic and annual evaluation of the co-mingling of hatchery and naturally-spawning fish.31 

Furthermore, a modern, centralized M&E database where information can be evaluated annually 

for adherence to regional and system-wide goals needs to be institutionalized, in order to 

adaptively manage the system. Individual hatcheries need to be equipped with computers and 

Internet access that allow them to use and share data from a record collection system developed by 

the co-managers, such as the HatPro system. 

31 See Appendix A, Scientific Framework, Monitoring and Evaluation for Accountability and Success. 
46 Applied Hatchery Reform – Program-Specific Regional Recommendations 

PROGRAM-SPECIFIC REGIONAL 

RECOMMENDATIONS 

In each of the regions reviewed, the HSRG found significant differences in the quality of the habitat, 

stock status, the goals the managers have prescribed for each region’s salmon and steelhead stocks, 

and the purposes of each region’s hatchery programs. The HSRG’s regional review process produced 

roughly 1,000 program-specific recommendations addressing these specific circumstances. 

Recommendations ranged from changes in broodstock management, to addressing water quality 

concerns, to removal of fish passage impediments, and many others. Some program-specific 

recommendations referenced system-wide recommendations; others were unique to the program. 

This synopsis includes the HSRG’s findings for each region reviewed and a list of regional 

participants. The full analysis and recommendations for hatchery programs in each region can be 

found in the three separate volumes that constitute this document’s Appendix I or electronically at 

www.hatcheryreform.org. 

Hatchery Reform Recommendations February 2002: 

Eastern Strait of Juan de Fuca, South Puget Sound, and 

Stillaguamish and Snohomish Rivers

Eastern Strait of Juan de Fuca 

This region includes the eastern portion of the Strait of Juan de Fuca, from Point Wilson to the 

Hoko River. Twelve hatchery programs were reviewed in this region, with 60 specific reforms 

recommended. Two major restoration efforts are planned in this region: dam removal/watershed 

restoration on the Elwha River and habitat restoration at the mouth of the Dungeness River. 

Historically, the Elwha River supported a genetically distinct run of Chinook salmon. These fish 

regularly attained sizes greater than 50 pounds. A hatchery supported population remains in the 

lower river with some natural spawning in the river itself, but these do not attain their historic 

sizes. What happens to an endangered run of Chinook salmon when a dam is removed and a 

hundred years’ of sediment flows downstream? The hatcheries on this river system will play a 

central role in protecting and restoring this run until the habitat is ready to support them again. 

Federal, state and tribal managers in this region must determine how best to do this, in keeping 

with the principle of operating hatchery programs in a scientifically defensible way. The regional 

review process has helped them answer questions about how long the fish should be reared in 

captivity and when and where their progeny should be released to reestablish a naturally spawning 

population. The co-managers are currently developing a detailed, Elwha River Restoration Plan 

that will prescribe the role of existing hatchery facilities, artificial propagation, and potential 

outplanting of hatchery-origin fish in the restoration process. The restoration effort will also 

include coho salmon, sockeye salmon, and steelhead. 
Applied Hatchery Reform – Program-Specific Regional Recommendations 47 

Regional Participants - Pat Crain, Mike McHenry and Larry Ward, Elwha Klallam Tribe; 

Scott Chitwood, Byron Rot and Ann Seiter, Jamestown S'Klallam Tribe; Marianna 

Alexandersdottir, Kyle Brakensiek and Willy Eldridge, Northwest Indian Fisheries Commission 

(NWIFC); Brian Winter, Olympic National Park; Chris Weller, Point no Point Treaty Council 

(PNPTC); Donald Haring, Washington State Conservation Commission; Ann Blakely, Chris 

Byrnes, Martin Chen, Bill Freymond, Randy Johnson, Thom Johnson, Mark Kimbel, Anne 

Marshall, Darrell Mills, Don Rapelje, Dick Rogers and Paul Seidel, Washington State Department 

of Fish and Wildlife (WDFW). 

South Puget Sound 

This region includes the portion of Puget Sound south of the Tacoma Narrows. The HSRG 

reviewed 16 hatchery programs in this region, and provided 64 specific recommendations. The 

region is highly urbanized. Habitat in the region is affected by population growth and 

development, although instream flows are expected to be relatively stable. Storm water, 

sedimentation from development, and beach and stream bank channelization are expected to still 

be significant in the future. Habitat restoration projects are underway in the region, most noteably 

in the Nisqually River and Delta. Other stream restorations projects such as removal of the 

Goldsborough dam are also underway, although most are only selected reach-scale restoration 

efforts. 

The managers designated this region a hatchery management zone for many stocks as part of their 

post-Boldt Decision efforts to provide opportunities for pre-terminal Puget Sound fisheries and 

adequate fishing opportunities for the Puyallup, Nisqually and Squaxin Island tribes, all of which 

have “usual and accustomed” fishing areas here. It includes several old trout facilities (formerly 

under the management of the Washington Department of Game prior to merger) not particularly 

suited for rearing salmon as well as many facilities without the capability to fully incubate or 

provided full-term rearing for their programs. These facilities therefore, have been used as 

intermediate rearing stations for fish from other facilities, requiring a series of interbasin stock 

transfers to meet program goals. This region previously released up to ten million coho smolts per 

year, around ten percent of the total releases in Puget Sound and coastal Washington, at its height 

of productivity. Despite increased smolt releases, adult returns of coho have declined. The 

scientists strongly recommend an analysis of the carrying capacity of the Sound with a decrease or 

cap in smolt releases in this region until more scientific understanding is established, in keeping 

with the principle of managing hatchery programs based on informed decision making. 

Regional Participants - Jeanette Dorner, Joan Miniken, Bill St. Jean, David Troutt and 

George Walter, Nisqually Tribe; Marianna Alexandersdottir, Jim Bertolini, Kyle Brakensiek, 

Willy Eldridge, NWIFC; Frankie John Jr., Russ Ladley, Chris Phinney and Blake Smith, Puyallup 

Tribe; Jeff Dickison, Will Henderson, Jim Peters and Andy Whitener, Squaxin Island Tribe; 

Donald Haring and John Kerwin, Washington State Conservation Commission; Charmane 

Ashbrook, Chuck Baranski, Debbie Carnevali, Martin Chen, Jeff Davis, Rich Eltrich, Jim Fraser, 

Darrell Mills, Don Nauer, Denis Popochock, Brian Quinton, Margie Schirato, Paul Seidel, Jack 

Tipping, Marc Wicke and Dan Wrye, WDFW. 
48 Applied Hatchery Reform – Program-Specific Regional Recommendations 

Stillaguamish/Snohomish Rivers 

This region includes the watersheds contained by the Stillaguamish and Snohomish rivers and 

Tulalip Bay. The HSRG reviewed 16 hatchery programs in this region and provided 94 specific 

recommendations. Habitat in the Stillaguamish River system has been heavily altered and 

compromised by land use activities such as logging, diking, housing development and dairy 

farming. This region is becoming increasingly urbanized, particularly in the lower reaches of the 

respective river valleys. The Skykomish River features relatively undisturbed habitat. While the 

Snoqualmie is wild-like above North Bend, in rural, eastern King County it has been affected by 

agriculture and development. When the Skykomish and Snoqualmie join and form the Snohomish, 

the effects of development are even clearer. In addition to programs operating within the larger 

river systems, the Tulalip Tribes operate a facility with numerous hatchery programs meant to 

contribute to terminal harvest in Tulalip Bay. The HSRG emphasized the need to determine 

whether adult fish from these and other programs are straying to other regional streams and 

presenting risks to naturally spawning salmon. Another distinguishing characteristic of this region 

is its popular steelhead sport fishery. This region is one where the HSRG’s “wild steelhead 

management zones” concept32 was a particular focus of the recommendations. 

Regional Participants - Marianna Alexandersdottir, Kyle Brakensiek, Willy Eldridge and 

Bruce Stewart, NWIFC; John Drotts, Kip Killebrew, Pat Stevenson and Shawn Yanity, 

Stillaguamish Tribe; Cliff Bengston, Marla Maxwell, Kurt Nelson, Kit Rawson and Francis 

Sheldon, The Tulalip Tribes; Kevin Amos, Charmane Ashbrook, Dave Brock, Mike Chamblin, 

Doug Hatfield, John Kerwin, Larry Klube, Curt Kraemer, Chuck Lavier, Darrell Mills, Steve 

Moore, Tony Opperman, Eric Pentico, Chuck Phillips, Jed Varney, Ron Warren and Dan Wrye, 

WDFW. 

Hatchery Reform Recommendations March 2003:

Skagit River Basin, Nooksack and Samish Rivers, and 

Central Puget Sound

Skagit River Basin 

This region includes the watersheds contained by the Skagit River Basin (including the mainstem 

Skagit, Baker, Sauk, Cascade and Suiattle rivers) and Whidbey Island. Eleven hatchery programs 

were reviewed in this region with 48 specific recommendations provided. The Skagit River Basin 

is the largest watershed in Puget Sound and supports all six species of anadromous salmonids 

native to Washington state. A significant amount of natural habitat is still available in this region, 

though it has been affected by hydropower and other land uses. The Skagit Basin is an important 

region for the recovery of Puget Sound salmon stocks. Strong spring, summer and fall Chinook 

runs existed in the past and there is still a fair amount of this diversity left. However, there are 

conservation concerns for several stocks, including Chinook, coho and steelhead. The region has a 

number of hatchery programs serving as indicator stocks for the US/Canada Treaty and other 

 

32 A full description of this concept is included in the Applied Hatchery Reform chapter, Principles and System-Wide Recommendations. 
Applied Hatchery Reform – Program-Specific Regional Recommendations 49 

processes. These are important to fisheries management, but not central to recovery or direct 

harvest. Natural production goals are key for all species in this region. Therefore, in keeping with 

the principle of operating hatchery programs based on clear goals for the resource, the HSRG 

recommended the managers size these indicator programs to meet indicator stock needs, but not 

above that level. The group also noted Baker Lake sockeye as an example of a hatchery program 

that is meeting its conservation purpose by maintaining a stock that would otherwise go extinct. 

Regional Participants - Steve Fransen, NOAA Fisheries; Marianna Alexandersdottir, Kyle 

Brakensiek, Ken Currens, Willy Eldridge, Grant Kirby, Bruce Stewart, NWIFC; Doug Bruland, 

Puget Sound Energy; Dave Pflug, Seattle City Light; Eric Beamer, Bob Hayman, Scott Schuyler, 

Larry Wasserman, Skagit System Cooperative; Charmane Ashbrook, Brett Barkdull, Kurt 

Buchanan, Pete Castle, Deborah Cornet, Chuck Johnson, John Kerwin, Kevin Kurras, Chuck 

Lavier, Darrell Mills, Steve Moore, Chuck Phillips, Gary Sprague, Steve Stout, Jack Tipping, Jed 

Varney, WDFW. 

Nooksack/Samish Rivers 

This region includes the watersheds contained by the Nooksack and Samish rivers and the San 

Juan Islands. Nineteen hatchery programs were reviewed in this region, with 89 specific 

recommendations provided. Some similarities exist between the Nooksack/Samish region and the 

Stillaguamish/Snohomish region where habitat has been altered by land use activities. Because of 

this, natural production has been severely impaired. Spring Chinook stocks, in particular, are 

dependent on hatchery programs for recovery. Management goals for the region’s stocks have 

emphasized hatchery production for harvest, especially on Chinook and coho. This region was in 

the past the center of Puget Sound Chinook harvest, but both hatchery production and harvest have 

been reduced over the last decade or so. The HSRG recommended the managers ensure their 

hatchery programs are consistent with conservation goals, in particular those for spring Chinook. 

The group pointed out the importance of making sure recovery programs do not produce numbers 

of fish that exceed the capacity of the limited habitat into which they are released and to which 

they return. If this occurs, a program might be rebuilding one stock, while at the same time 

producing strays that compete with natural stocks in other streams, thereby not meeting the 

principle of scientific defensibility. 

Regional Participants - Earl Steele, Bellingham Technical College; Michael O’Connell, 

Long Live The Kings (LLTK); Alan Chapman, Randy Kinley, Lummi Nation; Ned Currence, 

Nooksack Tribe; Marianna Alexandersdottir, Kyle Brakensiek, Deborah Cornett, Willy Eldridge, 

Grant Kirby, NWIFC; Scott Schuyler, Skagit System Cooperative; Charmane Ashbrook, Pete 

Castle, Chuck Johnson, John Kerwin, Darrell Mills, Chuck Phillips, Steve Seymour. Ted 

Thygesen, Jack Tipping, Jed Varney, WDFW. 

Central Puget Sound 

This region includes the central portion of Puget Sound, including the Puyallup River, Green 

River, Lake Washington and watersheds along the eastern shore of the Kitsap Peninsula. Thirtyone hatchery programs were reviewed in this region, with 149 specific recommendations 

provided. Central Puget Sound is where the largest concentration of the human population lives in 
50 Applied Hatchery Reform – Program-Specific Regional Recommendations 

 

Puget Sound and coastal Washington, putting particular focus on issues surrounding how salmon 

and people coexist. The HSRG reviewed four sub-regions within Central Puget Sound and found 

that each had its own distinct character. 

The Puyallup River sub-region has been affected by land use and hydropower and is home to 

White River Chinook, the last remaining spring Chinook stock in South and Central Puget Sound. 

White River Chinook owes its recent rebound to a successful hatchery intervention. The HSRG 

said this program has been successful enough that it is time to begin locally-adapting the stock, 

moving away from out-of-basin rearing and increasing the program’s scientific defensibility. 

The East Kitsap sub-region features smaller, shorter streams and is only now beginning to 

confront the rapid population growth and corresponding pressure on habitat that much of Central 

Puget Sound has already experienced. Consistent with its short streams, hatchery programs in this 

sub-region have emphasized chum production. Though the harvest benefits derived from these 

programs are not always large, the HSRG saw them as good examples of how hatcheries can be 

used for environmental education, in that they make extensive use of volunteers from the general 

public, many drawn from the new arrivals who need to learn about protecting salmon stocks and 

their habitat. 

Purposes other than conservation and harvest (i.e., education and research) are featured at hatchery 

facilities in the Lake Washington sub-region, such as Issaquah Hatchery and the University of 

Washington. Another major effort in this sub-region is the conservation and harvest hatchery 

program directed on Lake Washington sockeye. The HSRG provided a number of 

recommendations for allowing fish from this program to more closely emulate the natural life 

history pattern of sockeye in the Cedar River and Lake Washington, increasing its scientific 

defensibility. 

The Green River sub-region has more than a century’s history of hatchery and natural production 

existing side-by-side on a Chinook stock that has remained relatively healthy. The region also 

features several net pen programs, which acclimate and release smolts in marine areas where a 

targeted fishery of returning adults is desired. Accordingly, this region is one where the HSRG’s 

recommendations about reducing straying risks from outplanting and net pen programs33

 were a 

particular focus. 

Regional Participants - Paul Hage, Richard Johnson, Mike Mahovlich, Dennis Moore, 

Isabel Tinoco, Muckleshoot Tribe ; Marianna Alexandersdottir, Kyle Brakensiek, Ken Currens, 

Willy Eldridge, Bruce Stewart, NWIFC; Frankie John Jr., Russ Ladley, Chris Phinney, Blake 

Smith, Puyallup Tribe; Rich Brooks, Mike Huff, Rob Purser, Jay Zischke, Suquamish Tribe; 

Brodie Antipa, Charmane, Ashbrook, Chuck Baranski, Deborah Cornett, Tom Cropp, Jeff Davis, 

Bob Everitt, Steve Foley, Doug Hatfield, Chad Jackson, Chuck Johnson, John Kerwin, Kirk 

Lakey, John Long, Darrell Mills, Travis Nelson, Don Nauer , Chuck Phillips, Denis Popochock, 

Brian Quinton, Doris Small, Chad Stussy, Joan Thomas, Jack Tipping, WDFW. 

33 See Emerging Issues paper on Outplanting and Net Pen Releases; and recommendations on this subject in Principles and System-Wide 

Recommendations. 
Applied Hatchery Reform – Program-Specific Regional Recommendations 51 

Hatchery Reform Recommendations March 2004: Hood 

Canal, Willapa Bay, North Coast, and Grays Harbor

Hood Canal 

This region includes the watersheds draining into Hood Canal. Twenty-two hatchery programs 

were reviewed in this region, with 99 specific recommendations provided. The region featured 

primarily, but not entirely, hatchery harvest programs. Chum stocks are biologically significant 

here; and Hood Canal summer chum are listed as threatened under the Endangered Species Act. 

The HSRG found that the Summer Chum Salmon Conservation Initiative being conducted by a 

partnership of state, tribal, federal and non-governmental organizations represents a very well 

designed and operated approach to restoring Hood Canal summer chum, and recommended 

continuing this program. In one stream (the Big Quilcene River), the HSRG determined that the 

managers had met their rebuilding goal and recommended discontinuing this program a year 

earlier then planned. Summer-fall Chinook in Hood Canal are also listed as threatened under the 

Endangered Species Act as part of the Puget Sound ESU. The HSRG recommended developing a 

locally adapted, integrated stock of Chinook in the Skokomish River Basin that could biologically 

serve as a “core populations” for Hood Canal. This population will need to be sustained by 

hatcheries until the time that improved habitat can support a natural, self-sustaining population. 

Under the HSRG’s principle of managing hatchery programs based on clear goals, the group 

recommended that a number of hatchery programs within this region be adjusted to meet current 

harvest needs, either by reducing the number of fish released or by increasing harvest. And the 

HSRG determined that the managers need to take into account facility water and space availability 

in determining the optimum species mix at the region’s hatcheries. 

Regional Participants - Lee Boad, Dan Hannifous, Eileen Palmer, and Neil Werner, Hood 

Canal Salmon Enhancement Group; Rick Endicott and Joy Lee, LLTK; Kyle Brakensiek, Willy 

Eldridge and Marcia House, NWIFC; Chris Weller, PNPTC; Tim Seachord, Port Gamble 

S’Klallam Tribe; David Herrera, Skokomish Tribe; Dan Adkins, Martin Chen, Kent Dimmitt, Kirt 

Hughes, Thom Johnson, Ed Jouper, Steve Kalinowski, Bob Leland, Darrell Mills, Denis 

Popochock, Brad Sele, Doris Small, Jack Tipping and Ron Warren, WDFW; and Judy Gordon, 

Tom Kane, Sonia Mumford, Larry Telles, Ron Wong, Bob Wunderlich and Dave Zajac, USFWS. 

Willapa Bay 

This region includes the watersheds draining into Willapa Bay. Twenty hatchery programs were 

reviewed in this region, with 120 specific recommendations provided. This and the other two 

coastal regions (North Coast and Grays Harbor) differ from the Puget Sound regions in that they 

feature numerous, smaller, independent systems that drain into the bay or directly into the Pacific 

Ocean and the Strait of Juan de Fuca. This means the HSRG had many more stocks and programs 

to consider per region, as compared to Puget Sound where the smaller drainages tended to flow 

into larger rivers. Another difference is that the managers reported a higher number of relatively 

healthy natural stocks in this region, most likely due in large part to less urbanization. 
52 Applied Hatchery Reform – Program-Specific Regional Recommendations 

Unlike the other regions, all hatcheries in Willapa Bay are owned and operated solely by WDFW. 

However, the regional fisheries enhancement group has views that differ from WDFW as to which 

stocks should be a priority within the region. In light of this, the HSRG recommended that 

WDFW, along with local stake-holders, develop a region-wide strategic plan for managing all 

stocks. This will require developing a better understanding of stock structure and identifying core 

populations for each species, and designing hatchery programs and strategies around this structure. 

For Chinook, the HSRG determined that—given the limited potential for Chinook habitat in the 

Nemah River, the uncertainty of the stock structure, and the history of hatchery releases in this 

watershed—developing viable stocks in the Naselle and Willapa rivers may better meet the stock 

goals for the region than attempting to create a properly integrated Nemah River Chinook 

program. In this region, the HSRG re-emphasized the importance of using in-basin rearing and 

locally-adapted broodstocks. Importing and moving eggs and juveniles into and out of a watershed 

inhibits natural biological processes related to homing fidelity, viability, and local adaptation. 

Ensuring that naturally-spawning stocks drive the adaptation will require increasing the number of 

natural-origin fish brought into the hatchery broodstocks each year. Distinguishing hatchery and 

natural origin during spawning will also be necessary. The HSRG also found that there is less 

monitoring and evaluation occurring in this region than in any other. This lack of information 

prevents the managers from knowing what benefits the programs provide or risks they create. 

Regional Participants - Kyle Brakensiek and Willy Eldridge, NWIFC; Charlie Stenvall, 

USFWS; and Randy Aho, Robert Allan, Jim Bauer, William Campbell, Larry Durham, Rich 

Ereth, Manuel Fariñas, Kirt Hughes, Ken Jansma, Dave Kloempke, Darrell Mills, Ike Queral, 

Chad Stussy, Jack Tipping, and Ron Warren WDFW; Don Amend and Ron Craig, Willapa Bay 

Fisheries Enhancement Group; and Jim Mitby, Willapa Bay Gillnetters Association. 

North Coast 

This region includes the coastal drainages west of—and including—the Hoko River and north of 

Grays Harbor. Twenty-eight hatchery programs were reviewed in this region, with 188 specific 

recommendations provided. The North Coast provided several examples of hatchery programs—

Chinook in particular—that meet the HSRG’s guidelines for properly integrated programs, 

meaning that a sufficient number of natural-origin fish are included in the hatchery broodstock and 

the number of hatchery-origin fish on the spawning grounds is kept low enough to allow naturalorigin spawners to drive the adaptation of the stock. Meeting these guidelines also requires that the 

programs be sized to suit the available receiving habitat, so as not to compete with natural 

production. Hatchery programs also need to be sized to take into account facility limitations and 

conditions (such as water quality, quantity and temperature, and rearing space). The HSRG saw 

several such challenges in this region, especially at Makah National Fish Hatchery. 

In addition, the group expressed concern about the use of introduced stocks in Quillayute system. 

The HSRG agreed that improved rearing and incubation facilities were needed at several regional 

facilities in order to implement the group’s recommendations. Some of the tribes, in particular, are 

undertaking significant conservation programs without the necessary infrastructure to ensure the 

success of these programs, and are relying on creativity and patch-work solutions. The HSRG 

concluded that the tribal conservation program for Lake Ozette sockeye was well designed and 

efficiently operated and should continue as planned. Steelhead survival rates on the coast are 
Applied Hatchery Reform – Program-Specific Regional Recommendations 53 

currently significantly higher than in Puget Sound. Consequently, this region features the most 

successful steelhead harvest programs of any region the HSRG has reviewed in terms of making a 

significant contribution to harvest. However, the HSRG found that additional investment in adult 

capture facilities for steelhead may be necessary to reduced risks to naturally spawning 

populations. 

Regional Participants - Jim Jorgenson, Hoh Tribe; Joe Hinton, Al Jensen and Caroline 

Peterschmidt, Makah Tribe; John Meyer, National Park Service, Marianna Alexandersdottir, Kyle 

Brakensiek, Willy Eldridge and Sandy Zeiir, NWIFC; Mark Galloway and Kris Northcutt, 

Quileute Tribe; Guy McMinds, Mark Mobbs and Steve Meadows, Quinault Indian Nation; Ray 

Brunson, Joy Evered, Paul Hayduk, Tom Kane, Dan Sorensen and Dave Zajac, USFWS; and 

Martin Chen, Manuel Farinas, Mike Gross, Darrell Mills, Scott Moore, Don Rapelje, Jack 

Tipping, Ron Warren and Scott Williams, WDFW. 

Grays Harbor 

This region includes all the rivers and streams draining into Grays Harbor, including the Chehalis 

River Basin. Thirty-one hatchery programs were reviewed in this region, with 230 specific 

recommendations provided. The HSRG recommended that the managers identify fall, spring and 

summer Chinook stocks in this region; determine the status of these stock components; and 

minimize impacts on natural spawners during adult collections targeting a specific stock or race. 

In addition, the group called for marking and tagging all hatchery Chinook and coho, to determine 

their contribution to harvest and the proportion of hatchery-origin versus natural-origin fish on the 

spawning grounds. The HSRG also recommended the managers take steps to maintain and 

encourage regional coho diversity in this large, geographically diverse region. DNA analysis has 

shown that coho are more genetically diverse than was previously assumed. This will require 

further analysis of regional stock structure and the use of locally-adapted broodstocks. It was 

unclear to the HSRG that there was a need for the chum conservation programs in this region. The 

HSRG suggested an alternative to its Wild Steelhead Management Zones approach for this region 

because many of the Grays Harbor steelhead programs are using locally-derived integrated stocks, 

as opposed to the introduced, segregated stocks that typify steelhead programs in other regions. As 

part of this approach, the HSRG recommended that the managers dedicate WRIA 23 to integrated, 

native stocks only, and dedicate the Wishkah River to only natural production. Grays Harbor 

featured the largest amount of educational and cooperative programs the HSRG has seen. While 

strongly supportive of education programs, the HSRG said these need to exemplify proper 

program design and operations, with clear educational objectives, consistent with conservation 

needs. 

Regional Participants - Lonnie Crumley, Jim Dunn, Joe Durham, Doug Fricke and Dave 

Hamilton, Chehalis Basin Fisheries Task Force; Terry Baltzell, LLTK; Marianna Alexandersdottir 

and Kyle Brakensiek, NWIFC; Steve Meadows, Quinault Indian Nation; and Randy Aho, Rob 

Allan, Gary Bell, Bill Campbell, Rich Ereth, Manuel Farinas, Curt Holt, Kirt Hughes, Ken 

Isaksson, Joel Jaquez, Dave Kloempken, Joe Rothrock, Jack Tipping, Ron Warren and Kevin 

Young, WDFW. 

Conclusions – The Future of Hatcheries 55 

Conclusions 

THE FUTURE OF HATCHERIES 

Because of its Congressional mandate, the Hatchery Scientific Review Group (HSRG) has had a 

unique opportunity over the last four years to intensively study all aspects of salmon and steelhead 

hatchery management in Puget Sound and coastal Washington.34 As a result, the HSRG has 

formulated a number of conclusions about hatcheries and how they should be operated: 

• Hatcheries do have a role in the future, as part of an integrated strategy (alongside 

harvest management and habitat protection/restoration) to meet conservation and harvest 

goals on a sustainable basis. 

• Hatcheries of the future must be different from those of the past. There is both need and 

opportunity to make them better by ensuring that they are more consistent with ecological 

and genetic/evolutionary principles. 

• Sustainability of salmon stocks and harvest opportunities in the Pacific Northwest must be 

based on protection and restoration of natural populations and their habitats. Hatcheries 

cannot be simply regarded as surrogates for lost habitat. 

• Hatchery programs must be planned and operated with consideration of the potential for 

genetic and ecological interactions with natural stocks. 

• Hatcheries are by their nature a compromise, a balancing of benefits and risks to the target 

stock, other stocks, and the environment affected by the hatchery program. A hatchery 

program is the right solution only if it is better, in a benefit/risk sense, than alternative 

means for achieving the same or similar goals. 

• A detailed set of operational guidelines for all hatchery programs should be adopted and 

implemented by the co-managers. These guidelines should address all life stages of 

propagated fish, be derived from an explicit scientific framework, and be tailored to the 

specific purpose (conservation and/or harvest) and type (integrated or segregated) of each 

hatchery program. 

• While all hatchery programs are classified by intent as either integrated or segregated, 

most programs do not achieve the guidelines for proper integration or proper segregation. 

Plans should be developed and implemented for each program to meet those guidelines. 

 

34 The HSRG met monthly for four years, typically for three days, and systematically reviewed over 200 hatchery programs. 
56 Conclusions – The Future of Hatcheries 

• The performance of each hatchery program should be routinely evaluated and reported. 

This evaluation should address consistency with resource goals and coordination with 

other strategies to meet those goals. A system for effective and timely collection, analysis 

and dissemination of data and information must be implemented. 

• A research agenda must be established to guide funding for applied hatchery research in 

the Pacific Northwest. This agenda must be directed towards an increased understanding 

of the benefits and risks from hatchery programs. Knowledge and information gained 

from this research should be incorporated into an explicit and comprehensive scientific 

framework that informs decision-making. 

• Hatchery programs and resource management plans should be consistent with the 

principles of: 1) establishing well-defined goals, 2) being scientifically defensible, and 3) 

using informed decision making. Implications of this include: 

o Hatchery programs must have well-defined goals to direct their operations and 

permit meaningful program evaluation. Once the goals for the resource have been 

established, a scientific rationale for designing, building and/or operating each 

hatchery and hatchery program must be developed to guide the hatchery program 

in achieving its desired outcomes. The use of hatcheries as part of the strategy to 

meet these resource goals must be scientifically defensible. 

o Integrated hatchery programs are linked very closely to a naturally spawning 

stock. For these programs, some broodstock must be derived from the natural 

stock, and broodstock collection and hatchery operations must be consistent with 

allowing the natural environment to drive the adaptation of the combined natural-

/hatchery-origin population. 

o Local adaptation is important for the sustainability of all populations. Thus, stock 

transfers between watersheds are likely to interfere with local adaptation and 

should be avoided. Hatchery broodstock should be managed to foster local 

adaptation. 

o The sizing of hatchery programs (number of fish released) should take into 

account current and expected future conditions of the available habitat (including 

habitat limitations), potential genetic and ecological interactions with natural 

stocks, as well as economic and cultural goals. Hatchery program should always 

be sized to take into account the potential for negative effects on naturally 

spawning stocks and the environment. 

o Hatcheries can impair existing habitat and naturally spawning fish, by virtue of 

their associated structures. In designing hatcheries, particular care should be taken 

so that water intakes, effluent treatment facilities, juvenile release locations and 

adult collection structures do not impair habitat or naturally spawning fish. 
Conclusions – Examples of Successful Hatchery Programs 57 

o Because of inevitable uncertainty, hatcheries should be designed for flexibility 

and their operations adapted to changing environmental conditions, stock status 

and new scientific information. 

o To be successful, hatcheries must develop and maintain an up-to-date and unified 

database that allows resource managers to regularly evaluate and adjust hatchery 

programs, taking into account changes in the status of natural stocks, the carrying 

capacity of receiving waters, ocean productivity and harvest needs. 

o All watersheds are different. Thus, hatchery programs must be designed and 

operated consistent with current and expected future condition of habitats and the 

natural stocks that depend on those habitats. 

o Hatcheries must take into account the programs of other hatcheries occurring in 

the same watershed or region, so that they are complimentary to each other and 

are collectively consistent with resource goals in the watershed or region. 

o The value of hatcheries can no longer be judged solely by the number of fish 

released and returning. Rather, hatchery programs should also be evaluated based 

on: 1) the degree to which they have taken into account the ecosystems they might 

effect, 2) their willingness to adapt to changing conditions in those ecosystems, 

both freshwater and marine, 3) whether they are indeed the “best” strategy for 

meeting resource goals, and 4) whether they are compatible with (i.e., 

complementary to, and integrated with) other strategies. 

EXAMPLES OF SUCCESSFUL HATCHERY 

PROGRAMS 

During 2001–03, the HSRG reviewed over 200 hatchery programs, in ten identified regions of Puget 

Sound and coastal Washington. This systematic, science-based review found a number of programs 

that stand out as examples of hatchery programs that are being conducted in the context of clearly 

articulated goals for the resource, and are the right tool for helping to successfully achieve those goals, 

given the particular circumstances. A few of these programs are presented below as examples of 

hatchery programs that are: 1) helping to recover and conserve naturally spawning populations; 2) 

supporting sustainable fisheries; or 3) providing other benefits, such as education. This is not to say 

that these programs are all without flaw or could not be improved. But they are, overall, in keeping 

with the HSRG’s key principles of operating hatcheries in the context of clear goals, scientifically 

defensible programs, and informed decision making. The HSRG notes that for all integrated hatchery 

programs, success will ultimately depend on good habitat being available to both the hatchery- and 

natural-origin components of the population. 
58 Conclusions – Examples of Successful Hatchery Programs 

Conservation

White River Chinook 

In 1977, fewer than 50 naturally-spawning spring Chinook returned to spawn in the White River. 

Responding to this crisis, a multi-agency recovery effort by the Muckleshoot Indian Tribe, 

Puyallup Tribe of Indians, Washington Department of Fish and Wildlife (WDFW), US Fish and 

Wildlife Service (USFWS), US Forest Service, National Oceanic and Atmospheric 

Administration/National Marine Fisheries Service (NOAA Fisheries), Nisqually Tribe and 

Squaxin Island Tribe developed the White River Chinook Recovery Plan. This plan has used 

captive breeding and multiple juvenile rearing and release strategies to increase the number of 

adults returning to spawn. As a direct result of this program, nearly 1,000 adults returned to spawn 

naturally in each of the last two years. Without intervention, this unique stock of Chinook would 

be extinct today. 

Elwha Chinook 

This cooperative effort between WDFW, the Lower Elwha Tribe and the National Park Service is 

a good example of a long-term gene banking program. It is successfully maintaining a naturally 

spawning population of Elwha Chinook until recolonization of the upper watershed can occur, 

after the scheduled removal of two dams on the Elwha River that have blocked this unique 

Chinook stock’s access to pristine habitat for nearly 100 years. 

Snow Creek Coho 

This conservation program, operated by WDFW, is a well-conceived and science-based plan for 

recovering a threatened, native coho population. Prior to intervention, spawning escapement was 

below 100 fish (and often as low as 20), per year over a 20 year period. Every adult was captured, 

artificially spawned and its eggs were incubated in a hatchery. After that, groups of fry were 

exposed to a variety of rearing and release strategies, to increase the possibility that one or more 

would prove successful. A five-fold increase in adult survival has been realized from these efforts, 

thus avoiding imminent risk of extinction for this stock. 

Lake Ozette Sockeye 

The purpose of this well-designed and efficient program, operated by the Makah Tribe, is to 

achieve the recovery of this Endangered Species Act (ESA)-listed stock by augmenting the riverspawning component of the population and establishing self-sustaining runs in underused habitat 

in Lake Ozette tributaries. This stock is all the more valuable because genetics studies indicate it is 

a native stock, with little or no history of fish transfers into the basin, and no evidence of 

interbreeding. Reintroductions into the tributaries have been increasingly successful in 

reestablishing spawning aggregations. Domestication selection risk is reduced by the small size 

and early life history stage at which the fish are released from the hatchery. 
Conclusions – Examples of Successful Hatchery Programs 59 

Hood Canal Summer Chum Conservation Initiative 

Hood Canal and Strait of Juan de Fuca summer chum experienced a severe drop in abundance in 

the 1980s, and returns decreased to all-time lows of less than 1,000 spawners. The Summer Chum 

Salmon Conservation Initiative (SCSCI) is a well-designed, well-conducted program that appears 

to be achieving its goals of recovering these ESA-listed fish. Adult returns have increased 

substantially in chum streams across the program area. SCSCI is an example of a successful 

conservation program and partnership among state, tribal, private, and federal entities. Partners 

include WDFW, the Point No Point Treaty Council (PNPTC), Hood Canal Salmon Enhancement 

Group, Long Live the Kings (LLTK), NOAA Fisheries and USFWS. The program, which may 

serve as a prototype for similar efforts in the future, has met the HSRG’s first key principle of 

beginning with a solid goal setting process. The plan also calls for collecting and analyzing the 

data necessary to evaluate the program’s success. Ensuring complete monitoring and evaluation of 

this program will be crucial to meeting the HSRG’s second and third principles—scientific 

defensibility and informed decision making. 

Hamma Hamma Steelhead 

Hood Canal winter steelhead numbers began to show a serious decline two decades ago. The 

number of naturally spawning adults has remained precipitously low since then. A partnership 

between LLTK, HCSEG, NOAA Fisheries, PNPTC, USFWS, and WDFW, this well-designed and 

scientifically-sound recovery program for Hamma Hamma winter steelhead features the only 

captive brood and two year-old smolt programs in Washington state. Fish for this program are 

thought to be indigenous, with little or no history of stock transfers, introductions, or artificial 

propagation. The rearing program includes exercise for the captive brood fish, and smolts are fed 

on a schedule that mimics nature. Initial results indicate that the program has a good chance of 

achieving the goals for the stock, though low ocean survival trends for steelhead from this region 

may make this more difficult. If this program is successful in the long-term, it could serve as a 

model for steelhead conservation programs. 

Harvest

Green River Hatchery Fall Chinook 

The Washington Department of Fish and Wildlife’s Green River Hatchery has propagated 

Chinook and provided harvest on these fish for over 100 years. Harvest goals are consistently 

achieved within Washington waters. Significant numbers of natural-origin adults are used each 

year for broodstock, integrating this hatchery stock with the natural stock. As a result, the hatchery 

stock also contributes to meeting natural production goals for fall Chinook in a compromised 

habitat. 
60 Conclusions – Examples of Successful Hatchery Programs 

Tulalip Bay Hatchery Chum 

This hatchery program, operated by the Tulalip Tribes and directed at a stock that is kept 

genetically segregated from natural stocks in the region, meets its goal of high harvest rates, 

without apparent adverse effects on other regional stocks. The hatchery fish are marked and 

monitored, to ensure that straying into adjacent watersheds does not have an adverse affect on 

naturally spawning stocks. 

Wynoochee Winter Steelhead 

This program, operated by WDFW is a mitigation program for the Wynoochee River Dam. Fish 

for this WDFW program originated from—and are kept genetically integrated with—native 

Wynoochee River fish, unlike the non-local, segregated stocks that typify steelhead programs in 

other regions. The program is being operated consistent with short- and long-term stock goals, and 

is providing harvest benefits. The likelihood of attaining these goals is high, due to relatively good 

survival of coastal steelhead stocks in recent years. The HSRG recommended that the managers 

monitor the natural spawning population and take steps to reduce hatchery-origin fish spawning 

naturally by following HSRG spawning and integrated population management guidelines. 

Education

Issaquah Hatchery 

This Washington Department of Fish and Wildlife hatchery has become a cherished asset to the 

urban community in which it is located—Issaquah, Washington. A dedicated group of volunteers 

called Friends of Issaquah Salmon Hatchery (FISH) provides both casual visitors and organized 

classes with detailed information about salmon life history, species identification, migration 

patterns, the importance of functional habitat, and other environmental education topics. Signs, 

interactive displays, and viewing areas for observing daily operations are used heavily by the 

public. The hatchery is an integral part of Issaquah’s annual Salmon Days festival, when over 

300,000 visitors tour the facility during a single weekend. 

Pipers Creek Chum, Carkeek Park 

Located in a highly urbanized part of Seattle, this is another example of a grass-roots program 

whose efforts have expanded into a productive, environmental-based cooperative between local 

community supporters and public agencies. The program began as an effort to reintroduce salmon 

to a creek where they had been extirpated for several decades. The program has grown into a fullyfunctional, environmental education center. 

Cooperative Programs 

The managers are fortunate to have the dedication, energy and resourcefulness of many nongovernmental, educational and citizens groups to assist them in meeting conservation, harvest and 
Conclusions – Examples of Successful Hatchery Programs 61 

other goals for Puget Sound and coastal Washington salmonids. Fourteen Regional Fisheries 

Enhancement Groups, dozens of Salmon in the Classroom programs, a number of not-for-profit 

organizations, and hundreds of private citizens and volunteers augment and expand what the state, 

tribal and federal operators of the hatchery system are able to do on behalf of the area’s salmonids. 

In this way, their efforts go beyond meeting educational goals, to in fact playing an essential role 

in meeting conservation and harvest goals for the resource. 

Appendices 

Scientific Framework - Contents A-1 

A. Scientific Framework for the Artificial 

Propagation of Salmon and Steelhead 

CONTENTS

OVERVIEW............................................................................................................................................. A-3

CHAPTER 1. PURPOSES AND TYPES OF HATCHERY PROGRAMS.......................................................... A-5

1.1 Purposes of Hatchery Programs ......................................................................................................A-6

1.1.1 Conservation.............................................................................................................................................A-6

1.1.2 Harvest......................................................................................................................................................A-6

1.1.3 Education and Research............................................................................................................................A-6

1.2 Types of Hatchery Programs...........................................................................................................A-6

1.2.1 Genetically Integrated Programs...............................................................................................................A-7

1.2.2 Genetically Segregated Programs.............................................................................................................A-8

CHAPTER 2. HATCHERY PROGRAMS IN THE ECOSYSTEM CONTEXT: THE REGIONAL APPROACH ... A-9

2.1 Receiving Habitat............................................................................................................................A-9

2.1.1 Quality of the Receiving Environment ...................................................................................................A-10

2.1.2 Complexity and Connectivity of Receiving Environment ......................................................................A-10

2.1.3 Quantity of Receiving Habitat ................................................................................................................A-10

2.1.4 Temporal Climatic Changes Affecting Habitat.......................................................................................A-10

2.2 Habitat – Current Status and Short and Long-term Goals.............................................................A-11

2.3 Effects of Hatchery Operations on Habitat and Ecological Function............................................A-11

2.4 Effects of Hatchery Structures on Fish..........................................................................................A-13

2.4.1 Downstream Fish Passage ......................................................................................................................A-13

2.4.2 Upstream Fish Passage ...........................................................................................................................A-13

2.4.3 Volitional Entry to Hatchery...................................................................................................................A-13

2.4.4 Instream Flow.........................................................................................................................................A-14

2.4.5 Discharge Quality ...................................................................................................................................A-14

2.4.6 Modification of Riparian Areas..............................................................................................................A-14

2.4.7 Harassment from Humans ......................................................................................................................A-14

CHAPTER 3. HATCHERY PROGRAMS IN THE SPECIES/POPULATION CONTEXT ................................ A-15

3.1 Biological Significance .................................................................................................................A-15

3.1.1 Genetic Diversity....................................................................................................................................A-15

3.1.2 Local adaptation .....................................................................................................................................A-16

3.1.3 Genetic Structure ....................................................................................................................................A-17

3.2 Viability.........................................................................................................................................A-18

3.2.1 Effective population size ........................................................................................................................A-18

3.2.2 Age class structure..................................................................................................................................A-19

3.2.3 Trends and variance in abundance over time..........................................................................................A-19

CHAPTER 4: EFFECTS OF HATCHERY OPERATIONS ON HARVEST AND CONSERVATION OF THE 

PROPAGATED STOCK .......................................................................................................................... A-21

4.1 Hatchery Operations as they affect the genetic characteristics of the Propagated Stock...............A-21

4.1.1 Changes in Biological Significance ........................................................................................................A-22

4.1.2 Changes in Viability ...............................................................................................................................A-25
A-2 Scientific Framework - Contents 

4.2 Hatchery Operations as they affect the non-genetic characteristics of the Propagated Stock .......A-27

4.2.1 Changes in Physiology ...........................................................................................................................A-28

4.2.2 Changes in Morphology .........................................................................................................................A-29

4.2.3 Changes in Behavior...............................................................................................................................A-32

4.2.4 Changes in Fish Health...........................................................................................................................A-33

4.2.5 Nutrition .................................................................................................................................................A-34

4.3 Desired Qualities of Propagated Fish ............................................................................................A-35

4.4 Achieving Harvest Goals through the Hatchery Environment and Operational Protocols............A-37

4.4.1 Segregated Harvest Programs.................................................................................................................A-38

4.4.2 Integrated Harvest Programs ..................................................................................................................A-39

4.5 Achieving Conservation Goals through the Hatchery Environment and Operational Protocols...A-41

4.5.1 Segregated Conservation Programs........................................................................................................A-42

4.5.2 Integrated Conservation Programs..........................................................................................................A-43

CHAPTER 5: EFFECTS OF HATCHERY FISH ON HARVEST AND CONSERVATION OF OTHER STOCKS AND 

SPECIES................................................................................................................................................ A-46

5.1 Genetics Effects (including changes in biological significance and viability) ..............................A-46

5.1.1 Changes in Biological Significance ........................................................................................................A-46

5.1.2 Changes in Viability ...............................................................................................................................A-48

5.2 Ecological Effects (predation, competition, fish health, disease, nutrient enhancement)..............A-48

5.3 Harvest Effects..............................................................................................................................A-49

5.4 Actions to Achieve Desired Outcome ...........................................................................................A-50

5.4.1 Genetics Actions.....................................................................................................................................A-50

5.4.2 Ecological Actions..................................................................................................................................A-50

5.4.3 Harvest Actions ......................................................................................................................................A-52

CHAPTER 6: MONITORING AND EVALUATION: MANAGING HATCHERY PROGRAMS FOR 

ACCOUNTABILITY AND SUCCESS ....................................................................................................... A-53

6.1 Evaluating Hatchery Success.........................................................................................................A-53

6.2 Factors Necessary for a Successful Monitoring and Evaluation Program.....................................A-54

6.2.1. Decision Making at the Implementation, Effectiveness, Performance and Validation/Research 

Levels..............................................................................................................................................................A-54

6.2.2. Tools for Evaluating Hatchery Performance..........................................................................................A-55

6.2.3. An Accessible and Unified Data-Gathering System..............................................................................A-58

SOURCES AND REFERENCES ............................................................................................................... A-59
Scientific Framework - Overview A-3 

OVERVIEW

Early in the project’s first year (2000), the Hatchery Scientific Review Group (HSRG) agreed that 

hatchery programs should no longer be seen as surrogates for lost habitat. Instead, hatchery programs 

must be viewed as tools that can be managed as part of an integrated strategy to meet watershed or 

regional resource goals, in concert with actions affecting habitat, harvest rates, water allocation and 

other factors. Using current scientific knowledge, and consideration of the benefits and risks to all 

affected stocks, a hatchery program should be conducted only if it is deemed the best available tool for 

achieving those goals. 

Under this model, healthy, available habitat is essential to an effective hatchery program. In addition, 

resource managers have to consider whether a hatchery program is the best means to achieve the goal, 

once the risks and benefits from the program are considered. To scientifically evaluate the hatcheries 

in Puget Sound and coastal Washington in this new context, the scientists recognized the need for a 

scientific foundation for their work. 

The HSRG’s scientific framework is the foundation for evaluating the benefits and risks of hatchery 

programs in Puget Sound and coastal Washington. Its purpose is to provide a detailed review and 

evaluation of the scientific literature as justification for the recommendations developed through the 

Regional Review Process that occurred in 2001-2003. The results of this review effort are detailed in 

three separate volumes (Appendix I) and are available at www.hatcheryreform.org. 

The framework informs all the HSRG’s tools, processes and recommendations and provides the 

scientific approach for achieving Principle 2: Scientific Defensibility.35 The framework organizes the 

current state of knowledge, about how actions associated with hatcheries affect the environment and 

fishery resources, around six key topics: 

1) Hatchery Programs: Definitions of Purpose and Type 

2) Hatcheries in the Ecosystem Context: The Regional Approach 

3) Hatcheries in the Populations/Species Context 

4) Effects of Hatchery Operations on Harvest and Conservation of the Target Stock 

5) Effects of Hatchery Fish on Harvest and Conservation of Other Stocks and Species 

6) Monitoring and Evaluation: Managing Hatchery Programs for Accountability and Success 

The framework begins by classifying hatcheries in terms of their purpose and type. This classification 

reflects a new way of thinking about and defining hatcheries, and provides a foundation for describing 

and reviewing them in a systematic and scientific manner. The next two topics deal with the effects of 

hatcheries on the ecosystem and on other fish populations. Topics four and five address the effects of 

 

35 See Applied Hatchery Reform chapter, Principles and System-wide Recommendations 
A-4 Scientific Framework - Overview 

hatcheries on resource goals for the target stock and other stocks. The final topic deals with 

accountability through monitoring and evaluation. 

The framework was first released to the public in December 2000, after extensive peer and stakeholder 

review and prior to development of the review tools and inception of the regional review process. It 

has subsequently been updated to incorporate recent scientific and technical information that became 

available or was developed in 2001-2003 through the review process. 
Scientific Framework - Purposes and Types of Hatchery Programs A-5 

CHAPTER 1. PURPOSES AND TYPES OF HATCHERY 

PROGRAMS

Hatcheries have propagated Pacific salmon and steelhead in the Pacific Northwest for nearly 130 years 

(reviewed by Lichatowich 1999). The first hatchery in the Puget Sound area was established on the 

Baker River in 1896. Most hatcheries in Puget Sound and coastal Washington have been in operation 

for decades and were built to produce fish for harvest, compensating for declines in naturally 

spawning populations. Hatchery-origin fish are important to the North Pacific recreational and 

commercial fishing economy and to meeting tribal treaty harvest needs. 

The abundance and productivity of salmon and steelhead stocks has varied throughout the period that 

records have been maintained. For example, in 1977 returns of adult salmon and steelhead began to 

decline precipitously. These declines occurred despite increasing numbers of hatchery fish released 

during the preceding 20 years. This decline is presumed to be related to a major decadal shift in ocean 

conditions, associated with increased marine temperatures in the northeast Pacific Ocean (Cooper and 

Johnson 1992, Beamish and Bouillon 1993, Lichatowich 1993, Olsen and Richards 1994, Cramer 

2000). Increased urbanization and poor land-use practices also contributed to declines in the 

abundance of Pacific salmon and steelhead. These declines ultimately led to the 1999 threatened 

listing of Puget Sound fall Chinook and Hood Canal summer chum salmon under the federal 

Endangered Species Act (or ESA, Fed. Reg. 1999). 

Fishery scientists have identified hatcheries as one of the factors contributing to declines in abundance 

of naturally-spawning salmon populations (e.g., Waples 1991; Hilborn 1992; Reisenbichler and Rubin 

1999; Levin et al. 2001). For example, some facilities have negatively affected natural populations by 

inhibiting freshwater migrations of adult and juvenile fish and removing sexually mature adults for 

broodstock. In addition, ecological and genetic interactions between hatchery- and natural-origin fish 

have been postulated as factors affecting the viability of natural populations. The once-common 

practice of transferring and releasing hatchery fish between watersheds or rivers is now recognized as 

a potential risk to natural populations. 

As a consequence of the ESA listings, federal, state and tribal fishery managers must demonstrate that 

their hatcheries do not present unacceptable risks to naturally spawning populations. Harvest 

restrictions to protect natural populations, including compliance with ESA, limit the ability of 

commercial, tribal and recreational fishers to harvest relatively abundant fish from successful hatchery 

programs. Minimizing these risks, while at the same time maintaining sustainable fisheries, presents a 

major challenge to fishery managers. 

The HSRG has concluded that in order to review benefits and risks of hatchery programs in a 

systematic and scientific manner, each program must explicitly be defined in terms of its purpose and 

type. The purpose of the program spells out what the hatchery program is expected to accomplish in 

relation to goals set for the resource (e.g., harvest and/or conservation). The type of program defines 

its genetic management goal. This goal defines the relationship between the propagated stock and the 

natural stock (i.e., integrated or segregated). The purpose and type of each hatchery program must be 

defined before program components can be developed or evaluated. 
A-6 Scientific Framework – Purposes and Types of Hatchery Programs 

1.1 Purposes of Hatchery Programs

The HSRG recognizes two primary purposes of hatchery programs: 1) help conserve naturally 

spawning populations and their inherent genetic resources, and 2) provide fish for harvest. Many 

hatchery programs are designed to provide both harvest and conservation benefits. Other purposes of 

hatchery programs include scientific research, education, and providing cultural benefits, particularly 

for American Indian tribes. Each of these identified purposes is briefly described below. 

1.1.1 Conservation 

Hatchery programs with conservation goals vary substantially in size and scope. The ultimate goal 

of such programs is to conserve natural populations and their genetic resources. Captive breeding 

of endangered populations is one extreme example (Schiewe et al. 1997). On the other hand, a 

hatchery program propagating a native population for harvest may also have conservation 

objectives, if a long-term goal is to conserve the genetic resources of that population. 

Conservation goals impose additional operational requirements on hatcheries, as compared to 

simply producing fish for harvest. However, such conservation-motivated objectives may also 

help support sustainable fisheries in the long-term. Consequently, the HSRG recognizes 

conservation as a very important purpose of hatcheries, both from the standpoint of conserving 

genetic resources and supporting sustainable fisheries. 

1.1.2 Harvest 

Most hatchery programs in Washington state were developed for the single purpose of producing 

fish for harvest. That harvest can take place in recreational, commercial, ceremonial, and 

subsistence fisheries. Hatchery programs also provide fish for indicator/index stock programs that 

inform and direct harvest management. Harvest continues to be the primary purpose for the 

majority of hatchery programs. However, simply producing fish for harvest may not be sufficient 

to meet long-term resource goals; rather, hatcheries must be managed in a manner that helps 

support and maintain sustainable fisheries, while minimizing negative impacts to naturally 

spawning populations. 

1.1.3 Education and Research 

Hatcheries are in a unique position to provide educational and research opportunities because they 

represent “living laboratories” where the biology of the fish can be studied and populations 

monitored. As a place where citizens can see and work with salmonids from their egg to adult 

stages, each hatchery has the potential to serve as a venue for community involvement and 

education, and a source of data and information about salmonid biology, fisheries and ecology. 

1.2 Types of Hatchery Programs

Hatchery programs for Pacific salmon and steelhead can be classified as either integrated or 

segregated based on the genetic management goals and protocols for propagating a hatchery 
Scientific Framework - Purposes and Types of Hatchery Programs A-7 

 

broodstock. Hatchery programs are classified as genetically integrated if a principal goal is to manage 

the hatchery broodstock as a genetic component of a naturally-spawning population such that the 

natural environment drives the adaptation of the composite population made up hatchery and natural 

fish. Hatchery programs are classified as genetically segregated if the broodstock is propagated as a 

reproductively discrete population primarily, if not exclusively, with adult returns back to the 

hatchery. In segregated programs, little or no gene flow should occur from a naturally spawning 

population to the hatchery broodstock. In the context of managing salmon and steelhead hatcheries, all 

programs should be either genetically integrated or segregated relative to naturally spawning 

populations. This defines the intent of the program, therefore, no program can be classified as both or 

intermediate. 

1.2.1 Genetically Integrated Programs 

Hatchery programs can be classified as integrated if: a) a principal management goal is to 

minimize genetic divergence between the hatchery broodstock and a naturally spawning 

population; and b) natural-origin fish are regularly included in the hatchery broodstock at a level 

sufficient to prevent such genetic divergence. In an idealized integrated program, natural- and 

hatchery-origin fish simply represent two genetically-equal components of a common gene pool 

within the watershed where adults are trapped for broodstock and progeny fish released. A 

fundamental goal of an integrated program is to minimize genetic changes resulting from artificial 

propagation; thereby reducing genetic risks of hatchery-origin fish to a naturally spawning 

population.36 Another goal is for hatchery fish to represent a potential genetic repository for the 

natural population, in case of a major decline in abundance (e.g., as a result of stochastic 

environmental events, over-fishing, etc.). Under this idealized integrated concept, the hatchery 

represents an artificial extension of the natural environment, thereby increasing the total 

reproductive capacity of the target population. This increased reproductive capacity can 

conceptually yield both harvest benefits to fishers and demographic benefits to the target 

population. However, integrated programs will invariably represent trade-offs between ease of 

culture and achievement of genetic management goals. 

An integrated hatchery program does not imply that gene flow from the hatchery component into 

the naturally spawning component necessarily occurs or is desired; on the contrary, the goal of an 

integrated program is not for hatchery-origin fish to necessarily spawn naturally but, rather, to 

maintain the genetic characteristics of a natural population in the hatchery broodstock. This goal 

necessitates a minimum amount of gene flow from the natural population to the hatchery 

broodstock each generation, while controlling or restricting gene flow from the hatchery 

component to the natural component.37 Deliberate gene flow from the hatchery broodstock to a 

natural population relates strictly to the purposes and intended benefits of hatchery-propagated 

fish after release (e.g. restoration or recovery of natural populations) and not directly to the genetic 

management goals for the hatchery broodstock. Indeed, if the natural population component is 

self-sustaining and can supply natural-origin fish to the hatchery broodstock each year—albeit, 

36 See this Scientific Framework’s section on domestication. 

37 See Appendix B, Emerging Issues paper on Integrated and Segregated hatchery programs. 
A-8 Scientific Framework – Purposes and Types of Hatchery Programs 

without reducing natural productivity below a level necessary for the natural population to sustain 

itself—then no demographic need would exist for hatchery fish to spawn naturally. 

1.2.2 Genetically Segregated Programs 

Hatchery programs are classified as segregated if the hatchery population is propagated as a 

genetically discrete or segregated population relative to naturally spawning populations. The 

principal goal of a segregated broodstock program is to create a new, hatchery-adapted population 

to meet co-manager needs for harvest or other purposes. Hatchery broodstocks (and programs) are 

considered genetically segregated if the broodstock is maintained primarily or exclusively from 

adults returning back to the hatchery. As a consequence, little or no gene flow from a natural 

population to the hatchery broodstock is intended to occur in a segregated program. 

Segregated hatchery broodstocks are expected to diverge genetically from the source founding 

population or local natural populations, due to genetic drift and potential domestication effects. 

Moreover, segregated hatchery broodstocks are often selectively bred for particular traits (e.g., 

early run-timing) to facilitate ease of culture and/or to help achieve harvest benefits. Segregated 

programs are usually managed in a way that maximizes productivity or efficiency of hatchery 

operations. Natural spawning of returning adults from a segregated hatchery program is usually 

considered highly undesirable; because of the genetic risks those fish pose to natural populations. 

In addition, hatchery-origin fish from segregated programs may pose significant ecological risks if 

those fish directly compete with, or prey upon, natural-origin fish. Indeed, properly managed 

segregated programs must ensure that hatchery-origin fish do not stray or spawn naturally, or do 

so at very low rates to minimize biological risks to natural populations. In this context, not only is 

the broodstock segregated genetically from a natural population, but released fish from that 

broodstock must be ecologically and genetically segregated from natural-origin fish as much as 

possible in the natural environment. Consequently, segregated programs usually represent major 

trade-offs between maximizing operational efficiency of the hatchery program and minimizing 

biological risks to naturally spawning populations. 
Scientific Framework - Hatchery Programs in the Ecosystem Context A-9 

CHAPTER 2. HATCHERY PROGRAMS IN THE ECOSYSTEM 

CONTEXT: THE REGIONAL APPROACH

Hatcheries can no longer be regarded as surrogates for lost habitat. In operating hatcheries, 

consideration must be given not only to the receiving habitat in which they operate but also to the 

hatchery propagated and naturally-spawning fish that depend on the existing habitat. In addition, 

hatcheries must take into account the programs of other hatcheries occurring in the same watershed or 

region. Only in this way will adverse interactions between salmonid stocks in the watershed or region 

be recognized. Hatcheries also have the potential to impair existing habitat and naturally-spawning 

fish populations by virtue of their associated structures and by the inappropriate sizing of their 

programs. In designing hatcheries and their programs, these factors have, therefore, to be borne in 

mind. 

No longer can the value of hatcheries and their programs be judged solely by the size of their releases 

and returns. Rather, hatcheries and their programs will also have to be evaluated on the degree to 

which they have taken into account the ecosystem on which they might have an impact and on their 

willingness to adapt to changing conditions in the ecosystem, both freshwater and the marine. The 

fitness of naturally spawning populations, their productivity, and the numbers of adult salmon 

returning to individual watersheds, ultimately depend on the natural habitat and on climatic conditions 

affecting its productivity. 

Therefore, it is appropriate to review hatchery programs in Puget Sound and coastal Washington using 

a regional approach, taking into account the nature of the watersheds in which the programs occur and 

the goals set for the programs by the managers. Each watershed or region differs significantly in the 

quality and quantity of habitat, the status of salmonid stocks within those regions, and the regional 

goals. 

A review of the Puget Sound/coastal Washington hatchery system as a whole would result in general 

recommendations not suited to regional differences in habitat and management goals. Decision 

making program-by-program or hatchery facility would fail to consider how best to use the hatchery 

system as a whole and would fail to take into account cumulative, regional effects. 

2.1 Receiving Habitat

Healthy habitat that can support the life cycle of a salmon population is necessary to the success of any 

hatchery program. The environmental conditions experienced by hatchery fish following their release 

vary depending upon when and where they are released. The health and viability of hatchery 

populations are dependent upon quality, complexity and connectivity, and quantity of the receiving 

habitat; and temporal climatic changes affecting habitat. 
A-10 Scientific Framework - Hatchery Programs in the Ecosystem Context 

2.1.1 Quality of the Receiving Environment 

The quality of the receiving environment refers to the condition of the habitat available to 

hatchery-origin fish following their release from the hatchery (Bjornn and Reiser 1991; Reeves et 

al. 1991; Doppelt et al. 1993; Beechie et al. 1994; Bilby et al. 1996; Mobrand et al.1997). 

Significant departures from optimal habitat quality conditions may result in failure to meet natural 

productivity requirements. Factors affecting the quality of the receiving environment vary by 

habitat type (freshwater, estuarine, marine near-shore, and marine off-shore). Among the factors to 

consider are channel stability, riparian condition, habitat diversity, water flow, sediment load, 

nutrient load, obstructions, oxygen, chemicals, pathogens, temperature, competition, predation, 

food, and salinity (Lichatowich et al. 1995). 

2.1.2 Complexity and Connectivity of Receiving Environment 

The complexity and connectivity of the receiving environment affect survival and life history 

diversity of hatchery populations. Life history diversity, which is the species’ solution to a 

dynamic environment, is determined both by genetic and phenotypic traits and by the ability of the 

habitat to support multiple life history pathways (Mobrand et al. 1997). The latter is determined by 

the patterns of connected, high quality habitat segments (see also 2.3 and 3.1.3). 

2.1.3 Quantity of Receiving Habitat 

The abundance potential of a hatchery population is in part a function of the quantity of food and 

space available in the receiving natural habitat (Hall and Field-Dodgeson 1981; Nickelson et al. 

1986; Hunter 1991; Reeves et al. 1991; Nickelson et al. 1993). The availability of food and space 

affects the survival of hatchery fish through density-dependent mechanisms such as competition 

and predation. Generally, survival decreases with increasing population density. Density is 

determined by the quantity of key habitat, the abundance of hatchery fish and their rate of 

dispersal (Lestelle et al. 1996). 

The present hatchery system for Pacific salmon was developed to meet fishery demands and 

compensate for losses in salmonid habitat. The hatchery goal has traditionally been to produce 

increasingly higher numbers of fish that would grow to harvest size in an oceanic ecosystem, 

believed to be constant and near limitless in its capacity to provide food and space for hatchery 

salmon. The modern view of the ocean ecosystem is, however, one characterized by ecological 

uncertainty (Mahnken et al. 1998). 

2.1.4 Temporal Climatic Changes Affecting Habitat 

Decadal and inter-annual changes in productivity of salmon populations are an increasingly well 

recognized phenomenon, and it apparently reflects the stochastic and deterministic effects of 

environmentally driven changes in salmonid habitat. Studies on abundance of salmonid stocks in 

widely separate geographic areas over time have indicated oceanic conditions are primarily 

responsible for changes in annual returns of adult salmon (Cooper and Johnson 1992, Beamish and 

Bouillon 1993, Lichatowich 1993, Olsen and Richards 1994, Cramer 2000). The way in which 
Scientific Framework - Hatchery Programs in the Ecosystem Context A-11 

physical, chemical, and biological processes in the ocean impact fish populations and production 

trends is reasonably well known. 

2.2 Habitat – Current Status and Short and Long-term 

Goals 

One of the factors to be taken into account in reviewing hatchery programs is the status of the 

freshwater habitat into which the hatchery fish are to be released. Both the current and the future status 

of the habitat should be considered. Silt free incubation gravels and cool, stable incubating water are 

necessary for the survival of salmon embryos. Flowing streams with complex structure, riparian 

vegetation, seasonal flow stability, and productive estuaries are necessary to the survival of juvenile 

salmon. Flowing streams are also necessary for the successful passage and spawning of returning 

mature adults. In reviewing hatchery programs, several categories of freshwater habitat are recognized. 

These freshwater habitat categories are defined in some detail in the HSRG’s Benefit-Risk Tool.38 

In addition, there is increasing evidence that the size of hatchery releases should take into account 

changing marine conditions. Based on an analysis of climatic trends and the productivity of salmon 

fisheries in the North Pacific, Beamish and Bouillon (1993) noted that the strategy of releasing large 

numbers of artificially reared smolts during a period of decreasing marine survival is not scientifically 

defensible. Although harvest rates are generally scaled back when the abundance or productivity of 

naturally-spawning stocks is low and regime shifts become evident, hatchery production is not scaled 

back. Given that the carrying capacity of the ocean has a primary impact on salmon returns, it is 

eminently sensible that hatchery releases should be reduced during periods of poor ocean survival to 

protect naturally-spawning fish. Furthermore, regime shifts, or major changes in ocean productivity, 

are becoming increasingly predictable and therefore should be a consideration in managing hatchery 

programs. 

2.3 Effects of Hatchery Operations on Habitat and 

Ecological Function

The productivity of an ecosystem (e.g., a receiving habitat) can be gauged on the basis of the 

heterogeneity of life and habitat within it and by the biomass it supports. The productivity of the 

system is a function of the collection of biological, chemical, and physical factors/processes that 

govern the flow of energy and material through it. The ecological function of a particular event in an 

ecosystem is the effect that the event has on the system. As described below, hatchery structures and 

operations can affect ecological function. 

The functioning of an ecosystem is important because it affects the productivity of the system (Golley 

1993; Norton 1994; Haskell et al. 1992; Karr 1992). In this regard, the riparian environment is of 

primary importance to the proper functioning of riverine, aquatic ecosystems, and to resident or 

migratory salmonids. The structural complexity and species diversity of this habitat determine both the 

 

38 See Appendix G. 
A-12 Scientific Framework - Hatchery Programs in the Ecosystem Context 

carrying capacity and quality of smolts produced in (or introduced into) these habitats. Vegetation 

provides shade, moderates stream water temperatures, and provides cover in the form of large woody 

debris and stream bank overhangs created by roots. Riparian vegetation stabilizes stream banks, binds 

soil particles, holds water in the flood plain, and provides a source of carbon and nitrogen for the 

organisms upon which juvenile salmon feed. Rocks and gravel substrate provide structure and features 

around which salmon establish territory. These complex, dynamic ecosystems are essential for 

maintaining adaptive behavioral patterns and moderating stress in juvenile salmon. 

Nutrients released from hatcheries may affect the productivity of systems into which they drain, the 

resulting benefit or harm being based on the nutrient loading that occurs. Also, salmon released from 

hatcheries may serve as prey for a large number of native and non-native fishes. In addition, salmon 

produced in hatcheries may increase the productivity of a particular drainage by virtue of the nutrients 

brought back from the sea and released to the water and riparian environment from their carcasses 

following spawning (Bilby et al. 1996). Returning adult salmon are a unique vector for the delivery of 

marine nutrients into the freshwater ecosystem. The importance of these nutrients to consumers such 

as raccoons, bear, eagles, and even man, has been recognized for some time. Recent research also 

suggests that a significant portion of nitrogen in plants and animals in streams where adult salmon are 

abundant is derived from those returning adults (Mathison 1988, Kline et al. 1993). 

Marine-derived nutrients from returning adult salmon have been found to provide a significant 

contribution to riparian vegetation and even old growth forests (Reimchen 1994, Bilby et al. 1996). In 

streams in interior British Columbia, Johnston et al. (1997) found that where salmon carcasses were 

abundant, up to 60% of the nitrogen in benthic insects was derived from the carcasses. They also 

found that juvenile salmon show higher growth rates in streams after adult salmon spawn than in 

streams without spawning adults. Use of hatchery salmon carcasses as a source of these marine 

derived nutrients was found to increase the density of age 0+ coho salmon and age 0+ and l+ steelhead 

in small southwestern Washington streams (Bilby et al. 1998). Any structures (such as hatchery weirs; 

see below) or practices that reduce the nutrient influx from salmon carcasses may reduce the 

productivity of the system. 

The value of nutrient input has been demonstrated in British Columbia where artificial fertilization has 

been (and is being) used to enhance salmonid production in nutrient-deficient systems. In British 

Columbia, lake fertilization has been used in place of hatcheries for enhancing sockeye production 

(Hyatt and Stockner 1985), an approach that is currently also been used for kokanee. In addition, 

following on the earlier stream fertilization studies of Stockner and Shortreed (1978) and Mundie et al 

(1983, 1991), stream fertilization is being tested, with promising results, as an interim measure for 

recovering certain natural salmonid stocks that have been in decline for reasons not related to hatchery 

practices (McCubbing and Ward 2000, Larkin and Slaney 1996). 

Hatchery operations may impact the community structure of an ecosystem. When hatcheries release 

large numbers of fish, the capacity of the ecosystem to handle the released juveniles or returning 

adults may be exceeded. Alternately, when hatchery fish are released outside their historic range they 

may cause new competition and predation impacts to established communities. The end result may be 

increased competition between naturally-spawning and hatchery propagated fish for rearing or 

spawning areas and the displacement of naturally-spawning fish (RASP, 1992; see also Chapter 5). 
Scientific Framework - Hatchery Programs in the Ecosystem Context A-13 

2.4 Effects of Hatchery Structures on Fish

The physical structures of hatcheries are located in riparian areas. Sufficient infrastructure, space, and 

water are required for incubation of eggs, juvenile rearing, and adult collection, maturation and 

spawning. Some hatchery structures have severe adverse effects on naturally-spawning fish 

populations by creating (for example) obstacles to migration, changes in in-stream flows, and loss of 

water quality. Most effects of hatchery structures are quantifiable. Water quality of hatchery effluent 

and changes in in-stream flows are relatively easy to measure. Impassible barriers to migration are 

identifiable and delays in migration can be estimated. Hatchery structures may affect naturallyspawning fish and the environment in various ways. 

2.4.1 Downstream Fish Passage 

Hatcheries require sufficient water for juvenile rearing and adult attraction. Water is usually drawn 

from an adjacent stream via pumps or gravity. Improperly designed and maintained water intakes 

can impinge migrant or resident juveniles (Pearce and Lee 1991, Washington Department of Fish 

and Wildlife 2000). Improperly sized screens can allow natural-origin juveniles to enter and be 

trapped in hatchery rearing vessels. Many hatchery water intakes were designed over 40 years ago. 

These often do not meet current design standards for screen mesh size and approach velocity. 

Adequate maintenance of properly designed intakes is also important. 

2.4.2 Upstream Fish Passage 

Adult salmonids have a high fidelity for returning to their natal rearing areas to spawn and will 

return to their respective hatcheries or native spawning grounds if unimpeded (Brannon et al. 

1984, Van der Haegen and Doty 1995). Fish collected for broodstock require sufficient and unique 

flows for attraction and separation into the hatchery, but fish intended to spawn naturally need to 

be able to pass through hatchery structures, such as intake dams or adult weirs, in a timely manner 

(Clay 1961, Fleming and Reynolds 1991). Identification and passage of natural-origin and 

hatchery salmon is important to maximize use of natural habitat and minimize “broodstock 

mining”. Allowing separation of hatchery- and natural-origin adults to their respective natal 

rearing areas is also important to minimize negative ecological and genetic interactions (see 

sections 1.2.1, 1.2.2, 2.3, 4.1, 5.1 and 5.2). 

2.4.3 Volitional Entry to Hatchery 

Hatcheries can attract returning adults to an artificial stream created by water passing through 

hatchery rearing containers. The unique scent of attraction of the hatchery effluent can selectively 

influence the return of hatchery adults (Brannon 1982, Dittman et al. 1996). If attraction is 

sufficient to selectively influence the return of only hatchery fish, negative genetic and ecological 

interactions between natural-origin and hatchery-origin adults can be reduced (see sections 4.1,5.1 

and 5.2.) 
A-14 Scientific Framework - Hatchery Programs in the Ecosystem Context 

2.4.4 Instream Flow 

Hatcheries usually divert water from adjacent streams for fish cultural purposes. Diverted water is 

often returned at significant distances downstream. Water diversion through hatcheries from 

relatively small streams can significantly reduce the amount of water for juvenile rearing and 

upstream adult migration between the area of intake and discharge. In small streams, flows in the 

section of stream between the intake and discharge should not be reduced so that upstream 

migration by adult salmonids is not prevented or delayed during the usually dry fall season (Bell 

1986, Stalnaker et al. 1995, Washington Department of Ecology 2002). 

2.4.5 Discharge Quality 

Discharge quality is the physical and chemical qualities of water leaving the hatchery and entering 

the adjacent stream. These qualities include temperature, settleable solids, suspended solids, nitrite 

levels, nitrate levels, and phosphorous levels (Kendra 1991). Unregulated discharge and poor 

water quality can alter the native flora and fauna below the point of discharge (Willoughby et al. 

1972, Kanaga and Evans 1982). The United States Environmental Protection Agency and 

Washington State Department of Ecology require adherence to state and federal water quality 

standards at all hatcheries in the state (Boersen and Westers 1986, Cho and Bureau 1997). 

2.4.6 Modification of Riparian Areas 

The physical structures of hatcheries are often located adjacent to riparian areas where natural 

habitat has been replaced with hatchery buildings and juvenile rearing vessels. Negative effects of 

these physical structures, such as increased surface run-off, decreased near-shore cover, loss of 

shade and reduced water quality in the immediate vicinity, should be minimized (Shepherd 1991, 

Beechie and Sibley 1997, Keith et al. 1998). 

2.4.7 Harassment from Humans 

Adult salmonid collection facilities at hatcheries concentrate returning adults prior to spawning. 

These concentrations are often highly visible and predictable, attracting fishers and nonconsumptive users. Illegal activities such as poaching and harassment can also occur. These 

activities can have a negative effect by reducing spawning success. 
Scientific Framework - Hatchery Programs in the Species/Population Context A-15 

CHAPTER 3. HATCHERY PROGRAMS IN THE 

SPECIES/POPULATION CONTEXT

Hatchery populations of salmonids are subject to many of the same biological processes as their 

naturally-spawning counterparts. These biological processes shape the biological significance and 

viability of both hatchery and naturally-spawning populations. Assessment of the biological 

significance and viability of salmonid populations provides an important benchmark for developing 

both long- and short-term goals and management strategies for a particular population or stock. In the 

case of integrated hatchery programs, where the management strategy is to minimize genetic 

divergence between the hatchery broodstock and naturally-spawning population, the combined 

population shares similar characteristics for biological significance and viability. In the case of 

segregated hatchery programs, the biological significance is based solely on the biological origin and 

attributes of the hatchery population with the viability linked to the performance of the stock in both 

the hatchery and natural environments. 

3.1 Biological Significance 

The biological significance of a stock is a function of the origin of the stock and its inherent genetic 

diversity, its biological attributes, uniqueness, local adaptation, and the genetic structure of this 

population relative to other con-specific populations. A population can be considered highly 

significant if it exhibits unique genetic and biological attributes that are not shared with other adjacent 

stocks. These attributes may include unique life history, physiological, morphological, behavior, and 

disease resistance characters with a genetic basis. 

3.1.1 Genetic Diversity 

Genetic diversity refers to the magnitude and distribution of genetic variation among individuals. 

Genetic variation is important because it provides the foundation for responses to selection 

(natural or artificial) and local adaptations (Falconer and MacKay 1996). Phenotypic variation 

refers to the variation in measurable traits (e.g., size at reproduction) among individuals. It is 

determined by the combined effects of genetic and environmental variation among those 

individuals. 

Genetic diversity can be measured by molecular and quantitative genetic methods. Molecular 

methods examine genetic variation at the level of individual genes or DNA sequences. Most of the 

variation detectable at the molecular genetic level of biological organization is assumed to be 

“selectively neutral,” thus reflecting the ancestral history of a population. Quantitative genetic 

methods statistically partition the phenotypic variation (or variance) of measurable traits into 

genetic and environmental components. These latter methods attempt to understand the biological 

significance of phenotypic variation, in terms of fitness and potential responses to selection, under 

specific or varying environmental conditions. Estimating the genetic and environmental 

components of phenotypic variance requires knowledge of the familial relationships among a 
A-16 Scientific Framework - Hatchery Programs in the Species/Population Context 

portion, or sample, of individuals within a population. These kinds of data are extremely difficult 

to obtain for salmon because parental identities of individual fish are usually unknown. 

3.1.2 Local adaptation 

Local adaptation is the response of a local population, observed as changes of phenotypes and 

mediated by genetic change, to natural selection in a particular environment over time. The 

process of local adaptation occurs when the population’s phenotypes (traits related to survival and 

reproduction such as size, fecundity, and disease susceptibility) become ‘best suited’, or adapted, 

genetically to the population’s local environment. Local adaptation of many salmon population 

traits has been inferred from observations of trait differences between populations (Ricker 1972; 

Taylor 1991). 

Rigorous demonstration of local adaptation is difficult because it requires detection of a genetic 

basis for variations of fitness traits and demonstration that a local population has a higher mean 

fitness (viability, reproductive success, etc.) under its local conditions than do non-local 

populations (Chilcote et al. 1986; Leider et al. 1990; Fleming and colleagues 1992, 1993, 1994; 

McGinnity et al. 1997; Taylor 1991; see also series of experiments described by Gharrett and 

Smoker 1993a,b; Smoker et al. 1994; Smoker et al. 1998; Geiger et al. 1998; McGregor et al. 

1998; Hebert et al. 1998). Nevertheless, compelling examples apparently demonstrating local 

adaptation come from comparative studies of fitness traits among conspecific populations of 

sockeye and pink salmon. Several studies have demonstrated different rheotaxis in fry from inletand outlet-spawning sockeye salmon and indeterminate rheotaxis in intercrosses; Offspring of 

inlet spawners are appropriately negatively rheotactic and would, in nature, swim downstream to 

their native lake; Offspring of outlet spawners are positively rheotactic (Raleigh 1971; Brannon 

1967). With respect to reproductive fitness, pink salmon spawn earlier in cool, mainland streams 

and high altitude streams than in comparatively warmer, island and low altitude streams (Sheridan 

1962; Brannon 1987). The inference is that natural selection favors earlier spawners in cooler 

streams because developing eggs laid by later spawners would not have sufficient time to 

complete embryonic development before the onset of the spring growing season. In addition, mean 

embryonic development is more rapid in eggs from cool water populations than warm water 

populations, when incubated together at the same temperature. In addition, significant genetic 

variation for incubation rate exists within populations (Hebert et al. 1998). Genetic variation exists 

also for arrival date of pink salmon to their spawning streams (Smoker et al. 1998) and 

ovulation/spawn date of rainbow trout (Siitonen and Gall 1995). Collectively, these studies 

illustrate a wide of range of phenotypic responses—probably reflecting local adaptations—that 

have been shown experimentally to have significant genetic components. 

Some natural level of straying occurs continually among salmonid populations but observed local 

adaptation presumably results from the scarcity of strays or lower reproductive success relative to 

locally adapted salmon. This observation is consistent with the generally poor survival of 

transplanted salmon relative to naturally-spawning populations (Quinn 1997). 

Life history diversity within populations buffers the populations during periods of change or 

environmental instability (Hilborn et al. 2003). Salmonids inhabit variable environments 
Scientific Framework - Hatchery Programs in the Species/Population Context A-17 

characterized by annual, decadal, and other cyclical climatic events. Catastrophic habitat changes 

from natural occurrence such as floods, earthquakes, and droughts, as well as human-induced 

changes such as logging and stream diversion also characterize salmonid habitats. Genetic 

diversity of life history traits among individuals within populations contributes to successful 

reproduction and population persistence under variable habitat and climatic conditions 

3.1.3 Genetic Structure 

Genetic population structure refers to the spatial and temporal partitioning of genetic variation into 

populations, subpopulations, year classes, and other discernible groups (Gilpin 1993; Harrison and 

Taylor 1997). Structure reflects a deviation from random interbreeding among all individuals 

constituting a species or population. Population structure enhances the ability of species to persist 

over time in a variable environment and buffers populations during catastrophic events. 

Spatial Variability among Populations 

Spatial genetic structure refers to genetic heterogeneity among geographically separate 

spawning aggregations among which gene flow is restricted. Populations may be separated by 

spawning location, spawning substrate, or other geographic features (e.g. lake or river system, 

inlet or outlet, beach or stream). Spatial genetic structure is usually measured in terms of the 

phenotypic or genetic variance within and between populations or by Wright’s F-statistics (or 

gene diversity statistics), which reflect deviations from panmixia at various hierarchical levels 

of structure. Each spatially partitioned subclass may be characterized by an effective 

population size (see Section 3.2.1).Spatial structure buffers a species against localized, 

detrimental effects and provides a mechanism for fine-tuning natural selection and local 

adaptation. 

Temporal Variability 

Temporal genetic structure refers to the partitioning of a species’ gene pool into separate 

temporal classes. Temporal structure occurs both within years (e.g. early versus late run time) 

and among year classes. Many salmonid populations exhibit temporal genetic structuring 

within years through divergent run times. This structuring is often associated with specific 

life-history characteristics that have evolved in response to varying environmental conditions. 

Phelps et al. (1984) observed significant genetic differences between summer-run and fall-run 

chum salmon originating from Hood Canal. Fall-run chum salmon from Hood Canal are 

genetically more similar to other geographically-distant fall-run populations than to summerrun populations from Hood Canal. Summer-run chum salmon typically spawn in the mainstem 

of rivers in periods of high water temperature, suggesting a specialized life history adaptation. 

Similar temporal genetic divergence occurs between “even” and “odd” year classes of pink 

salmon, a species with a strict two-year life history, thus leading to two temporally-discrete 

populations that often spawn in the same stream, every other year. 
A-18 Scientific Framework - Hatchery Programs in the Species/Population Context 

Connectivity of wild salmonid populations 

Homing to natal streams is an important biological characteristic of salmonid fishes, allowing 

evolution of local adaptations in life history and other fitness traits (Quinn 1993; Altukhov and 

Salmenkova 1994; Quinn et al. 2001). Stock-specific, genetically-based adaptations include 

size and age at sexual maturity, adult return and spawn-timing, pre-hatch developmental rate, 

length of freshwater residence prior to outmigration, and marine migration patterns (Smoker et 

al. 1998; Sato et al. 2000). Despite the biological importance of homing, natural straying also 

plays an important function related to colonization of new habitats and maintaining 

connectivity between geographically adjacent populations (Quinn 1993). Many studies have 

shown that salmon and steelhead seek alternative spawning habitats if no appropriate habitat is 

immediately available (Pascual and Quinn 1994). Such behavior is most apparent when natal 

streams are blocked by catastrophic, environmental events. For example, siltation resulting 

from the 1980 eruption of Mount St. Helens resulted in significant numbers of Chinook 

salmon and steelhead straying from the Cowlitz River to the Kalama and Lewis rivers (Leider 

1989; Quinn et al. 1991). Although, some natural level of straying occurs continually among 

salmonid populations, observed local adaptation presumably results from the scarcity of strays 

or their lower reproductive success relative to locally adapted salmon. This observation is 

consistent with the generally poor survival of transplanted salmon relative to naturallyspawning populations (Quinn 1997). 

Historically, many salmonid populations could be characterized by a metapopulation structure 

and a level of connectivity between populations. Under these concepts, populations were 

spatially structured into assemblages of local breeding populations and migration among the 

local populations influenced local dynamics and provided the possibility of population 

reestablishment following extinction. However the cumulative effect of habitat degradation, 

dams, channelization, logging, and other effects of urbanization have resulted in a loss of 

connectivity among some populations of Puget Sound and coastal Washington. Some former 

metapopulations have been reduced to single isolated populations. While formerly a 

population within a larger metapopulation would not have been deemed highly significant 

because it shared biological attributes with other populations, an isolated remnant would now 

be considered highly biologically significant. 

3.2 Viability

3.2.1 Effective population size 

One of the most important parameters affecting genetic diversity is effective population size (Ne). 

Effective population size places an upper limit on the amount of genetic diversity that can be 

maintained in a population in relation to its pedigree history and potential losses due to genetic 

drift. Some general guidelines for maintaining minimum Ne in distinct, or semi-isolated, 

populations have been proposed: 

• Ne > 50 to prevent inbreeding depression and a detectable decrease in viability or 

reproductive fitness of a population (Franklin 1980). 
Scientific Framework - Hatchery Programs in the Species/Population Context A-19 

• Ne > 500 to maintain constant genetic variance in a population resulting from a balance 

between loss of variance due to genetic drift and the increase in variance due spontaneous 

mutations (Franklin 1980; Soule 1980; Lande 1988) 

• Ne > 5,000 to maintain a constant variance for quasi-neutral, genetic variation that can 

serve as a reservoir for future adaptations in response to natural selection and changing 

environmental conditions (Lande 1995). The rationale here is that Ne needs to be large 

enough to minimize genetic drift and the potential loss of “neutral” alleles that may 

confer fitness advantages under changing environmental conditions and new selection 

regimes. The Ne > 5,000 rule applies primarily to an entire ESU or species over 

evolutionary time spans, whereas Ne > 50 applies primarily to closed, local populations. 

A more detailed analysis of Ne in fluctuating populations similar to what might occur in a hatchery 

involves a distinction between the inbreeding effective number (NeI ) and the variance effective 

number (NeV) (Crow 1954; Simberloff 1988). The inbreeding effective size quantifies the increase 

in inbreeding while the variance effective size specifies the amount of genetic drift and the rate of 

loss of heterozygosity (Ryman et al. 1995). When population numbers are stable, NeI and NeV are 

identical and constant over time. In a rapidly growing population NeV may be much larger than NeI 

while the opposite is true for declining populations, and, in these situations, a distinction should be 

made between the two measures (Hedrick and Hedgecock 1994). 

3.2.2 Age class structure 

Age class structure leads to temporal structuring of populations across years and varies 

substantially among species. It must be taken into account in estimation of effective population 

size. Age class structuring is absolute in pink salmon, with a strict, two-year life cycle. It is 

slightly more diverse in coho salmon, where a three-year life cycle predominates but is augmented 

largely by jacks (two-year old spawners) and a small number of four-year old spawners Age class 

structures for sockeye salmon, Chinook salmon, and chum salmon are more complex with 

multiple year classes contributing to a single generation. Age class structures are even more 

complex in steelhead, cutthroat trout and other species that undergo repeat spawning at variable 

ages. A complex age structure also tends to diminish the likelihood of a small population going 

extinct in a particular year in which an environmental disaster occurs. 

Temporal structuring decreases as the variance in age at maturity increases. Populations showing 

temporal stability in abundance have comparatively low variances in the effective number of 

breeders per year. The effective population size of an entire population (and generation) is 

approximately the harmonic mean of the effective number of breeders per year, multiplied by the 

generation time in years (Waples 1990). Generation time is defined as the average age of parents 

at the time of reproduction. 

3.2.3 Trends and variance in abundance over time

Viable salmon populations, whether natural or hatchery subsidized, exhibit high intrinsic 

population growth. When abundance is reduced (e.g. due to catastrophic events or harvest) the 
A-20 Scientific Framework - Hatchery Programs in the Species/Population Context 

population will subsequently respond with a rapid increase in abundance, provided habitat of 

sufficient quantity and quality is available. When populations remain depressed over extended 

periods of time, it is evidence either of poor habitat (including the hatchery environment) or poor 

genetic viability. Thus trends and variance abundance over time can be indicators of population 

viability. More specifically trends in productivity (adult progeny per parent - recruits/spawner), 

under stable environmental conditions and when corrected for density dependent factors are good 

measures of population viability. 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-21 

CHAPTER 4: EFFECTS OF HATCHERY OPERATIONS ON 

HARVEST AND CONSERVATION OF THE PROPAGATED 

STOCK

Hatchery operations - including broodstock choice and collection, spawning, incubation, and rearing 

protocols - and the hatchery environment itself can affect the short and long-term survival and 

behavior of the propagated stock. Hatcheries can affect the achievement of harvest goals as well as the 

goals for biological significance and viability for the target stock. This is true whether the target stock 

represents a genetically segregated hatchery population or a component of the natural stock as a 

genetically integrated broodstock. Hatchery operations can affect both the long-term genetic 

constitution of a population and the short-term and the short-term phenotypic performance of the 

target population. 

4.1 Hatchery Operations as they affect the genetic 

characteristics of the Propagated Stock 

Hatcheries represent unique environments that are not part of the natural evolutionary history of 

anadromous salmonid fishes. However, hatcheries now represent a major component of the range of 

environmental conditions that salmon and steelhead experience during their lifetimes. Indeed, a 

significant proportion of all returning adults in Puget Sound, the Washington coast, and the Columbia 

River are the progeny of hatchery-spawned adults. Consequently, from a regional perspective, 

hatcheries represent a significant component of the overall, environmental landscape experienced by 

salmon and steelhead in Washington state (Williams et al. 2003). 

Hatcheries also represent unique environments that can cause populations to change genetically over 

time relative to naturally spawning populations. From a conceptual viewpoint, populations are 

characterized genetically by the suite of genotypes and genes represented by all individuals in a 

population. By definition, “genetic change” refers to changes in gene frequencies between generations, 

or between a parental population and a progeny population (offspring) when measured at the same life 

history stage. 

Populations can change genetically as a result of four fundamental processes: random genetic change, 

natural or artificial selection, migration (gene flow) from other populations, and mutation. Mutation is 

generally considered an important factor only over evolutionary time scales and will not be discussed 

here, although recent theoretical work suggests that it could be a factor in highly domesticated 

populations (Lynch and O’Hely 2001). 

In this section, we describe the mechanisms by which hatchery propagated populations can change 

genetically over time. These genetic changes can affect both the biological significance of a 

population and its viability. 
A-22 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

4.1.1 Changes in Biological Significance 

Biological significance, in the context of anadromous salmonid fishes, refers to the biological 

uniqueness of a population relative to other populations within an ESU (Section 3.1). For example, 

the spring Chinook population in the White River is considered biologically unique within the 

Puget Sound ESU and is thus classified as “high” biological significance. In contrast, a large 

number of coho salmon populations throughout Puget Sound express very similar life histories 

with respect to age class composition and run timing, and many of those coho populations are thus 

considered to have low biological significance. The concept of biological significance is 

associated with the concept of “local adaptation” and biological attributes. 

The biological significance of a hatchery-propagated population can change over time (i.e. 

generations) as a result of genetic changes to the population itself or changes in the abundance and 

significance of other populations within the ESU. The focus here is on genetic changes to hatchery 

propagated populations that directly affect their biological significance. These changes can occur 

via two principal processes: (1) domestication and (2) stock transfers into the hatchery. 

Domestication 

Domestication is the process of a population becoming genetically adapted over multiple 

generations to an artificial or human-controlled environment. Three principal factors can lead 

to domestication: (1) relaxation of natural selection that would otherwise occur in the wild 

(e.g. spawning behavior); (2) artificial or inadvertent selection imposed by the hatchery 

environment; and (3) direct selective breeding of adult spawners by hatchery personnel. In 

general, domestication results in increased fitness under hatchery conditions but decreased 

fitness under natural conditions (Price 1984; Kohane and Parsons 1988; Hemmer 1990). 

Domestication thus represents some level of local adaptation to hatchery conditions and 

reduced productivity under natural conditions (Reisenbichler and Rubin 1999). Domestication 

resulting from genetic change can be detected from morphological, physiological, and 

behavioral differences between fish from hatchery and natural populations when those fish are 

hatched and reared under identical, experimental conditions. 

Understanding the potential domestication effects of hatcheries and artificial propagation is 

currently an active research area. Many studies have demonstrated that fish from long standing 

hatchery populations exhibit greater swimming activity, greater surface orientation, and 

increased agonistic feeding behavior relative to fish from natural populations (Ruzzante 1994; 

Campton 1995; Berejikian et al. 1996; Reinhardt 2001). These domestication effects appear to 

reflect genetic responses to artificial selection for competitive ability under high density 

rearing and pulsed, surface feeding in hatchery environments. The progeny of hatchery-origin 

adults may also exhibit increased genetic vulnerability to predators under natural conditions 

(Berejikian 1995). Juvenile fish from domesticated hatchery populations may also displace 

locally adapted fish from their native habitats due to behavioral dominance and aggression 

(Nickelson et al. 1986; Berejikian et al. 1996). 

Differences in adult spawning behavior between fish from hatchery and natural populations 

have also been observed: adults from hatchery populations are generally less aggressive and 

behaviorally submissive to adults from natural populations (Fleming and Gross 1994; Fleming 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-23 

 

and Petersson 2001). These latter domestication effects may also affect reproductive success 

of hatchery-origin adults under natural conditions.39 

Domestication due to artificial selection within the hatchery environment is often difficult to 

detect or observe directly. For example, recent studies have confirmed earlier hypotheses that 

the benign conditions of a hatchery environment may directly select for increased fecundity of 

females with a correlated reduction in mean egg size (Heath et al. 2003). In general, egg size 

and egg number are negatively correlated within and among populations, both phenotypically 

and genetically (Fleming and Gross 1990; Beacham and Murray 1993; Kinnison et al. 1998; 

Einum and Fleming 2000a). As a consequence, artificial selection for increased egg number is 

expected to cause a decrease in mean egg size over multiple generations (but see Quinn et al. 

2004). Under natural conditions, egg size is believed to be under strong natural selection 

because a positive correlation exists among egg size, post-emergent fry size, and survival 

(Beacham and Murray 1990; Kinnison et al. 1998; Einem and Fleming 1999, 2000b). 

However, under the benign conditions of a hatchery environment, natural selection associated 

with large egg size and increased survival is relaxed. Consequently, females with higher 

fecundities for a given age are expected to produce more offspring and adult progeny relative 

to females of the same age with lower fecundities if survival probabilities of progeny are 

independent of fecundity. Sperm competition resulting from mixed-milt fertilizations in single 

containers (e.g. 5 males X 5 females) can also result in domestic changes in life history traits 

if those traits are correlated phenotypically with sperm potency and fertilization success in 

vitro (Campton 2004). 

Genetic change contributing to domestication can also result from direct selective breeding by 

hatchery personnel. Hatchery populations have often been selected for early within-season run 

timing and early spawn-timing by selecting the earliest returning fish and excluding latereturning fish from the broodstock. As a consequence, several hatchery stocks of steelhead 

coho salmon in Washington and Oregon now exhibit a range of return times and spawn times 

that are significantly earlier than natural populations (Ayerst 1977; Rosentreter 1977; Flagg et 

al. 1995; Mackey et al. 2001; Quinn et al. 2002). The biological significance of those hatchery 

stocks relative to natural populations is substantially reduced because those hatchery stocks no 

longer represent the genetic resources of the ESUs from which they were derived (i.e. due to 

domestication). Some of those hatchery stocks have been transplanted throughout western 

Washington resulting in several, independently propagated populations of the same, 

domesticated hatchery stock (e.g. Chambers Creek winter-run steelhead). 

Selective breeding for reduced age/size class variation has also been extensive, primarily by 

selectively breeding for larger, older fish and excluding “jacks” (two-year old coho, fall 

Chinook, and steelhead males) from broodstocks. For hatchery stocks of coho salmon, such 

selective breeding disrupts the natural genetic continuity among brood years (Van Doornik et 

al. 2002), thus resulting in three discrete populations of hatchery of coho salmon, each 

composed almost exclusively of three-year old fish, instead of a single genetic population 

composed of two or more age classes. Two year old “jack” males should, thus, be used for 

39 See framework Chapter 5. 
A-24 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

broodstock at a rate comparable to their relative abundance among returning adults. Increasing 

the proportion of jacks in coho broodstocks appears to have little effect on the proportion of 

jacks among returning adults relative to the much greater effects of accelerated growth rate 

and increased size at release of smolts (Appleby et al. 2003). Moreover, including jacks in 

coho broodstocks has little effect on post-release survival or mean size of age 3 adults 

(Appleby et al. 2003). On the contrary, excluding jacks from hatchery broodstocks represents 

a form of selective breeding that contributes to domestication. 

Potential solutions for retarding the deleterious effects of domestication include systematic 

gene flow from naturally-spawning populations to the hatchery population (Olson et al. 1995; 

Ford 2002), modified hatchery environments that more closely resemble natural conditions 

(Maynard et al. 1995; Berejikian et al. 2000, 2001; Fuss and Byrne 2002), protocols for 

selecting and mating spawners designed to minimize genetic change between adults and their 

progeny (Campton 2004), matching hatchery life cycles to local natural life cycles (e.g. 

subyearling fall Chinook rather than yearling smolts; but see Bugert et al. 1997 for 

compromised habitats), and limits on the duration of supplementation programs where the 

goal is to rebuild natural populations (Bugert 1998). 

Stock transfers and genetic introgression 

Backfilling egg or spawner shortages at one hatchery from surpluses at another hatchery has 

been a common practice among salmon hatcheries in Washington and other states in the 

Pacific Northwest. The net result of such transfers is a general decrease in between-population 

genetic variation (e.g. Simon et al. 1986; Utter et al. 1989). The transfer of eyed eggs among 

hatchery populations of coho salmon in Oregon may have especially contributed to genetic 

and phenotypic similarities among hatchery stocks and dissimilarities to wild stocks (Hjort 

and Schreck 1982). Such transfers can potentially compromise stock specific, or geographic 

specific, local adaptations related to run timing, spawn timing, embryonic developmental rate, 

disease resistance, and other traits known to be heritable and responsive genetically to local 

environmental conditions. In many instances, fish or gamete transfers have often taken place 

over hundreds of miles and between ecological provinces or regions (e.g. Puget Sound, 

Washington coast, and the Columbia River). Reductions in mean fitness of the receiving 

hatchery stock is the expected outcome of such transfers (Emlen 1991; Gharrett et al. 1999). 

Consequently, a shortage of adults returning to a particular hatchery should not be viewed as a 

deficiency, per se, but rather the result of natural selection acting on the hatchery population. 

The HSRG strongly discourages "fish transfers" or the "backfilling" of egg shortages at one 

facility with surpluses from another facility, particularly when the two facilities are in 

geographically-distinct watersheds or regions. The HSRG has concluded that egg or fish 

transfers inhibit the development of viable, self-sustaining populations in local watersheds, 

regardless of whether those populations are propagated by natural spawning or hatcheries. 

Homing fidelity in anadromous salmonid fishes has a heritable component; consequently, 

transferred fish and fish resulting from eyed egg transfers stray at a higher rate as returning 

adults than “native” fish that are released on site from where their parents returned and 

spawned (Quinn 1993, 1997). Not only does the transfer of fish between watersheds impose 

potential genetic risks to local populations, but increased straying from the release site (or 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-25 

 

facility) can result in undesirable natural spawning of transferred fish (or their progeny) in 

non-target watersheds.40 

The HSRG believes that hatchery programs incapable of sustaining their own broodstocks 

may be over-harvested and/or are not properly managed. The recommended solution to 

broodstock shortages is to address the hatchery or harvest management problem, not backfill 

shortages with transfers from another facility or watershed to meet a release "quota". As noted 

above, broodstock shortages may represent the results of "natural selection" at work. As a 

general working model, the basic biological principles used to manage natural populations of 

salmon and steelhead should be applied equally to hatchery-propagated populations. This 

working model precludes the transfer of fish or eyed eggs among regions, facilities, or 

watersheds to meet an escapement goal. 

4.1.2 Changes in Viability 

Viability refers to the ability of a population to sustain itself demographically over multiple 

generations. Population viability is a function of two independent factors: (1) the intrinsic genetic 

characteristics or fitness of the population and (2) the habitat or environmental conditions 

encountered by individuals of a population throughout their life cycle. Populations with high 

viability exhibit positive intrinsic rates of increase over time, whereas populations with low 

viability exhibit negative intrinsic rates of increase. Populations may exhibit low viability because 

of low genetic fitness, poor environmental conditions, or a mismatch between the genetic 

characteristics of the population and the particular environmental conditions encountered within a 

single generation. The principal emphasis here is on the genetic fitness of a population and how 

hatchery propagation can result in genetic changes in that fitness. 

Founder effects, genetic drift, and loss of genetic variation 

Hatchery-propagated populations can lose genetic variation by founder effects relative to their 

source, natural population. The founding broodstock of a hatchery population is simply all the 

adult fish that were used to initiate the hatchery program. These adults typically represent a 

finite sample from the source population. Genetic variation of the hatchery population cannot 

exceed that of the founding broodstock or source population. Founder effects occur when 

genetic variation of the founding broodstock is substantially less than that of the source 

population because a relatively small number of adults was used to initiate the broodstock. 

The genetic composition of the founding broodstock provides the genetic foundation for the 

phenotypic fitness and productivity of the hatchery population in future generations. Founder 

effects may be more problematic in segregated programs than integrated programs because the 

former are typically propagated exclusively with returnees back to the hatchery. Recent 

reviews of hatchery programs in the Puget Sound area by the HSRG have revealed a potential 

40 See framework Chapter 5. 
A-26 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

 

founder effect associated with the hatchery program for spring Chinook salmon on the Skagit 

River.41

Genetic drift can also lead to loss of genetic variation in artificially propagated populations. 

Genetic drift refers to random changes in allele or gene frequencies between brood years (e.g. 

spawners and recruits) and between generations due to small effective number of breeders and 

population sizes, respectively, resulting from the random sampling of genes from the parental 

gene pool to yield the offspring gene pool. As a result, alleles initially occurring at low 

frequencies (e.g p < 0.05) can easily be loss in genetically small populations due to genetic 

drift. Indeed, computer simulations indicate that low frequency alleles are subject to rapid 

extinction in populations of Pacific salmon with an Nb < 100 spawners per year (Waples 

1990). As noted in Section 3.2.1, effective population sizes should be greater than Ne = 500 to 

minimize genetic drift and the potential loss of alleles. 

Understanding the genetic composition of a hatchery population may require detailed records 

of the founding broodstock (e.g. population sources, number of male and female parents, 

mating protocols, etc.), the number of male and females spawners each year, and the manner 

in which male and female gametes are combined (i.e. breeding protocols). However, 

identification of founding broodstocks and their genetic contributions to existing hatchery 

populations may not be straightforward if multiple population sources were used to initiate a 

population. In addition, the manner in which males and females are mated is rarely 

documented in most hatchery programs. On the other hand, molecular genetic methods can be 

used to compare the genetic composition of existing hatchery populations to the source 

population (or populations) from which the hatchery population was derived. For example, 

several studies have documented significant losses of genetic variation or changes in allele 

frequencies for hatchery populations of non-anadromous salmonid fishes (Allendorf and 

Phelps 1980; Ryman and Stahl 1980; Cross and King 1983; Stahl 1983; Vuorinen 1984). 

Only a few published studies have actually documented loss of genetic variation, or significant 

allele frequency changes, in hatchery populations of Pacific salmon and steelhead relative to 

their source populations. For example, Steward and Bjornn (1990) noted that they “found few 

cases of reduced levels of genetic variability among hatchery stocks of Pacific salmon and 

steelhead.” On the other hand, considerable evidence now exists that hatchery populations of 

coastal coho salmon in Oregon have suffered significant genetic drift effects resulting from 

relatively small effective population sizes (Simon et al. 1986; Waples and Smouse 1990; 

Waples and Teel 1990; reviewed in Campton 1995). 

Sperm competition and reduced effective number of breeders 

Salmon hatcheries in the Pacific Northwest historically spawned adults by combining eggs fro 

several females with milt from several males in a single container. This mixed-milt approach 

leads to significant sperm competition and highly unequal genetic contributions from male 

spawners (Gharrett and Shirley 1985; Withler 1988; Withler and Beacham 1994; Gile and 

Ferguson 1995). Sperm competition substantially reduces the genetic effective number of 

41 See HSRG March 2003 regional recommendations for Skagit River Hatchery Spring Chinook Salmon 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-27 

breeders (Nb) relative to the actual number of spawners (Ns) such that Nb << Ns. Sperm 

competition in vitro can also result in undesirable artificial selection for life history traits (e.g. 

age/size at maturity) if those traits are correlated phenotypically with sperm potency and 

fertilization success (Campton 2004). For example, precocious male parr and other males 

exhibiting “sneaker” spawning behavior (e.g. “jacks”) produce milt with greater sperm 

concentrations and volumes relative to their body size than older larger males (Gage et al. 

1995; Taborsky 1998; Vladic and Järvi 2001; Koseki and Maekawa 2002; Liljedal and Folstad 

2003). Relationships between age/size at maturity and sperm characteristics have been 

demonstrated most conclusively with Atlantic salmon (Salmo salar) where sexually mature 

parr have greater proportions of motile spermatozoa and greater sperm ATP content than 

anadromous males, including greater fertilization success relative to anadromous males in 

experimental crosses (Vladic and Järvi 2001). Similarly, sperm concentration in the milt of 1-

year old rainbow trout males is greater than the concentration for three-year old males (Liley 

et al. 2002), and such variation can significantly influence in vitro fertilization success in 

mixed-milt spawnings (Gile and Ferguson 1995). 

A large number of salmon hatcheries in coastal Washington and Puget Sound continue to use 

mixed-milt fertilization (5 males X 5 females) despite documented genetic effects and 

potential risks. As a general rule, salmon hatcheries should discontinue mixed-milt 

fertilization and institutionalize alternative spawning protocols that preclude or minimize 

sperm competition in vitro. Three alternative protocols are recommended: pairwise spawning, 

nested spawning, and factorial or matrix spawning (Campton 2004). The underlying premise 

of these latter protocols is that every adult selected for broodstock should have an equal 

opportunity, and probability, of producing an equal number of progeny. One goal of most 

hatchery programs should be to minimize genetic change between the pool of returning adults 

available for broodstock each year and the progeny of parents selected for broodstock from 

that pool. To achieve this latter goal, spawning protocols should maximize the genetic 

effective number of breeders and minimize artificial selection associated with hatchery 

propagation. These goals and objectives may require increased genetic oversight of hatchery 

operations comparable to the level of fish health oversight (pathogen monitoring and disease 

prevention) currently practiced in salmon hatcheries throughout the Pacific Northwest. 

4.2 Hatchery Operations as they affect the non-genetic 

characteristics of the Propagated Stock 

In addition to their genetic makeup, the survival and reproductive success of juvenile hatchery fish 

depends upon their non-genetic characteristics at the time of release as well. These non-genetic 

characteristics include the physiological, morphological, behavioral, and health status of the fish being 

reared. Hatchery operations and the hatchery environment can affect each of these characteristics and 

influence the achievement of harvest or conservation goals for the propagated stock. 
A-28 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

4.2.1 Changes in Physiology 

Physiological fitness is the ability of fish to grow, smoltify and resist disease in the hatchery and 

natural environments. Following release, good physiological fitness allows hatchery fish to rapidly 

migrate downstream, adapt to seawater, survive in the ocean environment, and return to 

successfully reproduce. Physiological fitness is controlled by environmental factors such as 

weather, water quality, temperature, feed availability, and day length (photoperiod). These factors 

affect growth, development and metabolism, which ultimately influence genetically programmed 

variations in life history patterns that vary within and between populations. Various salmon stocks 

have evolved successful adaptive strategies and tactics based on emergence timing, freshwater 

residence, seasonal patterns of growth, age and timing of smoltification, periods of imprinting and 

homing, and age and timing of reproductive migration and maturation. 

Anadromous salmonids undergo a major metamorphic-like change, the parr-smolt transformation, 

as they prepare for migration to the sea. Fully smolted (transformed) juveniles exhibit rapid 

downstream migration, increased hypo-osmoregulatory capability, sustained growth in the ocean 

and high survival to adulthood. The link between smoltification, growth rate, seawater tolerance 

and migration rate has been observed and reported frequently in the literature (Wagner et al. 1969; 

Clarke et al. 1988; Varnavsky et al. 1992; Beckman et al. 1998, 1999). These processes are under 

hormonal control and are mediated primarily by photoperiod. The same hormones that control 

growth (growth hormone, insulin-like growth factor-I) also stimulate the development of seawater 

tolerance in salmonids (Sakamoto and Hirano 1993; Dickhoff et al. 1997). The sharp increase in 

growth of some species of wild fish concomitant with smoltification (Beckman et al. 2000) is 

similar to the rapid growth of high quality smolts in hatcheries (Beckman et al. 1999). Enhanced 

seawater tolerance is also characteristic of successful smoltification (Hoar 1988). 

Producing high quality hatchery smolts with greater smolt-to-adult survival will allow equivalent 

hatchery contribution to adult harvest with fewer smolts released. Releasing actively migrating, 

healthy smolts from hatcheries will reduce opportunities for hatchery-wild fish interactions and 

minimize negative impacts of hatchery fish on wild fish. Rapidly migrating smolts will be less 

likely to residualize and imprint on inappropriate stream sites. Therefore, they will be less likely to 

stray during their homing migration, thus reducing the likelihood of introgression of hatchery fish 

on non-target populations. The method of release is particularly important because it affects the 

rate of migration, predation, level of residualism, inter- and intra-species interactions, and 

imprinting or level of straying (Hillman et al. 1989; Vander Haegen and Doty 1995; McMichael et 

al. 1999). Additionally, the time of year and size at which smolts are released into the natural 

habitat can be used to minimize inter and intra-species competition, straying and residualism 

(Tipping and Blankenship 1993; Tipping 1997). Survival can be greatly increased if releases occur 

when food is abundant in the receiving habitat. The size and quality of a juvenile salmonid affects 

its ability to compete, escape predators, adapt to seawater, migrate rapidly, mature at the 

appropriate age, and most importantly recruit into the fishery or spawning population (see 4.2.2, 

and 4.2.3). 

Physiological fitness can be measured during the parr-smolt transformation and in reproductive 

adults. The timing, magnitude, and duration of the parr-smolt transformation are surrogates for 

physiological fitness. Some specific physiological measures of smoltification status include gil 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-29 

Na-K ATPase enzyme activity, blood concentrations of thyroid hormones, growth hormone, 

insulin-like growth factor, and body lipid levels, among others. Physiological fitness can also be 

estimated during the parr-smolt transformation by examining the pattern of juvenile growth 

(Beckman et al. 1999). In reproductive adults, physiological fitness can be measured in terms of 

their morphology (e.g. size and age at maturity); see section 4.2.2, development of secondary 

sexual characteristics, egg size and fecundity, and endocrine cycles. 

Hatcheries can affect the physiology of juvenile and adult salmon by creating an environment that 

either simulates or departs from the natural patterns in which the stock has evolved. For example, 

typically higher than natural water temperatures may result in earlier emergence by accelerating 

embryonic development. Higher growth rates due to high dietary ration in the hatchery may 

advance the timing of smoltification, e.g., autumn rather than spring smoltification in spring 

Chinook salmon. The lack of seasonal patterns of growth and development in hatchery fish 

contrast substantially to that seen in wild fish (Beckman et al. 2000). A more natural seasonal 

cycle of physiological development and high spring growth may enhance smoltification and 

survival to the adult stage (Beckman et al. 1999). High growth rates of fish in the hatchery may 

also alter the age of maturation, producing exceptionally high numbers of precocious males 

(Larsen et al. 2004). The use of high energy diets produce hatchery fish with greater body fat 

content compared to wild fish, which can also advance male maturation age (Silverstein et al. 

1998). Thus, it is important to regulate growth at appropriate times to enhance smoltification and 

migration, but not contribute to high rates of precocious male maturation. 

Water and feed quality including harmful contaminants will also affect physiology. Heavy metals 

such as copper, lead, zinc, cadmium, and mercury can be toxic to fish and can result in 

dysfunctional growth, poor reproduction, incomplete smoltification, and death. Likewise, organic 

chemicals like pesticides, polychlorinated biphenyls (PCBs), herbicides, and endocrine disruptors 

interfere with a variety of metabolic processes essential to growth, smoltification, reproduction 

and homing imprinting (Pennell and Barton 1996). 

4.2.2 Changes in Morphology 

Morphological fitness embodies a suite of visible traits including size, coloration, body form, fin 

shape and development, secondary sexual characteristics, body musculature, and fecundity. 

Morphological fitness is important to foraging, migration, reproduction, and juvenile camouflage. 

These morphological traits can be controlled or modified through hatchery rearing protocols prior 

to the release of juveniles and can affect the expression of morphological traits in returning adults. 

Juvenile Size—The size of a juvenile salmonid affects its ability to compete for food and space, 

escape predators, adapt to seawater, migrate rapidly, mature at the appropriate time, and most 

importantly survive and recruit into the fishery or spawning population. Natural populations 

generally contain fish within a size range governed by emergence time, available food resources, 

and climatic conditions. In intra-specific contests over food and space, all else being equal, the 

largest fish usually win and are able to establish prime territory (Hoar 1951; Chapman 1962; 

Mason and Chapman 1965; Jenkins 1969; Noakes 1980; Abbot et al. 1985; Maynard 1987). 
A-30 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

No other factor affects the development and growth of fish as much as water temperature. 

Metabolic rates of fish increase rapidly as water temperature increases. Biological processes such 

as spawning and egg hatching are governed by annual temperature changes in the natural 

environment. Successful hatchery operations depend on a detailed knowledge of such temperature 

influences relative to the operational goals of the hatchery. Time and fish size at release have been 

shown to affect overall survival, age at maturity and growth (Hager and Noble 1976; Fowler and 

Banks 1980; Bilton 1980, 1984; Hard et al. 1985; Hankin 1990; Holtby et al. 1990; Henderson and 

Cass 1991). 

Coloration—In nature, salmonid eggs incubate, and alevins develop in the darkened matrix-rich 

environment of the gravel substrate in the redd. Following hatch, juveniles rear in a complex, 

lighted environment of shade, sunlight filtering through riparian vegetation, and light-absorbing, 

dark, gravel substrate. This environment produces cryptic coloration and body camouflage 

patterns most likely to reduce vulnerability to predators. 

Body Shape—Body shape of wild salmonids changes with season and nutritional resources. 

During winter, a period of low feed availability or even starvation, body weight and condition 

(relationship between body length and weight) drops, resulting in a slimmer fish with lower body 

fat. In spring, prior to smoltification, resident non-migratory juveniles feed heavily and regain 

body fat and condition. During the parr-to-smolt transformation, as the period of downstream 

migration nears, the condition index changes again. A slimmer, more streamlined silver-colored 

smolt with reduced pigmentation is produced. 

Size at Maturity—Large body size has been shown to confer a competitive advantage to males 

competing for temporary access to females during spawning (Hanson and Smith 1967; Schroeder 

1981; Keenleyside and Dupuis 1988; Fleming et al. 1996; Berejikian et al. 1997). Breeding 

success of male coho salmon (O. kisutch) depends on their ability to obtain access to spawning 

females (Fleming and Gross 1992, 1994). Only males that enter the nest and release milt during 

oviposition have a chance of fertilizing eggs. Males that enter the nest first have the greatest 

fertilization success (Schroder 1982; Chebanov et al. 1983; Mjolnerod et al. 1998; but also see 

Foote 1997). Size at maturity can influence offspring survival. For example, larger females are 

better able to dig deeper redds, giving greater protection to ova against streambed movement. 

Secondary Sexual Characteristics—Certain morphological characteristics independent of body 

size have been demonstrated to influence male breeding success in Pacific salmon. For example, 

Quinn and Foote (1994) found that hump height was positively correlated with breeding success 

of male sockeye salmon. Those investigators also demonstrated that coho salmon males with 

longer snouts (kypes) attained greater access to spawning opportunities and greater estimated 

fertilization success than males with shorter snouts. Caudal peduncle depth has been correlated 

with female breeding success (Fleming and Gross 1994), perhaps related the capability to dig 

redds. Physical appearance has also been shown to be important in competitive asymmetries 

observed in other fish species. For example, male nuptial coloration plays an important role in 

determining dominance during reproduction (e.g., Kodric-Brown 1995; Baube 1997). The 

importance of spawner morphology in eliciting reproductive behavior has been seen in captively 

reared vs. wild coho salmon, implying that many of the differences between cultured and wild fish 

are a result of hatchery rearing (Berejikian et al. 1997; Hard et al. 2000). 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-31 

Fecundity —The fecundity (number of eggs per mature female) of Pacific salmon females 

represents the potential for production in the next generation. Fecundity is generally related to 

body size but varies by species, latitude, time of return and brood year, with Chinook being the 

most variable (Healey and Heard 1984; Healy 1991; Sandercock 1991; Beacham and Murray 

1993). 

Juvenile hatchery fish are normally reared under conditions were feed availability and rearing 

densities in hatcheries far exceed those found in natural streams. Growth rate, body size, and 

proximate body composition of hatchery fish are often quite different than wild fish (Forster and 

Hardy 1995, Beckman et al. 2000, Larsen et al. 2004). Hatchery reared fish generally have a 

higher percent body fat compared to wild fish (Beckman et al. 2000). In addition to having a 

different shape, juvenile hatchery reared fish are generally less variable in size than naturally 

reared fish (Taylor and Larkin 1986). Studies have indicated that hatchery-induced morphological 

differences can affect swimming speed and therefore the ability to escape predators (Bams 1967, 

Taylor and McPhail 1985). Studies have also suggested that hatchery rearing may result in 

decreased crypsis (camouflage coloration) for stream environments due to rearing against uniform 

(e.g., concrete) hatchery backgrounds (Donnelly and Whoriskey 1991; Maynard et al. 1995, 

1996). Feed and feed additives may also affect the external pigmentation of cultured salmonids, 

with fish fed natural prey supplements having more wild-like pigmentation than fish fed 

formulated feeds (Hickson and Leith 1996, Maynard et al. 1996). 

Inadequate rearing conditions may affect external morphological parameters (e.g., fin condition) 

and ultimate health. Several potentially causative factors have been identified, including under 

feeding, overcrowding, poor water quality, excess exposure to direct sunlight (sunburn), and 

abrasion from contact with raceway walls (Kindschi 1987, Kindschi et al. 1991, Winfree et al. 

1998). Hatchery management factors have been implicated in both decreases in age and size of 

maturity in Pacific salmon stocks (Bigler et al. 1996). Causative factors appear to be combinations 

of high hatchery growth rates triggering early onset of maturity (physiology), density-dependent 

growth after release (ocean carrying capacity), and size selection of larger, older fish by selective 

fisheries (genetic selection). Decreased body size at reproduction produces attendant potential 

reductions in reproductive behavior, fecundity, egg size, and survivorship of progeny (Bigler et al. 

1996; Berejikian et al. 1997, 1999, 2000; Heath et al. 2003). 

Underfeeding has often been cited as a cause of fin erosion in salmonids. Deterioration of fins 

among steelhead trout fed at restricted levels has been attributed to increased aggression and 

competition for a limited food resource (Larmoyeux and Piper 1971). Aggressive behavior in penreared juvenile steelhead includes frontal nipping and counterattacks directed toward the dorsal 

fin, resulting in loss of one-third or more of the tissue (Abbot and Dill 1985). According to Wolf 

(1938) and Klontz (1992), feeding to satiation can improve fin quality in trout, but results of other 

published studies have been inconsistent. Supplementation of diets based on fish meal with krill 

and squid protein or ash, or with sodium, magnesium, and copper have been found to improve 

dorsal fin quality of trout (Barrows and Lellis 1999). In nature, insects and other invertebrates are 

a rich source of copper in fish diets. 
A-32 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

4.2.3 Changes in Behavior 

Behavioral characteristics that are important to productivity can be grouped into four categories: 

1) social behavior including territoriality, schooling, and reproduction; 2) migration behavior 

including downstream migration, ocean migration, and homing migration; 3) predator avoidance 

behavior expressed through recognition of predators and escape response; and 4) foraging ability, 

the capability to recognize and capture suitable feeds. 

Territorial behavior allows stream-resident juveniles to establish feeding territories. Juvenile 

salmonids have been shown to reduce their territory size as fish density increases (McNicol and 

Noakes 1984). It has also been suggested that territory size may limit the maximum density of 

juvenile salmonids in streams (Grant and Kramer 1990). Photoperiod-induced changes in behavior 

allow smolts to aggregate in “schools” and migrate to the sea. Imprinting and subsequent homing 

behavior results in the return of adults to suitable home stream habitat and the perpetuation of 

locally adapted populations. Good predator avoidance behavior increases the probability that 

individuals will survive to adulthood. Foraging behavior assures an adequate food supply. 

Culture conditions within hatcheries can have a major effect on behavior. Migratory behavior, for 

instance, is under the complete control of the hatchery operator. Depending on the water 

temperature in the hatchery and its release protocols, this behavior in hatchery fish may coincide 

with natural out-migration in terms of timing and duration or may be completely different in either 

or both aspects. 

Social divergence of cultured fish may begin as early as the incubation stage. Unnatural hatchery 

incubation environments have been shown to induce excess alevin movement, resulting in lowered 

energetic efficiency, reduced size, and, in some wild stocks, death (Poon 1977, Leon and Bonney 

1979, Mighell 1981, Murray and Beacham 1986, Fuss and Johnson 1988). Feed availability and 

rearing densities in hatcheries far exceed those found in natural streams, and may contribute to 

increased aggressive behavior and lowered fright responses compared to wild fish (Symons 1968; 

Bachman 1984; Grant and Kramer 1990; Olla and Davis 1989, 1998; Uchida et al. 1989; Olla et 

al. 1998; Berejikian 1995a,b; Maynard et al. 1995; Berejikian et al. 1996). The traditional hatchery 

practice of providing feed at the water surface may condition hatchery fish to approach the surface 

of the water column (Maynard et al. 1995, Olla et al. 1998, Uchida et al. 1989), and this behavior 

may increase susceptibility to avian predation. Numerous studies have suggested that hatchery 

water supplies or temperature profiles that do not follow natural patterns (e.g., well water) may 

result in incomplete or inappropriately timed growth profiles, smoltification, outmigration, and 

homing (e.g., Pascual et al. 1995; Grant 1997; Beckman et al. 1999, 2000; Larsen et al. 2004) 

Studies have indicated that increased avian and piscivorous predator vulnerability of released 

hatchery fish may be related to decreased crypsis (camouflage coloration) for stream environments 

caused by rearing against uniform (e.g., concrete) hatchery backgrounds (Donnelly and Whoriskey 

1991; Maynard et al. 1995, 1996a). In addition, cultured and naturally-reared salmonids may 

respond differently to habitat in the post-release environment. In most cases, wild fish use both 

riffles and pools in streams, while newly released hatchery fish have been shown to primarily use 

pool environments that are similar to their raceway rearing experience (Allee 1974, Dickeson and 

MacCrimmon 1982, Bachman 1984, Uchida et al. 1989, Olla et al. 1998, Berejikian 1995a). 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-33 

 

4.2.4 Changes in Fish Health 

Fish health, in the fish hatchery context, is a term used when considering the well being of fish 

populations in hatcheries. The term does not indicate whether the fish are diseased or healthy. The 

latter are ones that are free of disease, be it of infectious or non-infectious cause. 

Health of the fish is important to the productivity and success of the hatchery for a number of 

reasons. First, losses experienced during rearing of healthy fish are usually much less than those 

for diseased fish. Second, the cost of trying to correct disease problems in hatcheries can be 

considerable. Third, rearing healthy fish obviates the need for using antimicrobial compounds.42

Finally, healthy fish are more likely than sick fish to survive following release from the hatchery. 

Fish health in a hatchery can be gauged by noting the absence or presence of epizootics (The reoccurrence of epizootics indicates that something is fundamentally wrong with the operation or 

physical set-up of the hatchery). In the absence of epizootics in the hatchery, there may be chronic 

health problems compromising efficient fish production. Evidence of such problems includes 

reduced growth and/or a high prevalence of abnormal gill structure, e.g., gill clubbing. A number 

of fish health manuals dealing with the identification and control of salmonid diseases exist. One 

of particular relevance to salmonid hatcheries in the Pacific Northwest is listed (see Washington 

Department of Fish and Wildlife 1997). In addition, excellent publications outlining cultural 

conditions optimal for the rearing of healthy salmonids are available (e.g., Piper 1992, Wedemeyer 

1996). Use of such publications will greatly assist in ensuring that disease problems are avoided in 

salmonid hatcheries. Finally, early diagnosis of disease problems and prompt action to implement 

needed treatments are critical if disease problems are to be successfully held to a minimum. 

The quality of the water supply in hatcheries has a strong bearing on fish health in hatcheries. 

Water supplies that are not fish-free can be source of a number of fish pathogens and the 

temperature regimes in some surface water supplies can be conducive to disease outbreaks 

because temperature extremes stress fish, thus allowing disease outbreaks to occur. Other water 

quality factors also influence hatchery fish performance. Several dissolved gases have 

implications for effective hatchery management, including oxygen and nitrogen. Levels of 

ammonia and nitrite are also important water quality parameters because both are toxic to fish. 

Fish excrete ammonia and nitrifying bacteria oxidize ammonia to nitrite. These products can occur 

in high concentrations, particularly where water is being reused through a culture system and 

biofilters are not functioning properly. The toxicity of these metabolites is pH dependent and 

varies with species of fish. Natural waters contain additional dissolved gases that must be kept 

below critical concentrations. Inappropriate concentrations of dissolved gases in source waters can 

create added expense for water treatment facilities. Excessive mortality in salmonids can occur at 

pH above 9.0 (Pennell and Barton 1996). As water passes through a hatchery, fish remove oxygen, 

excrete carbon dioxide, urea, and ammonia, and deposit feces. Long-term exposure to high levels 

of carbon dioxide may cause calcium deposits in the kidneys of fish. Chronic high levels can lead 

to increased stress on the fish, affecting their ability to use oxygen. Uneaten food can accumulate 

42 Some of these (e.g., formalin) may be harmful to hatchery personnel if not used strictly according to directions; others (e.g., antibiotics) 

can result in the selection/production of antibiotic resistant fish pathogens (Dixon 1994) and enhance the levels of the resistant forms present 

in the environment (Herwig et al 1997). 
A-34 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

in the pond and can be a source of disease, reduced growth, and reduced survival (Warren 1991; 

Piper et al. 1992; Wedemeyer 1996). Suspended solids, made up of waste feed and feces are 

particularly irritating to gills. This is a serious problem with newly ponded fry, where feeding is 

inefficient and gills seem to be sensitive to particulate matter. 

Culture conditions within hatcheries have a major bearing on the health status of fish being reared. 

As mentioned above, the accumulation of dead fish and the build-up of wastes in hatchery 

containers should be prevented if disease problems are to be avoided. In addition, practices and 

situations likely to result in chronic stress in hatchery fish should be avoided (e.g., frequent fish 

handling, holding of fish in high activity areas, overcrowding). Inappropriate rearing conditions 

can lead to diseases, both infectious and non-infectious, either of which can adversely affect 

growth and survival. The rearing of fish in hatcheries at densities exceeding guidelines often leads 

to disease outbreaks. Care must therefore be taken to ensure that overcrowding in hatcheries does 

not occur. 

4.2.5 Nutrition 

Nutrition is another important factor affecting fish health in the hatchery. The conditions under 

which diets are used and the way in which they are fed can influence the growth and health of 

hatchery fish. If the fish-holding units are difficult to clean or are not cleaned regularly enough, 

the build-up of uneaten feed and fecal matter can cause growth and health problems (Warren 

1991; Piper et al. 1992; Wedemeyer 1996). The effects can be direct or indirect. Direct effects, 

such as mechanical irritation of the gills in very young fish caused by “fines” in the ration, can 

result in mucus build-up on, and bacterial colonization of, the gills, and can lead to respiratory 

difficulty. Indirect effects can include reduced dissolved oxygen levels, due to the increased 

biological oxygen demand caused by the organic loading in the water, and the production of toxic 

substances such as ammonia or nitrite in the water. The indirect effects are more likely to occur in 

large ponds than in well-flushed raceways. In large ponds, unwitting overfeeding can compound 

this problem. In such ponds it is difficult to keep accurate track of fish losses and thus the biomass 

of fish to be fed is often not known with any accuracy. Further, manual cleaning of large ponds is 

often impractical (especially dirt-bottomed ponds), and flushing rates in ponds are usually 

insufficient to prevent the build-up of uneaten feed and fecal matter. 

Nutrition and diet management entails providing the correct amount and type of food to achieve 

desired growth rate, body composition, and condition factors, which are important for maximizing 

survival. Trace elements such as selenium have been implicated in disease resistance (Felton et al. 

1989). Fat and protein percentages have also been shown to be important. In general, wild smolts 

differ from hatchery smolts in three ways: 1) wild fish show rapid growth rate during the smolting 

period (as assessed by plasma levels of insulin-like growth factor-I); 2) wild smolts have less body 

fat than hatchery smolts (hatchery salmon are generally three to five times fatter than wild fish); 

and 3) wild smolts show a more dynamic change in physiological and metabolic status from overwintering to the spring smolting period. Growth rates, body composition and condition factors 

observed in local wild populations can serve as a guide or model for food and data management. 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-35 

Proper nutrition is a prerequisite for the growth and health of hatchery fish, and considerable 

research has been done in developing diets for salmonids. The research has identified the protein 

and amino acids, lipids and fatty acids, vitamins, and minerals that salmonids require (NRC, 1993; 

Higgs et al., 1995a; Li and Hardy, 2000; Higgs and Dong, 2000; Lall, 2002). Diets high in protein 

and lipids, preferably of fish origin, are ideal for salmonids (Higgs et al., 1995a; Higgs and Dong, 

2000) but because of the high cost of fish-derived proteins and lipids, research has shown that less 

costly vegetable sources can be used to satisfy some of these needs (Higgs et al., 1995b; Dosanjh 

et al., 1998; Higgs and Dong, 2000; Li and Hardy, 2000). Problems in diets related to the tendency 

of lipids to become rancid can now be avoided (Hardy and Roley, 2000) and the instability of 

certain vitamins (notably vitamin C) has now largely been solved (Gabaudan and Hardy, 2000). 

Moreover, dry and semi-dry diets that do not require refrigeration, and are capable of being stored 

for extended periods under cool, dry conditions have largely replaced the use of moist and semimoist diets that require frozen storage (WDFW 1996). Diets appropriate for the life-stage of the 

fish being fed are now available, both in terms of formulation and pellet size, and the feeding rates 

required to bring about desired growth rates are known (WDFW 1996). In short, if the feed 

manufacture’s instructions are followed, there is every reason to expect that the fish will do well, 

assuming that other cultural conditions are satisfactory. The only possible goal that current 

commercial diets do not apparently yet achieve is the production of hatchery smolts that mimic 

wild smolts in their chemical make-up. Research on this topic and on the advantages of producing 

such smolts is still in its infancy (Higgs et al., 1995a). 

The method of feeding fish can also affect fish health. If feeding is infrequent enough to cause 

significant hunger, and if the feed is dispensed in a highly localized manner rather than being 

broadcast over a wide area, the localized feeding frenzy that results can cause minor injuries such 

as scale loss that can contribute to infections. Further, such feeding is likely to produce fish that 

vary considerably in size due to intense competition (WDFW 1996). Various types of automatic 

feeders are available but some hand feeding is always advisable, particularly in ponds, as it allows 

the fish culturist to determine when to stop feeding, thereby reducing the chances of feed waste 

and organic matter accumulation. In addition, hand feeding allows the operator to assess fish 

health on the basis of feeding behavior (WDFW 1996). In short, hand feeding and cleaning are the 

two opportunities when hatchery workers can directly observe the behavior and overall health of 

the animals they are attending. 

4.3 Desired Qualities of Propagated Fish 

The success of hatchery programs is determined by the contribution of the propagated stock to 

meeting harvest goals, the conservation of the species, or other goals for the resource. This should be 

measured in terms of how many adults return to fisheries or return to the natural environment to 

reproduce and sustain the stock. It should also be measured by the age class structure, time of return, 

and genetic composition of those returning adults (i.e. measures of “quality”). In order to contribute to 

these goals, hatchery populations must survive and reproduce at rates sufficient to be self-sustaining 

and to support harvest or natural production objectives. One of the primary conditions for hatchery 

success is that anadromous salmon and steelhead populations reared in and released from the artificial 

environment must be healthy and viable. Population health and viability are measured in terms of 

productivity, abundance, diversity, and population structure (McEllaney et al. 2001). These factors are 
A-36 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

determined by the biological (phenotypic) characteristics of the population and the condition of the 

environment (hatchery and natural) available to the population. The population’s biological 

characteristics, in turn, are the influenced by both genetic and environmental factors. 

With rare exceptions, hatchery programs only have control over the propagated stock from the time 

adults return until juveniles are released. Hatcheries must, therefore, provide the type of rearing 

environment and operational protocols to produce juveniles with the proper genetic composition and 

diversity to ensure long-term survival of the hatchery population. Hatcheries must also produce 

juveniles with the biological characteristics that will allow them to survive to adulthood and have the 

desired qualities - as adults - to meet the goals of the hatchery program. 

The long-term survival of all hatchery populations, regardless of the type or purpose of an individual 

program, is influenced by the genetic compositions of those populations, which – in turn – are the 

products of the founding broodstock, local adaptation, domestication and gene flow resulting from 

stock transfers or natural straying. It is also influenced by the genetic diversity of the population, 

which, in the hatchery environment is controlled by the number of spawners, the selection of 

spawners, and the spawning protocols of the program. 

The desired qualities of propagated fish, in terms of genetic characteristics, depend on the purpose of 

the hatchery program (harvest or conservation) and the type of program (segregated or integrated). 

Where a hatchery program has conservation as one of its goals, maintaining the genetic composition 

and diversity of natural population among hatchery-origin fish is critical. Maintaining the 

characteristics of the local natural population requires a genetic management plan that maintains an 

adequate effective population size, mediates proper gene flow, and attempts to minimize the genetic 

effects of potential domestication (Campton 2004). These latter constraints and guidelines are 

particularly important in conservation programs. 

In segregated harvest programs, however, many characteristics of natural populations that are 

important to reproduction in the natural environment may be less important than the traits important to 

meeting the harvest goal or allowing efficient operation of the hatchery. In this case, certain genetic 

guidelines may be relaxed and broodstocks may be bred selectively for particular traits such as early 

run timing. Since the hatchery population is meant to be reproductively isolated from natural 

populations, certain types of artificial selection are acceptable. However, other principles such as 

maintaining adequate effective population sizes and fostering local adaptation are still applicable. 

There should also be recognition that purposeful artificial selection for one trait, such as early run 

timing may lead to inadvertent or correlated selection for another trait that may not be conducive to 

long-term survival of the population. Understanding the genetic and phenotypic correlations among all 

important traits is desirable. Hatcheries must also produce juveniles with biological qualities that will 

allow them as adults to meet the goals of the hatchery program. The survival and reproductive success 

of juvenile hatchery fish depends upon their physiological, morphological, behavioral, and health 

characteristics at the time of their release. One template for achieving healthy and viable hatchery 

populations is the biological characteristics of local wild fish populations. Since these populations 

have persisted for thousands of years, it is difficult to argue that these characteristics are not successful 

once the fish are released into the natural environment. Operators of hatchery programs need to 

understand the importance of these characteristics within the context of the natural environment and 

for certain types of programs should emulate them in the hatchery to the extent possible. Achieving 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-37 

the characteristics of these locally adapted stocks, including their physiology, morphology, behavior, 

and fish health, as well as their natural life history patterns, may provide benefits to hatchery stocks as 

well as reduce negative interactions with naturally produced fish. Deviation from this wild salmon 

template in terms of these factors, while possible and perhaps successful in the short-term may have 

significant consequences to hatchery and natural stocks in the long-term.43

Like genetic guidelines, certain biological guidelines are important no matter what the type and 

purpose of the program. Providing a hatchery environment and operational protocols that lead to good 

fish health is a necessity in every program. While the goal to produce fish with good physiological, 

morphological, and behavioral fitness is a desired outcome in every hatchery program, the means by 

which this is accomplished may vary depending on the type and purpose of the program. 

In integrated harvest and conservation programs for instance, mimicking the growth pattern, size, and 

out-migration timing of natural fish is likely to produce smolts prepared for rapid migration to saltwater, as well as having the ability to survive and grow. Adopting natural life history characteristics by 

allowing volitional out-migration during the normal timing of natural stocks may also provide longterm survival benefits when conditions in the receiving habitat vary. Following the wild fish template 

is also likely to produce adults with the morphological characteristics important to successful 

reproduction in the natural environment. 

In other types of programs such as segregated harvest or segregated conservation programs, producing 

fish with the proper physiological, morphological and behavioral characteristics is still necessary. 

However, using the wild salmon template, may not be the only way to accomplish the goals for such 

programs. In these cases, adoption of operational protocols that lead to better hatchery efficiency, or 

that maximize the survival of the propagated stock may be the overriding factor rather than the desire 

to produce adult fish more suited to reproducing in the wild. When these approaches are chosen, 

however, it must be recognized that deviation from the characteristics that have been derived through 

long-term adaptation of natural stocks, may have undesirable outcomes. 

4.4 Achieving Harvest Goals through the Hatchery 

Environment and Operational Protocols 

Meeting harvest goals requires that hatchery populations must be sufficiently productive and abundant 

to support fisheries. Harvestable fish must also be available at the proper time and place to allow 

fishery access. Harvest contribution is affected by the size of the hatchery program and the survival of 

hatchery fish through their life cycle. The health and viability of hatchery populations are affected by 

the environment in which the fish are reared and depends on the operational protocols of the hatchery 

program. Determining the requirements of the hatchery environment and the selection of operational 

protocols to meet harvest goals is dependent on the type of hatchery program being operated, either 

segregated or integrated. Certain requirements, such as the proper water quality for rearing and 

operational protocols that protect fish health are necessary in any program to meet the basic biological 

needs of the cultured fish. However, other environmental factors, such as the appropriate temperatures 

 

43 See Emerging Issue Paper ....add info here on location of Wild Fish Template 
A-38 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

 

for rearing, nutrition and diet management, and pond loading and densities may be different depending 

on the type of the hatchery program. Other operational protocols including broodstock choice and 

collection, incubation, rearing, and release strategies may also be different. 

4.4.1 Segregated Harvest Programs 

Segregated harvest programs are most appropriate when nearly all returning hatchery-origin adults 

can be harvested or recaptured, or where the habitat or natural environment cannot support natural 

populations of salmonids. They may also be the most appropriate where the only goal for the 

program is harvest and the potential for genetic and ecological interactions between hatcheryorigin and natural-origin fish is minimal, or the biological effects of those interactions are 

considered inconsequential. The size of segregated harvest programs must not exceed thresholds 

above which natural stray rates would pose significant genetic or ecological risks to natural 

populations in the target watershed or other watersheds. Stray rates as low as one to two percent 

for a large, segregated harvest program may pose unacceptable risks to natural populations. 

Hatchery environments appropriate for supporting segregated harvest programs may also have few 

limitations. It must simply provide an adequate water supply suitable for culture of salmonids. 

Other limitations such as the use of water temperatures that would synchronize development of 

hatchery stocks with their natural counterparts is not as important as it might be in other programs, 

therefore, the use of pathogen-free water for segregated harvest programs is preferable. 

Operational guidelines for segregated harvest programs should be appropriate to maximize the 

productivity of the hatchery stock prior to and after release. Since every hatchery stock 

experiences a unique combination of rearing conditions in the hatchery as well as in the receiving 

environment, these guidelines should be based on site-specific studies at each facility. 

Additionally, guidelines for genetic and biological characteristics including physiology, 

morphology, behavior, and fish health need to be followed to contribute to the long-term success 

of the program. Important guidelines to achieve this goal are provided below. These guidelines are 

not comprehensive but are meant to highlight the important factors that need to be achieved to 

meet the goals of a segregated harvest program relative to the hatchery stock only.44 

Important genetic guidelines include the following: 

• Maintain an effective population Ne of at least 500 fish; 

• Avoid the use of broodstock from natural populations or other hatchery populations; 

• Mark or tag all hatchery-released fish, so that the proportions of natural- and hatcheryorigin fish among natural spawners and in the broodstock can be monitored and 

controlled. 

44 A complete compilation of guidelines for segregated harvest programs can be found in Appendix B, p.2-25. Important guidelines that are 

pertinent to the effects of propagated fish on other stocks are provided in framework Chapter 5. 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-39 

Important guidelines for physiological, morphological, and behavioral characteristics include the 

following: 

• Produce fish that have the physiological fitness to migrate rapidly to saltwater and to 

survive in that environment through growth regimes that promote smoltification; 

• Produce fish that have the morphological characteristics to meet harvest goals; 

• Produce fish that have the behavioral characteristics, such as adult migration timing, to 

meet harvest goals. 

Important measures for controlling/preventing diseases in hatcheries include the following: 

• Avoid crowding and build-up of wastes and dead fish in fish holding units; 

• Monitor fish health regularly and implement needed treatments immediately; 

• Use prophylaxis by vaccination where feasible; 

• Use adequate diets that have been stored for only short periods; 

• Avoid practices and situations likely to result in chronic stress (e.g., frequent fish 

handling, holding of fish in high activity areas, overcrowding); 

• Use locally-adapted stocks that are likely to have developed reasonable resistance to any 

pathogens likely to be present in the water supply. 

These measures for controlling/preventing diseases apply to each type and purpose of hatchery 

program. 

4.4.2 Integrated Harvest Programs 

A fundamental goal of an integrated harvest program is to minimize genetic divergence of the 

hatchery broodstock from the naturally spawning population in areas where fish are released 

and/or collected for broodstock. The long-term goal of an integrated harvest program is to 

maintain genetic characteristics of a local, natural population among hatchery-origin fish by 

minimizing genetics changes resulting from artificial propagation and potential domestication. In 

an idealized integrated program, natural-origin and hatchery-origin fish are genetically equal 

components of a common gene pool. 

Integrated harvest programs may be most appropriate when conservation is one of the purposes of 

the program or when significant genetic and ecological interactions cannot be avoided through the 

use of a segregated harvest program. 

The hatchery environment that is appropriate for supporting an integrated harvest program has 

more requirements than the environment necessary to support a segregated harvest program. In 

addition to the water supply being simply suitable for the culture of salmonids, the hatchery 
A-40 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

 

should use a water supply with a temperature regime that would synchronize development of 

hatchery stocks with their natural counterparts. In this case, it is likely that this will require the use 

of surface water, which is not likely to be pathogen-free. 

Since the goal of integrated harvest programs is to minimize divergence from the naturally 

spawning population, strict broodstock management protocols as well other hatchery management 

practices that minimize the potential domestication effects of the hatchery environment should be 

used. Operational guidelines for integrated harvest programs should not be designed to maximize 

the productivity of the hatchery stock, as in segregated harvest programs. Rather, they should 

focus on producing fish with life history strategies providing sufficient productivity to meet 

harvest goals, while minimizing the potential ecological and genetic risks to the composite 

population. In this case, the wild fish in the watershed may provide the best template for how 

hatchery fish should be produced: that is, they should attempt to emulate natural fish in size, 

growth rate, physiology, morphology, and behavior. Important guidelines to achieve this goal are 

provided below. These guidelines are not comprehensive but are meant to highlight the important 

factors that need to be achieved to meet the goals of an integrated segregated harvest program 

relative to the propagated stock.45 

Important genetic guidelines include the following: 

• Develop a detailed genetic management plan for the hatchery broodstock and the 

naturally spawning population in the watershed where adults are trapped for broodstock; 

• Maintain an effective population size (Ne) in the hatchery of at least 500 fish; 

• Ensure that an average of 10 – 20% of the hatchery broodstock is composed of naturalorigin adults each year; 

• Collect and spawn adults randomly with respect to time of return, time of spawning, size 

and other characteristics related to fitness 

• Rear in a hatchery environment and with operational protocols that ensure all portions of 

the population are treated equally and have the same opportunity to contribute to the 

release population; 

• Mark or tag all hatchery-released fish, so that the proportions of natural- and hatcheryorigin fish among natural spawners and in the broodstock can be monitored and 

controlled; 

• Monitor and control natural spawning by hatchery origin adults, so that the percentage of 

natural spawners composed of hatchery-origin fish is less than the percentage of the 

hatchery broodstock derived from natural-origin fish. 

Important guidelines for physiological, morphological, and behavioral characteristics include the 

following: 

45 A complete compilation of guidelines for integrated harvest programs can be found in Appendix B, p.2-25. Guidelines that are pertinent 

to other stocks are provided in Chapter 5 of Appendix A. 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-41 

• Use a hatchery environment that allows synchronization of adult maturation, incubation 

and emergence, and out-migration with natural populations; 

• Use a hatchery environment and rearing protocols that produce juvenile fish similar to 

natural populations in growth rate and size to reduce competition with natural 

counterparts and to maintain the age structure of the natural population; 

• Rear fish at reduced densities in enriched environments to improve cryptic coloration, 

territorial fidelity, and social behavior; 

• Allow some controlled contact with predators to acquire a predator avoidance response; 

• Release fish volitionally during the out-migration timing of the natural stock. 

The important measures for controlling/preventing diseases in hatcheries are the same as for 

segregated harvest programs. 

4.5 Achieving Conservation Goals through the Hatchery 

Environment and Operational Protocols 

Conservation hatcheries46 can play a vital part in the recovery of threatened and endangered species by 

maintaining their genetic diversity and natural behavior, and by reducing the short-term risk of 

extinction. Under proper conditions, conservation hatcheries can maintain severely depleted natural 

stocks in captive culture in gene banks to avoid extinction. Hatcheries have the capability to maintain 

large breeding populations of wild stocks to minimize the risk of demographic loss from unpredictable 

environmental events. Hatcheries, when operating in the conservation mode, can supplement underrecruited wild populations that are below their natural carrying capacity. Finally, in cases where wild 

stocks have been extirpated, conservation hatcheries have the capability to introduce and maintain 

naturally spawning stocks until they are self-sustaining. The conservation hatchery concept implies 

that following the recovery of target populations and receiving habitat, these programs will be 

terminated. In order to be effective, conservation hatchery programs must be integrated with habitat 

and harvest management programs that provide for rebuilding of self-sustaining, naturally spawning 

populations. 

It is well recognized that the artificial rearing conditions within a hatchery can produce fish distinctly 

different from their wild cohorts in behavior, morphology, and physiology. Hatchery methodologies 

can impose different selective pressures on fish, and these can change overall fitness in many ways. 

Conventional hatchery rearing practices can alter genetic fitness through spawning, fertilization and 

rearing protocols. Hatcheries can inadvertently select for fish adaptable to high densities and feeding 

levels, and fish that cannot adapt may be selected against and not survive to release. Similarly, 

conventional practices may deliberately seek to reduce size variability. Within a hatchery population 

this may be desirable, but in the long-term this can be detrimental if fish are expected subsequently to 

rear and spawn in the wild. The wide natural variability in development and timing characteristics of 

 

46 A conservation hatchery is defined as one where the purpose is to recover and conserve naturally spawning populations. 
A-42 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

 

wild fish may be inherent factors that enable these fish to adapt to changing freshwater and marine 

conditions. 

As in harvest programs, determining the requirements of the hatchery environment and the selection of 

operational protocols to meet conservation goals is dependent on the type of hatchery program being 

operated, either segregated or integrated. Again, certain requirements, such as the proper water quality 

for rearing and operational protocols that protect fish health are necessary in any program. 

Additionally, since the stocks propagated in conservation programs usually exist in relatively low 

numbers that are maintained primarily in the hatchery environment, special care must be taken to 

provide security for the stocks to prevent against catastrophic loss. Other recommended environmental 

factors and operational protocols may change depending on the type of conservation program being 

operated. 

4.5.1 Segregated Conservation Programs 

Segregated conservation programs are appropriate in extreme circumstances where the natural 

environment can no longer support an important stock, and the stock is in rapid decline or is in 

imminent risk of extinction. The goal of these programs is to conserve the population and maintain 

its genetic resources while habitat supporting the stock is recovered or adverse environmental 

conditions leading to decline are corrected. At some point in time, the goal of these programs is to 

re-introduce the stock to a natural environment; consequently, it is critical that operational 

protocols are designed to maintain the genetic diversity of the propagated stock. Rearing and 

release protocols should generally be designed to maximize the productivity of the stock, but when 

there are multiple approaches with a high likelihood for success, different strategies should be 

employed to reduce risk. 

The hatchery environment appropriate for supporting a segregated conservation program will vary 

depending on the rearing approach that is used. Security of the stock, however, is critical, and 

hatcheries involved in these types of programs should have multiple water supplies that are 

pathogen-free and redundant systems to provide security. It is also advisable to use multiple 

facilities to provide added security. 

Since the goal of segregated conservation programs is to maintain the propagated stock until it can 

be re-introduced into the natural environment, broodstock protocols should be employed that 

maximize the genetic diversity of the stock, including the potential use of cryo-preserved gametes 

when necessary. Operational guidelines for segregated conservation programs should focus on 

producing juvenile fish similar to their natural counterparts. In extreme cases, the need to 

maximize the survival of each individual may be important enough to use alternative approaches 

such as captive rearing. Important guidelines to achieve the goals of segregated conservation are 

provided below. These guidelines are not comprehensive but are meant to highlight the important 

factors that need to be achieved to meet the goals of a segregated harvest program relative to the 

hatchery stock only.47 

47 A complete compilation of guidelines for segregated conservation programs can be found in Appendix B, p.2-25. Important guidelines 

that are pertinent to the effects of propagated fish on other stocks are provided in framework Chapter 5. 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-43 

Important genetic guidelines include the following: 

• Collect and spawn adults randomly with respect to time of return, time of spawning, size 

and other characteristics related to fitness; 

• Use mating protocols that maximize the effective population size (Ne) in the hatchery, 

including factorial mating, maintenance of individual pedigrees and cryopreserved 

gametes when necessary; 

• Rear in a hatchery environment and with operational protocols that ensure all portions of 

the population are treated equally and have the same opportunity to contribute to the 

release population; 

• Tag all hatchery-released fish to ensure correct identification for use in future 

broodstocks or in other monitoring programs. 

Important guidelines for physiological, morphological, and behavioral characteristics include the 

following: 

• Use a hatchery environment that allows synchronization of adult maturation, incubation 

and emergence, and out-migration with natural populations; 

• Rear fish at reduced densities in enriched environments to improve cryptic coloration, 

territorial fidelity, and social behavior; 

• Release fish volitionally during the out-migration timing of the natural stock; 

• Use a hatchery environment and operational protocols that maximize the survival of each 

individual including captive rearing. 

The important measures for controlling/preventing diseases in hatcheries are the same as for 

segregated harvest programs. 

4.5.2 Integrated Conservation Programs 

Integrated conservation programs are similar to integrated harvest programs with the exception 

that the fish produced are intended to contribute to natural production rather than harvest, and 

might be viewed at a transitional step between a segregated conservation program and an 

integrated harvest program. They are appropriate when demographic risks to the natural 

population outweigh the genetic risk from allowing hatchery-origin fish to spawn naturally. 

Broodstock management protocols should be designed to maintain the genetic diversity of the 

propagated stock, but strict adherence to a specific goal for the composition of the hatchery-origin 

or natural-origin fish on the spawning grounds is relaxed. However, as the number of naturalorigin fish returning to the watershed increases over time, the number of hatchery-origin adults 

allowed to spawn naturally would be restricted in order to allow selection in the natural 

environment to overcome any natural selection in the hatchery. Rearing and release protocols in 
A-44 Scientific Framework - Effects of Hatchery Operations on the Propagated Stock 

 

the hatchery should be similar to those used in integrated harvest programs and should produce 

fish similar to the naturally produced fish of the same species. 

The hatchery environment that is appropriate for supporting an integrated conservation program 

would be the same as that for an integrated harvest program. Integrated harvest programs may also 

have conservation goals, although natural spawning by hatchery-origin fish may not be an explicit 

purpose of a harvest-motivated program. 

Important guidelines to achieve the goals for integrated conservation programs are provided 

below. These guidelines are not comprehensive but are meant to highlight the important factors 

that need to be achieved to meet the goals of an integrated harvest program relative to the 

propagated stock.48 

Important genetic guidelines include the following: 

• Develop a detailed genetic management plan for the hatchery broodstock and the 

naturally spawning population that adapts to changes in the number of natural-origin 

spawners in the watershed; 

• Maintain an effective population size (Ne) in the hatchery of at least 500 fish; 

• Collect and spawn adults randomly with respect to time of return, time of spawning, size 

and other characteristics related to fitness; 

• Rear in a hatchery environment and with operational protocols that ensure all portions of 

the population are treated equally and have the same opportunity to contribute to the 

release population; 

• Mark or tag all hatchery-released fish, so that the proportions of natural- and hatcheryorigin fish among natural spawners and in the broodstock can be monitored and 

controlled. 

Important guidelines for physiological, morphological, and behavioral characteristics include the 

following: 

• Use a hatchery environment that allows synchronization of adult maturation, incubation 

and emergence, and out-migration with natural populations; 

• Use a hatchery environment and rearing protocols that produce juvenile fish similar to 

natural populations in growth rate and size to reduce competition with natural 

counterparts and to maintain the age structure of the natural population; 

48 A complete compilation of guidelines for integrated conservation programs can be found in Appendix B, p.2-25. Guidelines that are 

pertinent to other stocks are provided in framework Chapter 5. 
Scientific Framework - Effects of Hatchery Operations on the Propagated Stock A-45 

• Rear fish at reduced densities in enriched environments to improve cryptic coloration, 

territorial fidelity, and social behavior; 

• Allow some controlled contact with predators to acquire a predator avoidance response; 

• Release fish volitionally during the out-migration timing of the natural stock. 

The important measures for controlling/preventing diseases in hatcheries are the same as for 

segregated harvest programs. 
A-46 Scientific Framework - Effects of Hatchery Fish on Other Stocks and Species 

CHAPTER 5: EFFECTS OF HATCHERY FISH ON HARVEST 

AND CONSERVATION OF OTHER STOCKS AND SPECIES

Depending on the number, size, location and other release factors, hatchery fish may directly or 

indirectly affect other stocks and species through genetic or ecological interactions. The presence of 

hatchery fish may also alter fishing patterns and thereby affect harvest rates on natural produced 

stocks. In the following section we describe these potential effects and identify management actions 

that can help alleviate adverse impacts. 

5.1 Genetics Effects (including changes in biological 

significance and viability)

5.1.1 Changes in Biological Significance 

Hatchery populations directly affect the genetic composition and biological significance of natural 

populations through gene flow, the transfer of genes from hatchery populations into naturally 

spawning populations. Gene flow is influenced by the straying or stocking rate of hatchery 

populations into natural populations, as well as by the reproductive success of the hatchery fish. 

The effects of this gene flow are unpredictable and depend on the genetic composition of the 

hatchery population. 

Genetic changes in natural populations, particularly those related to fitness, are difficult to 

measure. Genetic effects on natural populations depend on factors including the frequency and 

consequence of the interaction. Hatchery fish contribute to gene flow only when they reproduce 

successfully. The magnitude of genetic effects is also influenced by genotypic and phenotypic 

dissimilarity between hatchery and wild populations. The greater the genetic distance, and the 

more dissimilar the hatchery and wild fish, the greater the potential deleterious effects (Withler 

1997). Further, the duration and magnitude of interbreeding, as well as the size of the natural 

population, also influence the potential for genetic effects. The proportion of genes incorporated 

into the local population (rather than the absolute size of the local population) determines the rate 

of gene flow and the potential genetic effects. 

Although the factors influencing genetic effects are well characterized (Grant 1997), predicting the 

magnitude of genetic effects is difficult due to their inherent complexity and our inability to 

accurately measure natural processes on salmonid populations (Busack and Currens 1995; 

Campton 1995). 

Change of Diversity Among Populations 

Hatchery populations can cause a loss or, less commonly, an increase in diversity among 

natural populations. These changes are measured as changes in numbers of alleles, in the 

relative frequencies of alleles, and in the distribution of alleles across populations (within and 

among-population diversity). 
Scientific Framework - Effects of Hatchery Fish on Other Stocks and Species A-47 

A reduction in among-population diversity can result from propagation of a single hatchery 

stock over a wide area, if these fish successfully interbreed with wild fish (Hindar et al. 1991; 

McGinnity et al. 1997). Loss of variation is influenced both by the level of straying (stray or 

stocking rate) and the success of hatchery fish in reproducing in the wild (rate of gene flow). 

As these rates increase, allele frequency differences among populations decrease. The loss 

may be particularly rapid if the hatchery population has reduced within-population variability 

as a result of hatchery practices and successfully interbreeds in large numbers with wild fish 

(Hjort and Schreck 1982; Simon et al. 1986; Waples and Teel 1990). 

Increases in among-population genetic variation can result from a non-native hatchery stock 

interbreeding extensively with a wild population, if the hatchery population is not straying to 

adjacent wild populations. However, the general expectation is that such interbreeding is 

likely to result in a decrease in fitness (Campton 1995; Reisenbichler and Rubin 1999). 

Studies have attempted to specifically address not only the rate of gene flow, but also the 

success of hatchery fish in reproducing in the wild. These studies have typically used genetic 

tagging or marking, so the progeny of hatchery fish can be detected and monitored (Leider et 

al. 1990; Seeb et al. 1990; Tallman and Healey 1994). New DNA methods now allow 

complete reconstruction of pedigrees, thus allowing the reproductive success of individual fish 

to be estimated. 

Some studies suggest that hatcheries have substantial genetic effects in reducing diversity, 

while others support the hypothesis that wild patterns of diversity have been maintained 

despite repeated stock transfers. Bugert et al. (1995) suggest that high rates of straying of 

Columbia River fall Chinook into the Snake River have influenced the genetic composition of 

Snake River fall Chinook salmon. Other studies found that wild patterns have been 

maintained, despite large levels of stocking of non-native fish, presumably because the 

introduced fish were poorly adapted to the environment (Wishard et al. 1984; Currens et al. 

1990). 

Change of Diversity Within Populations 

The same processes that lead to changes in diversity among populations can lead to change of 

diversity within individual populations receiving hatchery fish. In addition to replacement of 

alleles, a reduction in diversity and in the effective size of the wild population can result from 

“genetic swamping,” where a large number of hatchery fish from relatively few parents 

interbreed with wild fish. This is particularly likely if the effective population size of the 

hatchery population is substantially less than that of the wild population (Ryman and Laikre 

1991; Ryman et al. 1995). 

An increase in within-population diversity may result from interbreeding of hatchery fish into 

a population with very low effective population numbers. The consequence of this 

interbreeding would depend on the origin of the hatchery individuals. 
A-48 Scientific Framework - Effects of Hatchery Fish on Other Stocks and Species 

5.1.2 Changes in Viability 

Decreases in viability can occur when two genetically divergent populations interbreed or 

hybridize. These decreases are commonly termed outbreeding depression (Emlen 1991; Lynch 

1991). Outbreeding depression has two possible sources: 1) loss of adaptation (Hindar et al. 1991; 

Reisenbichler and Rubin 1999); and 2) breakup of favorable gene complexes (Templeton 1986; 

Lynch 1997). Loss of adaptation occurs when non-local genes that evolved in a different 

environment replace locally adapted genes, reducing the frequency of favorable genes. This loss 

may be immediately apparent in the first generation. The second cause of outbreeding depression 

occurs as a result of breakup of favorable combinations of genes or gene complexes and may not 

be apparent until the second generation or later (Lynch 1997). 

Reisenbichler and Rubin (1999) reviewed evidence for genetic changes from artificial propagation 

that affect productivity and viability of wild populations. They concluded that fitness in natural 

spawning and rearing environments can be rapidly and substantially reduced by artificial 

propagation. 

Decreases in viability can be measured as a change in productivity between the original local 

population and the hatchery fish. As individuals mate with increasingly genetically-dissimilar 

individuals, outbreeding depression is expected to increase. However, the effects of outbreeding 

depression may not appear for a few generations. Empirical evidence of outbreeding depression 

can be found in experiments in which outbred and control fish are released into natural 

environments and is more likely to be detected if the source populations are genetically different, 

either as a consequence of isolation or of local adaptation. Gharrett and Smoker (1991) evaluated 

hybrids of genetically isolated odd- and even-year pink salmon from the same stream by fertilizing 

eggs with cryo-preserved milt, releasing marked fry into the sea, and recovering marked adults at 

maturity at the natal stream. The returns of F2 individuals were apparently low, and the F2s had 

increased bilateral asymmetry, apparent evidence that co-adapted allele complexes were disrupted 

by outbreeding depression, Decreased survival of F2 hybrids was confirmed in a later study of two 

generations in two independent brood lines of pink salmon naturally spawning in the same stream 

(Gharrett et al. 1999). Gilk et al (2003) observed second-generation hybrids of pink salmon 

populations naturally isolated by 1000km of geographic distance and naturally adapted to different 

local environments; they detected reduced fitness (survival at sea) in both even-year and odd-year 

broodlines, evidence again of disruption of favorable gene complexes. Granath et al (2003) 

observed evidence of diminished adaptation in first-generation hybrids formed among three coho 

salmon populations naturally separated by 220 – 400km; they observed maladaptive embryonic 

development rates in hybrids compared to embryos formed within the three populations and 

observed in a laboratory environment shared in common with the hybrids. 

5.2 Ecological Effects (predation, competition, fish 

health, disease, nutrient enhancement)

Flagg et al. (2000) reviewed almost 300 references on ecological and behavioral impacts of artificial 

production on wild salmonids. The intent of the review was to determine the major impacts of 

different salmonid hatchery production strategies on abundance, competitive social interactions, 
Scientific Framework - Effects of Hatchery Fish on Other Stocks and Species A-49 

predation, health, migration, and population trends. Based on a combination of theoretical 

considerations and available data, the review was in most cases able to identify the directional trend of 

the effects to wild populations of release of hatchery fish. In general, the review indicated that: 1) 

Except in situations of low wild fish density, increasing release numbers of hatchery fish can 

negatively impact wild fish. This appeared true regardless of whether out-of-basin or local stocks were 

released. 2) Competition of hatchery fish with wild fish almost always has the potential to displace 

wild fish from portions of their habitat even where hatchery fish are less competitive on a one-to-one 

basis. 3) Only species that spend extended periods in freshwater habitats after their release have a 

strong potential to decrease the food resources available to wild fish. 4) Potential predation effects 

were documented whenever hatchery fish were significantly larger than comingling wild fish. 

Negative effects of hatchery fish on predator/prey dynamics, through such mechanisms as predator 

concentration, appeared possible at all life stages. 5) Releases of hatchery fish appeared to have the 

potential to affect the health of wild fish, although there was little evidence to suggest that disease 

transmission to wild stocks is routine. 6) Some reports have indicated that the presence of large 

numbers of outmigrating hatchery smolts may hasten the migration of wild smolts. However, neither 

the frequency of the phenomenon, the conditions under which it occurs, nor the effect on ultimate 

survival of wild fish has been documented. 

The ecological effects on freshwater habitat carrying capacity from nutrients derived from 

decomposing salmon carcasses (marine-derived nutrients) are recognized to play an important role in 

the ecology of anadromous salmonids (Bilby et al. 1996, Gresh et al. 2000). In the Northwest, river 

systems in which salmon spawn and rear are often nutrient poor and the delivery of marine-derived 

nutrients by returning salmon carcasses is a key component to potential growth and survival of 

juvenile fish in the system (Larkin and Slaney 1997, Bilby et al. 1996, 1998, 2001; Cederholm et al. 

1999). However, currently only a small fraction of historic marine-derived biomass (returning adults) 

is available to rivers in the Northwest. Thus, in many stream systems in the Northwest the macroinvertebrate communities may currently be below thresholds necessary to sustain increased fish 

production from supplementation releases without causing potential severe competitive interactions 

between supplemented and naturally produced fish. While the deliberate distribution of hatchery 

salmon carcasses into watersheds for purposes of nutrification can have a positive ecological benefit to 

natural salmonid stocks. It is well recognized that disease organisms present in salmon carcasses can 

be transmitted to other salmonids following the release of these organisms into water or through their 

direct consumption. Thus, this practice may also pose a fish health risk to these stocks if not properly 

managed. 

5.3 Harvest Effects 

Hatchery fish can indirectly affect natural stocks through harvest in two ways. First, hatchery 

populations typically can sustain far greater harvest rates than natural stocks, hence mixed stock 

fisheries that are conducted to harvest abundant and productive hatchery stocks will cause natural 

stock to be over harvested (e.g. Flagg et al. 1995). Secondly, abundant hatchery populations may mask 

the abundance of co-mingled natural stocks, causing imprecision in stock assessment and perhaps 

failure to recognize when a natural stock is depressed and in need of protection. 
A-50 Scientific Framework - Effects of Hatchery Fish on Other Stocks and Species 

5.4 Actions to Achieve Desired Outcome

5.4.1 Genetics Actions 

Actions to minimize detrimental genetic effects of hatchery populations on other stocks can be 

taken both within and outside the hatchery environment. Within the hatchery environment, actions 

include choosing an appropriate broodstock (Section 3.1) and using appropriate mating strategy to 

maintain a viable and genetically diverse broodstock (Section 4.1.1). Actions outside the hatchery 

environment include controlling the number of hatchery fish allowed on the spawning grounds 

(Section 4.2.2), and minimizing straying of hatchery fish to the non-target stock from both 

integrated and segregated programs. These latter actions will typically require identification of the 

hatchery stocks through tagging or marking programs to properly control interactions with 

naturally-spawning populations. 

Programs relying on outplanting may pose an elevated genetic risk by promoting stray rates, often 

exceeding natural levels, to freshwater areas where interbreeding with naturally spawning 

populations is undesirable. Tagging and genetic studies have shown that outplanting and net pen 

programs promote stray rates that far exceed natural levels (Candy and Beacham 2000; Mackey et 

al. 2001). Steelhead programs in Puget Sound and coastal Washington have often used outplanting 

to support sport fisheries in a large number of small streams. Similarly, saltwater net pens are used 

to acclimate and release salmon smolts in marine areas where a targeted marine fishery on 

returning adults is desired. A common feature of these programs is that they release fish where no 

or limited facilities exist to trap returning adults that escape target fisheries. Outplanting and netpen releases from segregated hatchery programs carry a potentially higher level of risk, because of 

the likelihood of significant genetic divergence between the hatchery and natural populations (see 

Section 5.1) and the potential for loss of among population diversity should hatchery populations 

interbreed with natural fish. 

5.4.2 Ecological Actions 

As described in Flagg et al. (in press), in order to reduce ecological and behavioral interactions 

between hatchery and wild fish, conservation-minded hatchery operations should include 

incubation and rearing vessels with options for habitat complexity to produce fish more wild-like 

in appearance, and with natural behaviors and higher survival. Rearing goals should be based on 

growth patterns of natural fish and size at emigration on natural population parameters. 

Conservation hatcheries should use low rearing densities to improve juvenile survival during 

rearing and to increase adult quality and return percentage. 

Recommended guidelines for reducing ecological and behavioral interactions include: 

• Determine growth rates, body size and composition, spawning, hatching, and emergence 

times of fish in the local populations and duplicate these in the hatchery by controlling 

factors such as photoperiod, water temperature, and diet composition and feeding rate to 

natural profiles; 
Scientific Framework - Effects of Hatchery Fish on Other Stocks and Species A-51 

• Provide matrix substrates, darkened environments, and temperature control for egg 

incubation and alevin development; 

• Rear fish for their entire juvenile freshwater lives in water from the intended return 

location to imprint natural odors and reduce straying of returning adults, or acclimate 

juveniles at selected release sites where this approach is not possible; 

• Reduce rearing density and maximize fish health; 

• Promote development of body camouflage coloration in juvenile fish by creating more 

natural environments in hatchery rearing vessels; for example through use of overhead 

cover, and in-stream structure, and substrate; 

• Condition young fish to orient to the bottom rather than the surface of the rearing vessel 

by using appropriately positioned feed delivery systems; 

• Release smolts within the size range of wild smolts from which the population is derived 

(except in a case when imminent extinction requires maximal survival, where release of 

large smolts may be warranted); 

• Allow fish to emigrate volitionally to maintain within-population variability in 

outmigration timing found in local wild populations and allow non-smolts (parr) to 

remain in the hatchery, and either smolt, residualize, or perish through natural selection; 

• Adopt strategies for restricting numbers of hatchery-reared juveniles released to not 

exceed carrying capacities of receiving waters and migration pathways (e.g., estuaries). 

In this regard, it appears critical to provide for increases in freshwater habitat carrying capacity 

through such things as nutrient enhancement in order for supplementation programs to minimize 

competitive interactions between hatchery releases and wild fish. 

Recommended guidelines when using hatchery carcasses for nutrient enhancement include: 

• Certifying that adult broodstock is free of viral pathogens prior to planting. The adult 

sampling level should be a minimum of 60 fish for carcass plantings within the same 

watershed and 150 fish for plantings in different watersheds within the same fish health 

management zone; 

• Freezing carcasses prior to planting to reduce the infectious titers of pathogenic 

organisms in the salmon carcasses. This measure will decrease the risk of transmission of 

certain of these disease organisms (see, for example, Margolis 1977 for a metazoan 

parasite, and Evelyn 2001 for two important bacterial fish pathogens); 
A-52 Scientific Framework - Effects of Hatchery Fish on Other Stocks and Species 

• Planting carcasses only within the historic range of the species being used for nutrient 

enhancement; 

• Avoiding the planting of adults or juveniles that may have died of infectious disease. This 

would include pre-spawning adult mortalities and juvenile mortalities from hatchery 

ponds. 

5.4.3 Harvest Actions 

The requirement to protect stocks of concern has increasingly imposed more frequent and 

significant limitations on harvest opportunities. These increased restrictions have created 

challenges to fully harvesting many hatchery populations. Tools available to provide harvest 

access to productive stocks, while protecting weaker ones, include: location of hatchery and 

release sites, selection of broodstock, and time-area harvest management policies. Additional 

tools, such as mass marking of hatchery fish coupled with harvest methods that allow fishers to 

release unmarked fish unharmed, are being developed, and may be appropriate to supplement 

traditional fishery management methods. New and creative ways to target hatchery fish without 

harming stocks of concern should be developed, tested, and implemented if successful.
Scientific Framework - Monitoring and Evaluation A-53 

CHAPTER 6: MONITORING AND EVALUATION: MANAGING 

HATCHERY PROGRAMS FOR ACCOUNTABILITY AND 

SUCCESS

Today’s salmon and steelhead hatcheries are called upon to help meet conservation, harvest, and/or 

other goals (e.g., education, research, cultural and ceremonial needs, and indicator stocks), while 

minimizing adverse impacts on natural-origin salmonids within the watersheds or regions in which 

they operate. To be successful at meeting these goals, accountability for decisions and actions is 

required at all levels within the agencies responsible for management and operation of hatcheries. 

Success will also require an accurate and timely management information system that can measure 

benefits, evaluate actions, and provide information for hatchery management and operations. This 

means that information about hatchery programs and natural stocks must be available in an up-to-date 

database that allows the managers to regularly adjust hatchery programs in response to changing 

conditions in their watersheds. These include changes in the status of natural stocks, carrying capacity 

of the receiving waters, ocean productivity, and harvest needs. 

The co-managers and the HSRG are currently engaged in an effort to develop a comprehensive 

operational monitoring and evaluation plan. This chapter should be viewed as a preliminary report on 

a work in progress. 

6.1 Evaluating Hatchery Success

Managers routinely monitor the operation of hatcheries to evaluate the biological and operational 

performance of individual hatcheries. This information must be used to evaluate the overall 

effectiveness of the system in meeting predetermined goals, and translated into performance measures 

for the system as a whole. Thus it is important that each hatchery program have clearly stated goals, 

not only for the performance of the hatchery stock, but for stocks affected by the hatchery program as 

well. These goals need to be sufficiently detailed to provide accountability for performance and for 

evaluating the benefits actually derived. Currently, protocols for monitoring are determined and 

reported separately by each of the co-managers, often in different dimensions and formats. This makes 

system-wide evaluation difficult. Furthermore, there is little standardization of monitoring criteria both 

within and between the co-management systems. To address these complex issues, managers and 

operators of hatchery programs must have access to, and must use, common tools and procedures that 

aid in: a) recording, organizing and reporting existing and emerging data and information; and b) 

monitoring and evaluating biological uncertainties. 

Monitoring hatchery programs for success must include two major phases: 

Hatchery Culture Phase - This phase involves the tracking of fish culture procedures within 

the hatchery to determine whether conditions in the hatchery are conducive to the production 

of healthy and viable fish, and whether the hatcheries are operating in the most cost-effective 

manner. 
A-54 Scientific Framework – Monitoring and Evaluation 

Post-Release Phase - This phase involves the tracking of released juveniles and returning 

hatchery adults to determine the ecological and genetic interactions between hatchery and wild 

fish in the natural environment, and the contribution of hatchery fish to the stated goals for the 

target stock(s). 

In order to evaluate the success of a program, specific performance indicators for each phase need to 

be identified. Success should be measured in terms of specific goals (validation monitoring) and 

performance benchmarks (performance and effectiveness monitoring) and based on adequate data. 

Further, because of the dynamic nature of ecosystems and the likelihood that interaction effects may 

be small but cumulative, the data gathering and evaluation process must be ongoing and 

comprehensive. 

Effective monitoring and evaluation programs, including implementation, performance, effectiveness, 

and validation monitoring should be developed for all hatchery programs. Data collection protocols 

should be developed and implemented to assure that the data needed for evaluation of both the 

hatchery culture and post-release phase of hatchery programs are available. In particular, standard data 

collection protocols should be developed to assure that information is available to evaluate the genetic 

and ecological consequences of hatchery actions on fish and habitat outside the hatchery. Hatchery 

reporting should document results from the monitoring program as well as any requirements from the 

agencies and funding sources. Tools that streamline standardized record keeping and data storage 

should be implemented. 

Timely and reliable information feedback at all levels of decision making and hatchery operation is an 

absolute requirement for hatchery programs to meet their goals without unnecessary costs. Effective 

feedback systems require that the necessary data be collected and disseminated in a manner that is 

useful and timely to decision makers, operators, scientific advisors and the public. Effectiveness of 

this system presumes a decision making process that is receptive and prepared to act on the 

information provided. 

Coordinated data collection protocols and information dissemination procedures are absolutely 

essential for informed decision making at all levels. Without them, the goals of hatchery reform cannot 

be achieved. 

6.2 Factors Necessary for a Successful Monitoring and 

Evaluation Program 

6.2.1. Decision Making at the Implementation, Effectiveness, 

Performance and Validation/Research Levels 

Existing hatchery programs should be regularly examined to determine whether they are being 

conducted in a manner consistent with resource goals. Managers should use the following 

recommendations in planning new hatchery programs, or altering existing programs when 

monitoring and evaluation (M&E) provides data indicating that changes are needed. This process 

of change and adaptive management must include staff at all levels of hatchery decision making 

and operation—hatchery personnel, field biologists, support scientists and management. 
Scientific Framework - Monitoring and Evaluation A-55 

An inevitable consequence of any hatchery M&E program is that decisions have to be made about 

hatchery operations that are found to be not meeting the stated goals. Effective M&E programs 

including four levels of decision making (implementation, effectiveness, performance, and

validation/research) should be developed for all hatchery programs. Using fish health as an 

example, and starting at the hatchery level of decision making upwards to the management level, 

one might ask the following questions: 

1) Implementation Level: What are the most significant disease problems at the hatchery? 

Are disease control measures being undertaken in an attempt to control them? 

2) Effectiveness Level: Are the disease control measures being used actually effective at 

controlling the disease? The forgoing question focuses on the effectiveness or adequacy of 

the current disease control policies and approaches. 

3) Performance Level: Are the program objectives being met in terms of the number of 

healthy fish released and the number of adults that return to spawn successfully? Do 

disease control methods assure that harvest and conservation goals for the stock are 

achieved? Are the disease risks posed to the target stock and other stocks of such a 

magnitude that, given the treatment options available, the program should be changed or 

even terminated? 

4) Validation/Research Level: What are the critical uncertainties in disease management? 

Where should research be focused to permit better decision making at the three lower 

levels relating to disease control? 

6.2.2. Tools for Evaluating Hatchery Performance 

The hatchery operational guidelines developed by the HSRG49 contain a list of critical questions 

used to determine if individual hatcheries are being operated according to their stated goals. They 

also provide a general checklist of evaluation questions to be asked during the operation of a 

hatchery program. These guidelines, in turn, lead to the HSRG’s monitoring and evaluation 

criteria,50 which identify the type of data that must be collected to permit evaluation to occur. The 

HSRG envisions that the co-managers will develop a detailed list of standardized, system-wide 

monitoring parameters that will be recorded at all hatcheries and that will address both segregated 

and integrated programs. 

The HSRG’s monitoring and evaluation criteria for the hatchery culture phase are organized 

according to six chronological hatchery culture stages, from broodstocking to release: 

1) Broodstock choice 

2) Broodstock collection 

3) Spawning 

 

49 See Appendix C, Hatchery Operational Guidelines. 

50 See Appendix D, Monitoring and Evaluation Criteria. 
A-56 Scientific Framework – Monitoring and Evaluation 

 

4) Incubation 

5) Rearing 

6) Release 

The HSRG Monitoring and Evaluation criteria for the post-release phase are organized into four 

categories: 

1) Habitat quality/quantity 

2) Genetic interactions 

3) Ecological Interactions 

4) Migration barriers 

In the hatchery culture phase, evaluation questions are posed with respect to: 1) genetics, 2) 

physiology, morphology and ecology, and 3) culture of the stock on which the program is 

targeted. In the post-release phase, questions are posed with respect to the interactions between 

hatchery-origin fish, or recruits (HORs), and natural-origin fish, or recruits (NORs). The net result 

is that there are 130 evaluation questions to be considered for each hatchery program, which, in 

turn lead to 60–85 monitoring criteria for which data should be collected, depending on whether 

the hatchery program is integrated or segregated30. In addition to the standardized set of 

parameters that would be monitored at all hatcheries, other parameters could be selected for 

monitoring, based on the goals for stocks subject to individual hatchery programs. 

Evaluation Modules 

Monitoring data gathered during the two collection phases can be assembled into evaluation 

modules, depending on the performance level being evaluated. For example, the hatchery 

culture phase might be comprised of the following evaluation modules: 

• A hatchery water quality module containing measures of settleable solids, pH, 

ammonia, and phosphorus can be used to determine if Washington State Department 

of Ecology (DOE) or US Environmental Protection Agency (USEPA) standards are 

being met. 

• A physiology, behavior and morphology module containing measures of silvering, 

migration readiness, condition index and gill Na-K ATPase can be employed to 

determine if the hatchery fish are smolting properly or meeting the “wild salmonid 

template.”51

• An operational efficiency module could be developed to contain a variety of measures. 

The cost of supplies, utilities, labor and overhead will be some of the inputs required 

to determine the cost effectiveness of the hatchery, along with how the cost per unit of 

smolt produced compares with other hatcheries in the system. 

51 See Emerging Issues in Hatchery Reform paper on this topic, Appendix B 
Scientific Framework - Monitoring and Evaluation A-57 

• A growth evaluation module would be used to compare in-hatchery growth to a predetermined standard, based on feeding rate and water temperature, or to evaluate 

growth modulation. 

• A broodstock module would allow managers to determine, for example, if sufficient 

NORs had been incorporated into the hatchery population, or if spawning protocols 

had been met. 

• A survival module would allow managers to evaluate where within the hatchery 

culture phase any unusual mortality was taking place. 

• A tagging/marking module would be essential in determining adult survival, 

contribution to fisheries and the number of HORs spawning naturally. 

Examples of modules that might be developed to aid in evaluating the success or failure of 

hatchery fish during the post-release phase might include the following: 

• A genetic integration module might be used to determine the ratio of HORs to NORs 

on the spawning grounds, and the relative reproductive success of the two 

components. 

• A freshwater survival module would provide a census of wild and hatchery fish within 

a seeded area until migration. The census would depend on population counts at weirs 

and smolt traps, and on other methods such as snorkeling or other appropriate 

techniques. 

• A habitat suitability module would map rearing and spawning habitat and evaluate 

both the quantity and quality of habitat suitable for spawning and rearing. 

• A freshwater habitat carrying capacity module would require a census of all wild 

juveniles, their residence time and average size, and an estimate of the capacity of the 

receiving habitat to accommodate additional hatchery smolts of a given size and 

population density. 

• A predation module would evaluate the capacity of hatchery fish to prey on, or be 

preyed upon by, wild salmonids. Input would require knowledge on the size (length) 

of hatchery fish at release, the size range of all resident wild fish and the distribution 

in time and space of predators and prey species. 

• A competition module would evaluate the competitive interaction between wild and 

hatchery fish for food resources and space. It would require measures of territoriality, 

gut contents, habitat carrying capacity, and hatchery release procedures. 

• A juvenile migration module would be comprised of measures of the timing and 

magnitude of juvenile outmigration, and would evaluate the emigration of juvenile 

hatchery fish in relation to wild fish emigration. These data are important in matching 

the wild salmonid template, determining the duration of predation, and estimating 

survival of the populations. 
A-58 Scientific Framework – Monitoring and Evaluation 

• An adult migration module would map the distribution of naturally-spawning NORs 

and HORs in the target watershed. Measures of reproductive success, distribution of 

spawning adults (redds), timing of spawning, redd superimposition, and age 

distribution would be required. 

These evaluation modules for the hatchery culture phase and the post-release phase would 

vary in their monitoring parameters, depending on the objectives of the hatchery program and 

whether the hatchery program is segregated from or integrated with the local natural 

population. The above list of modules is by no means complete but it should serve as an 

example of the types of data required to evaluate the Puget Sound and coastal Washington 

hatchery system. 

6.2.3. An Accessible and Unified Data-Gathering System 

The HSRG envisions a readily accessible, computerized and unified data repository of information 

assembled by the co-managers, allowing them to provide descriptive and quantitative information 

on the state of their hatcheries and programs in a timely manner. Co-managers would be 

responsible for analysis of information, evaluation of results and the publication of an annual 

report on the “state of the hatchery system”. The database would be available to all interested 

parties. 

Funding to provide the necessary hardware, software, and personnel may be required to facilitate 

the gathering, recording, and processing of M&E information so that it is immediately available 

to, and comprehendible by, all who need to act on it. 
Scientific Framework – Sources and References A-59 

SOURCES AND REFERENCES

The references section of this appendix lists sources cited in the framework and other relevant 

literature. In addition to the sources cited in the text, this framework draws ideas from several key 

background reports. These include the National Marine Fisheries Service’s Viable Salmonid 

Populations and the Recovery of Evolutionarily Significant Units, the co-managers’ Policy of 

Washington Department of Fish and Wildlife and Western Washington Treaty Tribes Concerning Wild 

Salmonids, the Washington Department of Fish and Wildlife’s additional policy guidance on deferred 

issues concerning wild salmonid policy, the Integrated Hatchery Operations Team’s Policies and 

Procedures for Columbia Basin Anadromous Salmonid Hatcheries, the Independent Scientific 

Advisory Board’s Review of the Draft Performance Standards and Indicators for Artificial Production 

in the Northwest Power Planning Council’s Artificial Production Review and Jim Lichatowich's 

Salmon Without Rivers: A History of the Pacific Salmon Crisis. 

References

Abbot, J. C., R. L. Dunbrack, and C. D. Orr. 1985. The interaction of size and experience in 

dominance relationships of juvenile steelhead trout (Salmo gairdneri). Animal Behavior 92: 

241-253. 

Allee, B. J. 1974. Spatial requirements and behavioral interaction of juvenile coho salmon 

(Oncorhynchus kisutch) and steelhead trout (Salmo gairdneri). Ph.D. Thesis, Univ. 

Washington, Seattle. 

Allen, K. R. 1969. Limitations on production in salmonid populations in streams. Pages 3-18 in T. G. 

Northcote, editor. Symposium on salmon and trout in streams. University of British Columbia. 

Altukhov, Y.P. and Salmenkova, E.A. 1994. Straying intensity and genetic differentiation in salmon 

populations. Aquaculture and Fisheries Management 25: 99-120. 

Bachman, R. A. 1984. Foraging behavior of free-ranging wild and hatchery brown trout in a stream. 

Transactions of the American Fisheries Society 113: 1-32. 

Bams, R. A. 1967. Difference in performance of naturally and artificially propagated sockeye salmon 

migrant fry, as measured with swimming and predation tests. J. Fish. Res. Board Can. 

24:1117-1153. 

Bams, R. A. 1976. Survival and propensity for homing as affected by presence or absence of locally 

adapted paternal genes in two transplanted populations of pink salmon (Oncorhynchus 

gorbuscha). J. Fish. Res. Bd. Can. 33: 2716-2725. 

Banks, J. L. 1994. Raceway density and water flow as factors affecting spring Chinook salmon 

(Oncorhynchus tshawytscha) during rearing and release. Aquaculture 119: 201-207. 
A-60 Scientific Framework – Sources and References 

Barrows, F.T., and W.A. Lellis. 1999. The effect of dietary protein and lipid sources on dorsal fin 

erosion on dorsal fin erosion in rainbow trout, Oncorhynchus mykiss. Aquaculture 180:167-

175. 

Bartley, D., M. Bagley, G. Gall, and B. Bentley. 1992. Use of Linkage Disequilibrium Data to 

Estimate Effective Size of Hatchery and Natural Fish Populations. Conservation Biology 6: 

365-375. 

Baube, C. L. 1997. Manipulations of signaling environment affect male competitive success in threespined sticklebacks. Anim. Behav. 53: 819-833. 

Beacham, T. D. and C. B. Murray. 1993. Fecundity and egg size variation in North American Pacific 

salmon (Oncorhynchus). Journal of Fish Biology 42: 485-508. 

Beacham, T. D. and T. P. T. Evelyn. 1992. Genetic variation in disease resistance and growth of 

Chinook, coho, and chum salmon with respect to vibriosis, furunculosis, and bacterial kidney 

disease. Trans. Amer. Fish. Soc. 121: 456-485. 

Beamesderfer, R. C. and B. E. Rieman. 1991. Abundance and distribution of northern squawfish, 

walleyes, and smallmouth bass in John Day Reservoir, Columbia River. Transactions of the 

American Fisheries Society 120: 439-447. 

Beamish, R.J. and D. Bouillon. 1993. Pacific salmon production trends in relation to climate. Can. J. 

Fish. Aquat. Sci. 50:1002-1016. 

Beckman B.R., DA Larsen, C Sharpe, B Lee-Pawlak, CB Schreck, and WW Dickhoff. 2000. 

Physiological status of naturally reared juvenile spring chinook salmon in the Yakima River: 

Seasonal dynamics and changes associated with smolting. Transactions of the American 

Fisheries Society. 129 (3): 727-753. 

Beckman, B. R., D. A. Larsen, C. Sharpe, B. Lee-Pawlak, C. B. Schreck, and W. W. Dickhoff. 2000. 

Physiological status of naturally-reared juvenile spring chinook salmon in the Yakima River: 

Seasonal dynamics and changes associated with smolting. Transactions of the American 

Fisheries Society 129:727-753. 

Beckman, B.R., D.A. Larsen, B. Lee-Pawlak and W.W. Dickhoff. 1998. Relation of fish size and 

growth rate to migration of spring chinook salmon smolts. North American Journal of 

Fisheries Management 18:537-546. 

Beckman, B.R., D.A. Larsen, C. Sharpe, B. Lee-Pawlak, C.B. Schreck, and W.W. Dickhoff. 2000. 

Physiological status of naturally reared juvenile spring chinook salmon in the Yakima River: 

Seasonal dynamics and changes associated with smolting. Trans. Am. Fish. Soc. 129:727-753. 

Beckman, B.R., W.W. Dickhoff, W.S. Zaugg, C. Sharpe, S. Hirtzel, R. Schrock, D.A. Larsen, R.D. 

Ewing, A. Plamisano, C.B. Schreck and C.V.W. Mahnken. 1999. Growth, smoltification, and 
Scientific Framework – Sources and References A-61 

smolt-to-adult return of spring chinook salmon (Oncorhynchus tshawytscha) from hatcheries 

on the Deschutes River, Oregon. Trans. Am. Fish. Soc. 128:1125-1150. 

Beckman, B.R., W.W. Dickhoff, W.S. Zaugg, C. Sharpe, S. Hirtzel. 1999. Growth, smoltification, and 

smolt-to-adult return of spring chinook salmon from hatcheries on the Deschutes River, OR. 

Transactions of the American Fisheries Society. 128: 1125-1150. 

Beckman, BR, DA Larsen, B. Lee-Pawlak, and WW Dickhoff. 1996. Physiological assessment and 

behavior interaction of wild and hatchery juvenile salmonids: The relationship of fish size and 

growth to smoltification in spring Chinook salmon. BPA Report, October 1996. 

Beechie, T. J., and T. H. Sibley. 1997. Relationships between channel characteristics, woody debris, 

and fish habitat in northwestern Washington streams. Transactions of the American Fisheries 

Society 126: 217-229. 

Beechie, T., E. Beamer, and L. Wasserman. 1994. Estimating coho salmon rearing habitat and smolt 

production losses in a large river basin, and implications for habitat restoration. 14: 797-811. 

Bell, M.C. 1986. Fisheries handbook of engineering requirements and biological criteria. Fish passage 

development and evaluation program, Corps of Engineers, North Pacific Division. 

Berejikian, B. A. 1995. The effects of hatchery and wild ancestry and experience on the relative ability 

of steelhead trout fry (Oncorhynchus mykiss) to avoid a benthic predator. Can. J. Fish. Aquat. 

Sci. 52: 2476-2482. 

Berejikian, B. A. 1995. The effects of hatchery and wild ancestry and experience on the relative ability 

of steelhead trout fry (Oncorhynchus mykiss) to avoid a benthic predator. Can. J. Fish. Aquat. 

Sci. 52: 2476-2482. 

Berejikian, B. A., E. P. Tezak, A. LaRae, T. A. Flagg, E. Kummerow, and C. V. W. Mahnken. 2000. 

Social dominance, growth and habitat use of age-0 steelhead (Oncorhynchus mykiss) grown in 

enriched and conventional hatchery rearing environments. Can. J. Fish. Aquat. Sci. 57: 628-

636. 

Berejikian, B. A., E. P. Tezak, S. L. Schroder, C. M. Knudsen, and J. J. Hard. 1997. Reproductive 

behavioral interactions between wild and captively reared coho salmon (Oncorhynchus 

kisutch). ICES Journal of Marine Science, 54: 1040-1050. 

Berejikian, B. A., E. P. Tezak, S. L. Schroder, C. M. Knudsen, and J. J. Hard. 1997. Reproductive 

behavioral interactions between wild and captively-reared coho salmon (Oncorhynchus 

kisutch). ICES J. Mar. Sci. 54: 1040-1050. 

Berejikian, B. A., E. P. Tezak, S. L. Schroder, K. M. Knudsen, and T. A. Flagg. 1999. Competitive 

differences between newly emerged offspring of captively reared and wild coho salmon 

(Oncorhynchus kisutch). Trans. Am. Fish. Soc. 128:832-839. 
A-62 Scientific Framework – Sources and References 

Berejikian, B. A., E. P. Tezak, S. L. Schroder, T. A. Flagg, and C. M. Knudsen. 1999. Competitive 

differences between newly emerged offspring of captive-reared and wild coho salmon. Trans. 

Am. Fish. Soc. 128: 832-839. 

Berejikian, B. A., S. B. Mathew, and T. P. Quinn. 1996. Effects of hatchery and wild ancestry and 

rearing environments on the development of agonistic behavior in steelhead trout 

(Oncorhynchus mykiss) fry. Can. J. Fish. Aquat. Sci 53: 2004-2014. 

Bigler, S. B., D. W. Welch, and J. H. Helle. 1996. A review of size trends among north Pacific salmon 

(Oncorhynchus spp.). Can. J. Aquat. Sci. 53:455-465. 

Bilby, R. E., B. R. Fransen, and P. A. Bisson. 1996. Incorporation of nitrogen and carbon from 

spawning coho salmon into the trophic system of small streams: evidence from stable 

isotopes. Can. J. Fish. Aquat. Sci. 53: 164-173. 

Bilby, R. E., B. R. Fransen, P. A. Bisson, and J. K. Walter. 1998. Response of juvenile coho salmon 

(Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss) to the addition of salmon 

carcasses to two streams in southwestern Washington, U.S.A. Canadian Journal of Fisheries 

and Aquatic Sciences 55: 1909-1918. 

Bilby, R.E., B.R. Fransen, J.K. Walter, C.J. Cederholm, W.J. Scarlett. 2001. Preliminary evaluation of 

the use of nitrogen stable isotope ratios to establish escapement levels for Pacific salmon. 

Fisheries 26:6-14. 

Bilby, R.E., B.R. Fransen, P.A. Bisson, and J.K. Walter. 1998. Response of juvenile coho salmon 

(Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss) to the addition of salmon 

carcasses to two streams in southwestern Washington, U.S.A. Can. J. Fish Aquat. Sci. 53:164-

173. 

Bilton, H. T. 1980. Returns of adult coho salmon in relation to mean size and time release of juveniles 

to the catch and escapement. Can. Tech. Rep. Fish. Aquatic Sci. 941. 

Bilton, H. T. 1984. Returns of Chinook salmon in relation to juvenile size at release. Can. Tech. Rep. 

Fish. Aquatic Sci. 1245. 

Bisson, P. A., K. Sullivan, and J. L. Nielsen. 1988. Channel hydraulics, habitat use, and body form of 

juvenile coho salmon, steelhead, and cutthroat trout in streams. Transactions of the American 

Fisheries Society 117: 262-273. 

Bjornn, T. C., and D. W. Reiser. 1991. Habitat requirements of salmonids in streams. Pages 83-138 in 

W. R. Meehan, editor. Influences of forest and rangeland management on salmonid fishes and 

their habitats. American Fisheries Society, Bethesda, Maryland. 

Boersen, G., and H. Westers. 1986. Waste solids control in hatchery raceways. Progressive Fish 

Culturist 48: 151-153. 
Scientific Framework – Sources and References A-63 

Brannon, E. L. 1967. Genetic control of migrating behavior of newly emerged sockeye salmon fry. Int. 

Pac. Salmon Fish. Comm. Prog. Rep. 16: 31p. 

Brannon, E. L. 1987. Mechanisms stabilizing salmonid fry emergence timing. Pages 120-124 in E. L. 

Margolis and C. C. Woods, editors. Sockeye salmon (Oncorhynchus nerka) population 

biology and future management. Can. Spec. Pub. Fish. Aquat. Sci. 96. 

Brannon, E. L., K. P. Currens, D. Goodman, J. A. Lichatowich, W. E. McConnaha, B. E. Riddell, and 

R. N. Williams. 1999. Review of Artificial Production of Anadromous and Resident Fish in 

the Columbia River Basin, Part 1: A Scientific Basis for Columbia River Production Program, 

Northwest Power Planning Council, 139 pp. 

Brannon, E.L. 1982. Orientation mechanisms of homing salmonids. Pages 219-227 in E.L. Brannon 

and E.O. Salo, Editors. Proceedings of the salmon and trout migratory behaviour symposium. 

School of Fisheries, University of Washington, Seattle. 

Brannon, E.L., R.P. Whitman and T. P. Quinn. 1984. Responses of returning adult coho salmon to 

home water and population-specific odors. Transactions of the American Fisheries Society 

113:374-377. 

Bugert, R. M. 1998. Mechanics of supplementation in the Columbia River. Fisheries 23: 11-20. 

Bugert, R. M., Hopley, C. W., Busack, C. A., and Mendel, G. W. 1995. Maintenance of stock integrity 

in Snake River Fall Chinook Salmon. Am. Fish. Soc. Symp. 15: 267-276. 

Busack, C. A., and K. P. Currens. 1995. Genetic risks and hazards in hatchery operations: 

Fundamental concepts and issues. Pages 71-80 in H. L. Schramm , Jr. and R. G. Piper, editors. 

Uses and effects of cultured fishes in aquatic ecosystems. American Fisheries Society 

Symposium 15, Bethesda, MD. 

Campton, D. E. 1995. Genetic effects of hatchery fish on wild populations of Pacific salmon and 

steelhead: What do we really know? Pages 337-353 in H. L. Schramm, Jr. and R. G. Piper, 

editors. Uses and effects of cultured fishes in aquatic ecosystems. American Fisheries Society 

Symposium 15, Bethesda, MD. 

Campton, D.E. 2004. Sperm competition in salmon hatcheries: the need to institutionalize geneticallybenign spawning protocols. Transactions of the American Fisheries Society 133: in press. 

Candy, J. R. and T. D. Beacham. 2000. Patterns of homing and straying in southern British Columbia 

coded-wire tagged Chinook salmon (Oncorhynchus tshawytscha) populations. Fisheries 

Research 47: 41-56. 

Cannamela, D. A. 1993. Hatchery steelhead smolt predation of wild and natural juvenile Chinook 

salmon fry in the upper Salmon River, Idaho. Idaho Dept. of Fish and Game. 42 pp. 
A-64 Scientific Framework – Sources and References 

Cederholm, C.J., M.D. Kunze, T. Murota, and A. Sibantani. 1999. Pacific salmon carcasses: essential 

contributions of nutrients and energy for aquatic and terrestial ecosystems. Fisheries 24:6-15. 

Chapman, D. W. 1962. Aggressive behavior in juvenile coho salmon as a cause of emigration. J. Fish. 

Res. Board Can. 19: 1047-1080. 

Chebanov, N. A. and B. E. Riddell. 1998. The spawning behavior, selection of mates, and 

reproductive success of Chinook salmon (Oncorhynchus tshawytscha) spawners of natural and 

hatchery origin under conditions of joint spawning. J. Ichthyol 38: 517-526. 

Chebanov, N. A., N. V. Varnavskaya, and V. S. Varnavsky. 1983. Effectiveness of spawning of male 

sockeye salmon, Oncorhynchus nerka (Salmonidae), of differing hierarchical rank by means 

of genetic-biochemical markers. J. Ichthyol 23: 51-55. 

Chilcote, M. W., S. A. Leider, and J. J. Loch. 1986. Differential reproductive success of hatchery and 

wild summer-run steelhead under natural conditions. Transactions of the American Fisheries 

Society 115: 726-735. 

Cho, C.Y., and D. P. Bureau. 1997 Reduction of waste output from salmonid aquaculture through 

feeds and feeding. Progressive Fish Culturist 59: 155-160. 

Clarke, W. C., J. E. Shelbourne, T. Ogasawara, and T. Hirano. Effect of initial day length on growth, 

seawater adaptability and plasma growth hormone levels in under-yearling coho, Chinook, 

and chum salmon. Salmonid Smoltification III. Proceedings of a workshop sponsored by the 

Directorate for Nature Management, Norwegian Fisheries Research Council, Norwegian 

Smolt producers Association and Statkraft, held at the University of Trondheim, Norway, 27 

June-1 July 1988., Elsevier, Amsterdam (Netherlands), 1989 pp. 51-62 Aquaculture. vol. 82. 

no. 1-4. 

Clay, C.H. 1961. Design of fishways and other fish facilities. Canada Department of Fisheries, 

Ottawa. 

Collis, K., R. E. Beaty, and B. R. Crain. 1995. Changes in catch rate and diet of northern squawfish 

associated with the release of hatchery-reared juvenile salmonids in a Columbia River 

reservoir. North American Journal of Fisheries Management 15: 346-357. 

Columbia Basin Fish and Wildlife Authority. 1994. Integrated Hatchery Operations Team. Columbia 

Basin anadromous salmonid hatchery policies and procedures. Portland, Oregon. 

Cooper, R. and T. Johnson. 1992. Trends in steelhead abundance in Washington and along the Pacific 

Coast of North America. Washington Department of Wildlife and Fisheries, Management 

Report 92-20. 

Cramer, S.P. 2000. The effect of environmentally driven recruitment variation on sustainable yield 

from salmon populations. p. 485-503. In E. E. Knudsen, C. R Steward, D. D. MacDonald, J. 
Scientific Framework – Sources and References A-65 

E. Williams, and D. W. Reiser, eds. Sustainable fisheries management: Pacific salmon. Lewis 

Publishers, Boca Raton, Florida. 

Crow, J. F. 1954. Breeding structure of populations. II. Effective population number. Pages 543-556 in 

O. Kempthorne, T. A. Bancroft, J. W. Gowen, and J. L. Lush, editors. Statistics and 

mathematics in biology. Iowa State College Press, Ames, Iowa. 

Currens, K. P., C. B. Schreck, and H. W. Li. 1990. Allozyme and morphological divergence of 

rainbow trout (Oncorhynchus mykiss) above and below waterfalls in the Deschutes River, 

Oregon. Copeia 1990: 730-746. 

Dickhoff, W.W., B.R. Beckman, D.A. Larsen, C. Duan and S. Moriyama. 1997. The role of growth in 

the endocrine regulation of salmon smoltification. Fish Physiol. Biochem. 17:231-236. 

Dickson, T.A. and H.R. MacCrimmon. 1982. Influence of hatchery experience on growth and 

behavior of juvenile atlantic salmon (salmo-salar) within allopatric and sympatric stream 

populations. Canadian Journal of Fisheries And Aquatic Sciences 39 (11): 1453-1458. 

Dittman, A. H., T. P. Quinn, and G. A. Nevitt. 1995. Timing of imprinting to natural and artificial 

odors by coho salmon (Oncorhynchus kisutch). Can. J. Fish. Aquat. Sci. 53: 434-442. 

Dittman, A.H., T.P. Quinn, and G.A. Nevitt. 1996. Timing of imprinting to natural and artificial odors 

by coho salmon. Canadian Journal of Fisheries and Aquatic Sciences 53:434-442. 

Dixon, B. A. 1994. Antibiotic resistance of bacterial pathogens. J. World Aquacult. Soc. 25: 60-63. 

Donnelly, W. A. and F. G. Whoriskey, Jr. 1991. Background-color acclimation of brook trout for 

crypsis reduces risk of predation by hooded mergansers Lophodytes cucullatus. North 

American Journal of Fisheries Management 11: 206-211. 

Donnelly, W. A., and F. G. Whoriskey Jr. 1991. Background-color acclimation of brook trout for 

crypsis reduces risk of predation by hooded mergansers (Lophodytes cucullatus). North 

American Journal of Fisheries Management 11:206-211. 

Doppelt, B., M. Scurlock, C. Frissell, and J. Karr. 1993. Entering the watershed: a new approach to 

save America's river ecosystems. Island Press. Covelo, California. 

Dosanjh, B.S., D.A. Higgs, D.J. McKenzie, D.J. Randall, J.G. Eales, N. Rowshandeli, M. 

Rowshandeli, and G. Deacon. 1998. Influence of dietary blends of menhaden oil and canola 

oil on growth, muscle lipid composition, and thyroidal status of Atlantic salmon (Salmo salar) 

in sea water. Fish Physiology And Biochemistry. 19 (2): 123-134 

Egglishaw, H. H. 1967. The food, growth and population structure of salmon and trout in two streams 

in the Scottish Highlands. Freshwater Salmon Fish. Res 38: 1-32. 
A-66 Scientific Framework – Sources and References 

Emlen, J. M. 1991. Heterosis and outbreeding depression: a multi-locus model and an application to 

salmon production. Fisheries research (Amsterdam) 12: 187-212. 

Evelyn, T. P. T., L. Prosperi-Porta, and J. E. Ketcheson. 1986a. Persistence of the kidney disease 

bacterium, Renibacterium salmoninarum, in coho salmon Oncorhynchus kisutch, eggs treated 

during and after water hardening with povidone-iodine. J. Fish. Dis. 9: 461-464. 

Evelyn, T. P. T., L. Prosperi-Porta, and J. E. Ketcheson. 1986b. Experimental intra-ovum infection of 

salmonid eggs with Renibacterium salmoninarum and vertical transmission of the pathogen 

with such eggs despite their treatment with erythromycin. Dis. Aquat. Org. 1: 197-202. 

Ewing, R. D. and S. K. Ewing. 1995. Review of the effects of rearing density on survival to adulthood 

for Pacific salmon. Progressive Fish Culturist 57: 1-25. 

Falconer, D. S. and T. D. F. MacKay. 1996. Introduction to Quantitative Genetics, 4th ed. Longman 

Press. London. 

Fausch, K. D. 1984. Profitable stream positions for salmonids: relating specific growth rate to net 

energy gain. Can. J. Zool. 62: 441-451. 

Felsenstein, J. 1997. Population differentiation and evolutionary processes. Pages 31-43 in W. S. 

Grant, editor. Genetic effects of straying on non-native hatchery fish into natural populations: 

Proceedings of the workshop. W. S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSDC30, 130 p. 

Felton, S. P., L. S. Smith, W. Ji, and J. E. Halver. 1989. Implications of selenium involvement during 

chemical and physical stresses in salmonids. Proc. Soc. Exp. Biol. and Med. 190 (3): 303. 

Fenderson, O. C. and M. R. Carpenter. 1971. Effects of crowding on the behavior of juvenile hatchery 

and wild landlocked Atlantic salmon (Salmo salar L.). Anim. Behav. 19: 439-447. 

Fenderson, O. C., W. H. Everhart, and K. M. Muth. 1968. Comparative agonistic and feeding behavior 

of hatchery-reared and wild salmon in aquaria. J. Fish. Res. Board Can. 25: 1-14. 

Flagg, T. A., B. A. Berejikian, J. E. Colt, W. W. Dickhoff, L. W. Harrell, D. J. Maynard, C. E. Nash, 

M. S. Strom, R. N. Iwamoto, and C. W. W. Mahnken. 2000. Ecological and behavioral 

impacts of artificial production strategies on the abundance of wild salmon populations. U. S. 

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-41: 92 p. 

Flagg, T. A., F. W. Waknitz, D. J. Maynard, G. B. Milner, and C. V. W. Mahnken. 1995. The effect of 

hatcheries on native coho salmon populations in the Lower Columbia River. Pages 366-375. 

in H. L. Schramm, Jr. and R. G. Piper, editors. Uses and effects of cultured fishes in aquatic 

ecosystems. American Fisheries Society Symposium 15, Bethesda, MD. 

Flagg, T.A., R.N. Iwamoto, and C.V.W. Mahnken. In press. Conservation Hatchery Protocols for 

Pacific Salmon. Am. Fish. Soc. Symp. Series., Prop. Fish Res. Manag. xx:xx-xx. 
Scientific Framework – Sources and References A-67 

Flagg, T. A., F. W. Waknitz, D. J. Maynard, G. B. Milner, and C. V. W. Mahnken. 1995. The effect of 

hatcheries on native coho salmon populations in the Lower Columbia River. Pages 366-375. 

in H. L. Schramm, Jr. and R. G. Piper, editors. Uses and effects of cultured fishes in aquatic 

ecosystems. American Fisheries Society Symposium 15, Bethesda, MD. 

Fleming, D.F., and J. B. Reynolds. 1991. Effects of spawning-run delay on spawning migration of 

Arctic grayling. In J. Colt and R. White, Editors. Fisheries Bioengineering Symposium. 

American Fisheries Society Symposium 10:299-305. 

Fleming, I. A. 1996. Captive breeding and the conservation of wild salmon populations. Cons. Biol. 8: 

886-888. 

Fleming, I. A. and M. Gross. 1993. Breeding success of hatchery and wild coho salmon 

(Oncorhynchus kisutch): does it differ? Ecological Applications 3: 230-245. 

Fleming, I. A. and M. R. Gross. 1989. Evolution of adult female life history and morphology in a 

Pacific salmon (coho: Oncorhynchus kisutch). Evolution 43: 141-157. 

Fleming, I. A. and M. R. Gross. 1992. Reproductive behavior of hatchery and wild coho salmon 

(Oncorhynchus kisutch): does it differ? Aquaculture 103: 101-121. 

Fleming, I. A. and M. R. Gross. 1994. Breeding competition in a Pacific salmon (coho: Oncorhynchus 

kisutch) : measures of natural and sexual selection. Evolution 48: 637-657. 

Fleming, I. A., B. Jonson, M. R. Gross, and A. Lamberg. 1996. An experimental study of the 

reproductive behavior and success of farmed and wild Atlantic salmon (Salmo salar). J. Appl. 

Ecol. 33: 893-905. 

Foote, C. J., G. S. Brown, and C. C. Wood. 1997. Spawning success of males using alternative mating 

tactics in sockeye salmon, Oncorhynchus nerka. Can. J. Fish. Aquat. Sci. 54: 1785-1795. 

Forster, I. P. and R. W. Hardy. 1995. Captive broodstock literature review. Bonneville Power 

Administration annual report for Project 93-56, 4:1-38. 

Fowler, L. G. and J. L . Banks. 1980. Survival rates for three sizes of hatchery reared fall Chinook 

salmon. U.S. Fish and Wildlife Service, Abernathy Salmon Cultural Development Center. 

Technology Transfer Series 80-1. 

Franklin, I. R. 1980. Evolutionary change in small populations. Pages 135-149 in M. E. Soule and B. 

A. Wilcox, editors. Conservation biology: An evolutionary-ecological perspective. Sinauer 

Assoc., Sunderland, MA. 

Fresh, K. L. 1997. The role of competition and predation in the decline of Pacific salmon and 

steelhead. Pages 245-275 in D. Stouder and R. Naiman, editors. Pacific salmon and their 

ecosystems. Chapman Hall Inc. 
A-68 Scientific Framework – Sources and References 

Fresh, K. L. and S. L. Schroder. 1987. Influence of the abundance, size, and yolk reserves of juvenile 

chum salmon (Oncorhynchus keta) on predation by freshwater fishes in a small coastal stream. 

Can. J. Fish. Aquat. Sci. 44: 236-243. 

Fuss, H. J. and C. Johnson. 1988. Effects of artificial substrate and covering on growth and survival of 

hatchery-reared coho salmon. Progressive Fish-Culturist 50: 232-237. 

Gabaudan, J. and R.W. Hardy. 2000. Vitamin sources for fish feeds. In: The Encyclopedia of 

Aquaculture, R.R. Stickney (Ed.), John Wiley and Sons, Inc., New York, pp. 961-965. 

Geiger, H. J., W. W. Smoker, L. A. Zhivotovsky, and A. J. Gharrett. 1997. Variability of family size 

and marine survival in pink salmon has implications for conservation biology and human use. 

Canadian Journal of Fisheries and Aquatic Sciences 54: 5684-2690. 

Gharrett, A. J. and S. M. Shirley. 1985. A genetic examination of spawning methodology in a salmon 

hatchery. Aquaculture 47: 245-256. 

Gharrett, A. J. and W. W. Smoker. 1991. Two generations of hybrids between even-year and odd-year 

pink salmon (Oncorhynchus gorbuscha): a test for outbreeding depression. Can. J. Fish. 

Aquat. Sci. 48: 1744-1749. 

Gharrett, A. J. and W. W. Smoker. 1993b. A perspective on the adaptive importance of genetic 

infrastructure in salmon populations to ocean ranching in Alaska. Fishery Research 18: 45-58. 

Gharrett, A. J., and W. W. Smoker. 1993a. Genetic components in life history traits contribute to 

population structure. Pages 197-202 in J. G. Cloud and G. H. Thorgaard, editors. Genetic 

conservation of salmonid fishes. Plenum Press, New York. 

Gharrett, A. J., W. W. Smoker, R. R. Reisenbichler, and S. G. Taylor. 1999. Outbreeding depression in 

hybrids between odd- and even-brood year pink salmon. Aquaculture 73: 117-130. 

Gilk, S. E., Wang, I. A., Hoover, C. L., Smoker, W. W., Taylor, S. G., Gray, A. K., and Gharrett, A. J. 

2004. Outbreeding depression in hybrids between spatially separated pink salmon, 

Oncorhynchus gorbuscha, populations: Marine survival, homing ability, and variability in 

family size. Environmental Biology of Fishes In Press. 

Gilpin, M. 1993. Metapopulations and wildlife conservation: approaches to modeling spatial structure. 

Pages 11-27 in D. R. McCullough, editor. Metapopulations and wildlife conservation. Island 

Press, Washington D. C. 

Ginetz, R. M. and P. A. Larkin. 1976. Factors affecting rainbow trout (Salmo gairdneri) predation on 

migrant fry of sockeye salmon (Oncorhynchus nerka). J. Fish. Res. Board Can. 33: 19-24. 

Golley, F. G. 1993. A history of the ecosystem concept in ecology: more than the sum of its parts. 

Yale University Press. New Haven. 
Scientific Framework – Sources and References A-69 

Granath, K. L., Smoker, W. W., Gharrett, A. J., and Hard, J. J. 2004. Effects on embryo development 

time and survival of intercrossing three geographically separate populations of southeast 

Alaska coho salmon, Oncorhynchus kisutch . Environmental Biology of Fishes In Press. 

Grant, J. W. A. and D. L. Kramer. 1990. Territory size as a predictor of the upper limit to population 

density of juvenile salmonids in streams. Can. J. Fish. Aquat. Sci. 47: 1724-1737. 

Grant, W. S. 1997. Genetic effects of straying on non-native hatchery fish into natural populations: 

Proceedings of the workshop. W. S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSDC30, 130 p. 

Grant, W.S. (editor). 1997. Genetic effects of straying of non-native fish hatchery fish into natural 

populations: proceedings of the workshop. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-30, 130 p. 

Gresh, T., Lichatowich, J., Schoonmaker, P. 2000. An estimation of historic and current levels of 

salmon production in the Northeast Pacific Ecosystem. Fisheries 25: 15-21 

Groot, C. and L. Margolis. 1991. Pacific Salmon Life Histories. UBC Press. Vancouver, B. C. 

Hager, R. C. and R. E. Noble. 1976. Relation of size at release of hatchery-reared coho salmon to age, 

size and sex composition of returning adults. Progressive Fish-Culturist 38(3): 144-147. 

Hall, J. D., and M. S. Field-Dodgeson. 1981. Improvement of spawning and rearing habitat for 

salmon. Pages 21-28 in C. L. Hopkins, editor. Proceedings of the salmon symposium. New 

Zealand Ministry of Agriculture and Fisheries Research Division, Occasional Publ. 30, 

Wellington. 

Hankin, D. G. 1990. Effects of month of release of hatchery-reared Chinook salmon on size at age, 

maturation schedule and fishery contribution. OR Dept. Fish and Wildlife Information Report 

90-4. 

Hankin, D. G., J. W. Nicholas, and T. W. Downey. 1993. Evidence for inheritance of age maturity in 

Chinook salmon (Oncorhynchus tshawytscha). Can. J. Fish. Aquat. Sci. 50: 347-358. 

Hanson, A. J. and H. D. Smith. 1967. Mate selection in a population of sockeye salmon 

(Oncorhynchus nerka) of mixed age groups. J. Fish. Res. Board Can. 24: 1977-1995. 

Hard, J. J. and W. R. Heard. 1999. Analysis of straying variation in Alaskan hatchery Chinook salmon 

(Oncorhynchus tshawytscha) following transplantation. Can. J. Fish. Aquat. Sci. 56: 578-589. 

Hard, J. J., A. C. Wertheimer, W. R. Heard, and R. M. Martin. 1985. Early male maturity in two 

stocks of Chinook salmon (Oncorhynchus tshawytscha) transplanted to an experimental 

hatchery in Southeastern Alaska. Aquaculture 48: 351-359. 
A-70 Scientific Framework – Sources and References 

Hard, J. J., and W. K. Hershberger. 1995. Quantitative genetic consequences of captive broodstock 

programs for anadromous Pacific salmon (Oncorhynchus spp.) . Page (2)1-(2)75 in T. A. 

Flagg and C. V. W. Mahnken (editors), editor. An assessment of the status of captive 

broodstock technology for Pacific salmon. 

Hard, J. J., B. A. Berejikian, E. P. Tezak, S. L. Schroder, C. M. Knidsen, and L. T. Parker. 2000. 

Evidence for morphometric differentiation of wild and captively reared adult coho salmon: a 

geometric analysis . Environmental Biology of Fishes 59: 61-73. 

Hard, J. J., G. A. Winans, and J. C. Richardson. 1999. Phenotypic and genetic architecture of juvenile 

morphometry in Chinook salmon. Journal of Heredity 90: 597-606. 

Hardy, R.W. and D.D. Roley, 2000. Lipid oxidation and antioxidants. In: The Encyclopedia of 

Aquaculture, R.R. Stickney (Ed.), John Wiley and Sons, Inc., New York, pp. 470-476. 

Harrison, S., and A. D. Taylor. 1997. Empirical evidence for metapopulation dynamics. Pages 27-42 

in I. Hanski and M. E. Gilpin, editors. Metapopulation Biology. Academic Press Inc, San 

Diego. 

Haskell, B. D., B. G. Norton, and R. Costanza. 1992. Introduction: what is ecosystem health and why 

should we worry about it? Pages 3-20 in R. Costanza, B. G. Norton, and B. D. Haskell, 

editors. Ecosystem Health: new goals for environmental management. Island Press, Covelo, 

California. 

Healey, M. C. 1991. Life history of Chinook salmon (Oncorhynchus tshawytscha) . Pages 311-394 in 

C. Groot and L. Margolis, editors. Pacific salmon life histories. University of British 

Columbia Press, Vancouver, B.C. 

Healey, M. C. and W. R. Heard. 1984. Inter- and intra-population variation in the fecundity of 

Chinook salmon (Oncorhynchus tshawytscha) and its relevance to life history theory. Can. J. 

Fish. Aquat. Sci. 41: 476-483. 

Healey, M.C. 1991. Life history of chinook salmon. Pages 311-393 in C. Groot and L. Margolis, 

editors. Pacific salmon life histories. University of Briths Columbia Press, Vancouver. 

Heath, D. D. 1992. Genetic, environmental, and physiological factors involved in the precocious 

sexual maturation of Chinook salmon (Oncorhynchus tshawytscha). Ph. D. Thesis. University 

of British Columbia, Vancouver, Canada. 166 p. 

Heath, D.H., J. W. Heath, C.A. Bryden, R. A. Johnson, and C.W. Fox. 2003. Rapid evolution of egg 

size in captive salmon. Science 299:1738-1740. 

Hebert, K. P., P. L. Goddard, W. W. Smoker, and A. J. Gharrett. 1998. Quantitative genetic variation 

and genotype by environment interaction of embryo development rate in pink salmon 

(Oncorhynchus gorbuscha). Canadian Journal of Fisheries & Aquatic Sciences. 55: 2048-

2057. 
Scientific Framework – Sources and References A-71 

Hedrick, P. W. and Hedgecock, D. 1994. Effective population size in winter-run chinook salmon. 

Conservation Biology 890-892. 

Hemmingsen, A. R., R. A. Holt, R. D. Ewing, and J. D. McIntyre. 1986. Susceptibility of progeny 

from crosses among three stocks of coho salmon to infection by Ceratomyxa shasta. 

Transactions of the American Fisheries Society 115: 492-495. 

Henderson, M. A. and A. J. Cass. 1991. Effect of smolt size on smolt-to-adult survival for Chilko Lake 

sockeye salmon (Oncorhynchus nerka). Can. J. Fish. Aquat. Sci. 48: 988-994. 

Herwig, R. P., J. P. Gray, and D. P. Weston. 1997. Antibacterial resistant bacteria in surficial 

sediments near salmon net-cage farms in Puget Sound, Washington. Aquacult. 149: 263-283. 

Hickson, B., and D. Leith. 1996. Review of feeds and feed delivery systems suitable for the 

NATURES program. Bonneville Power Administration annual report for Project 91-005, Pp. 

191-216. 

Hickson, B., and D. Leith. 1996. Review of feeds and feed delivery systems suitable for the 

NATURES program. Bonneville Power Administration annual report for Project 91-005, Pp. 

191-216. 

Higgs, D.A., and F.M. Dong. 2000. Lipids and fatty acids. In: The Encyclopedia of Aquaculture, R.R. 

Stickney (Ed.), John Wiley and Sons, Inc., New York, pp. 476-496. 

Higgs, D.A., J.S. Macdonald, C.D. Levings and B.S. Dosanjh. 1995a. Nutrition and feeding habits of 

Pacific salmon (Oncorhynchus species) in relation to life history stage. In: C. Groot, L. 

Margolis and W.C. Clarke (Eds). The Physiology Ecology of Pacific Salmon, U.B.C. Press, 

Vancouver, B.C., pp. 159-315. 

Hilborn, R. and C. Walters. 1992. Quantitative fisheries stock assessment: choice, dynamics & 

uncertainty. Routledge, Chapman and Hall. New York. 

Hilborn, R., T. P. Quinn, P., D.E. Schindler, and D.E. Rogers. 2003. Biocomplexity and fisheries 

sustainability. Proc. Natl. Acad. Sci. 100: 6564-6568. 

Hillman, T. W., and J. W. Mullan. 1989. Effect of hatchery releases on the abundance and behavior of 

wild juvenile salmonids. Pages 265-285 in D. W. Chapman Consultants, editor. Summer and 

winter ecology of juvenile Chinook salmon and steelhead trout in the Wenatchee River, 

Washington. Report of D. W. Chapman Consultants, Boise, Idaho, to Chelan County Public 

Utilities District, Wenatchee, Washington. 

Hindar, K., N. Ryman, and F. Utter. 1991. Genetic effects of cultured fish on natural fish populations. 

Can. J. Fish. Aquat. Sci. 48: 945-957. 
A-72 Scientific Framework – Sources and References 

Hjort, R. C. and C. B. Schreck. 1982. Phenotypic differences among stocks of hatchery and wild coho 

salmon, Oncorhynchus kisutch, in Oregon, Washington and California. Fishery Bulletin 80(1): 

105-119. 

Hoar, W. S. 1951. The behavior of chum, pink, and coho salmon fry in relation to their seaward 

migration. J. Fish. Res. Board Can. 12: 178-185. 

Hochachka, P. W. 1961. Liver glycogen reserves of interacting resident and introduced trout 

populations. J. Fish. Res. Board Can. 18: 125-135. 

Holtby, L. B., B. C. Andersen, and R. K. Kadowski. 1990. Importance of smolt size and early ocean 

growth to interannual variability in marine survival of coho salmon (Oncorhynchus kisutch). 

Can J. Fish . Aquat. Sci. 47:2181-2194. 

Holtby, L. B., D. P. Swain, and G. M. Allan. 1993. Mirror-elicited agonistic behavior and body 

morphology as predictors of dominance status in juvenile coho salmon (Oncorhynchus kisutch 

). Can. J. Fish. Aquat. Sci. 50: 676-684. 

Hunter, C. J. 1991. Better trout habitat. A guide to Stream Restoration and Management. Island Press. 

Covelo, CA. 

Hyatt, K. D. and J. G. Stockner. 1985. Responses of sockeye salmon (Oncorhynchus nerka) to 

fertilization of British Columbia coastal lakes. Can. J. Fish. Aquat. Sci. 42: 320-331. 

Ibarra, A., R. Hedrick, and G. A. E. Gall. 1994. Genetic analysis of rainbow trout susceptibility to the 

myxosporean, Ceratomyxa shasta. Aquaculture 120: 239-262. 

Integrated Hatchery Operations Team. 1994a. Implementation plan for integrating regional hatchery 

policies. Portland, Oregon: Bonneville Power Administration. 

Integrated Hatchery Operations Team. 1994b. Columbia Basin anadromous salmonid hatchery policies 

and procedures. Portland, Oregon: Columbia Basin Fish and Wildlife Authority. 

Integrated Hatchery Operations Team. 1997. Audit Reports . Notes: (Section 2 of each Hatchery 

report), Bonneville Power Administration, Portland, OR. 

Jenkins, T. M. 1969. Social structure, position choice and micro-distribution of two trout species 

(Salmo trutta and Salmo gairdneri) resident in mountain streams. Anim. Behav. 2: 57-123. 

Johnston, N.T., J.S. Macdonald, K.J. Hall, and P.J. Tschaplinski. 1997. A preliminary study of the role 

of sockeye salmon (Oncorhynchus nerka) carcasses as carbon and nitrogen sources for benthis 

insects and fishes in the 'Early Stuart' stock spawning streams, 1050 km from the ocean. 

Fisheries project report no. RD55, Fisheries Branch, Ministry of Environment, Lands, and 

Parks, British Columbia, Canada. 
Scientific Framework – Sources and References A-73 

Jonasson, B. C., R. W. Carmichael, and T. A. Whitesell. 1993. Residual hatchery steelhead: 

Characteristics and potential interactions with spring Chinook salmon in Northeast Oregon. 

Report to U. S. Fish and Wildlife Service, Contract number 14-16-0001-92541. 39 p. 

Jonasson, B. C., R. W. Carmichael, and T. A. Whitesell. 1994. Residual hatchery steelhead: 

Characteristics and potential interactions with spring Chinook salmon in Northeast Oregon. 

Report to U. S. Fish and Wildlife Service, Contract number 14-48-0001-93538. 45 p. 

Jonasson, B. C., R. W. Carmichael, and T. A. Whitesell. 1995. Residual hatchery steelhead: 

Characteristics and potential interactions with spring Chinook salmon in Northeast Oregon. 

Report to U. S. Fish and Wildlife Service, Contract number 14-48-0001-93538. 39 p. 

Kanaga, D., and E.D. Evans. 1982. The effect of the Platte River Anadromous Fish Hatchery on fish, 

benthic macroinvertebrates and nutrients in the Platte Lake. Michigan Department of Natural 

Resources, Water Quality Division, Lansing. 

Kapuscinski, A. R. 1996. Rehabilitation of Pacific salmon in their ecosystems: What can artificial 

propagation contribute? Pages 493-512 in Pacific Salmon and their ecosystems. Chapman 

Hall, Inc.. 

Karr, J. R. 1992. Ecological integrity: protecting earth's life support systems. Pages 223-238 in R. 

Costanza, B. G. Norton, and B. D. Haskell, editors. Ecosystem Health: New Goals for 

Environmental Management. Island Press, Covelo, CA. 

Keenleyside, M. H. A. and H. M. C. Dupuis. 1988. Courtship and spawning competition in pink 

salmon (Oncorhynchus gorbuscha). Canadian Journal of Zoology 66: 262-265. 

Keith, R. M., T. C. Bjorn, W. R. Meehan, N. J. Hetrick, and M. A.Brusven. 1998. Response of 

juvenile salmonids to riparian and instream cover modifications in small streams flowing 

through second-growth forests of SE Alaska. Transactions of the American Fisheries Society 

127: 889-907. 

Kendra, W. 1991. Quality of salmonid hatchery effluents during a summer low-flow season. 

Transactions of the American Fisheries Society 120:43-50. 

Kindschi, G. A. 1987. Method for quantifying degree of fin erosion. Prog. Fish Cult. 49:314-315. 

Kindschi, G. A., H. T. Shaw, and D. S. Bruhn. 1991. Effects of baffles and isolation on dorsal fin 

erosion in steelhead trout, Oncorhynchus mykiss (Walbaum). Aquac. Fish. Manage. 22:3443-

350. 

Kindschi, G.A. 1987. Method for quantifying degree of fin erosion. Progressive Fish-Culturist. 49 (4): 

314-315. 

Kindschi, G.A., R.G. Thompson, and A.P. Mendoza. 1991. Use of raceway baffles in rainbow-trout 

culture. Progressive Fish-Culturist. 53 (2): 97-101. 
A-74 Scientific Framework – Sources and References 

Kirn, R. A., R. D. Ledgerwood, and R. A. Nelson. 1986. Increased abundance and the food 

consumption of northern squawfish (Ptychocheilus oregonensis) at river kilometer 75 in the 

Columbia River. Northwest Science 60: 197-200. 

Kline, T.C. Jr., J.J. Goering, O.A. Mathisen, P.H. Poe, P.L. Parker. 1990. Recycling of elements 

transported upstream by runs of Pacific salmon. 15N and 13C evidence in Sashin Creek, 

southeastern Alaska. Can. J. Fish. Aquat. Sci. 47: 136-144. 

Klontz G.W., M.G. Maskill, and H. Kaiser. 1991. Effects of reduced continuous versus intermittent 

feeding of steelhead. Progressive Fish-Culturist. 53 (4): 229-235. 

Kodric-Brown, A. 1995. Does past reproductive history predict competitive interactions and male 

mating success in pupfish? Anim. Behav. 50: 1433-1440. 

Kramer, D. L., D. Manley, and R. Bourgeois. 1983. The effect of respiratory mode and oxygen 

concentration on the risk of aerial predation in fishes. Can. J. Zool. 61: 653-665. 

Lall, S.P. 2002. The minerals. In Fish Nutrition, 3rd Edition, (J. R. Halver and R.W. Hardy, eds.), 

Academic Press, San Diego, California, pp. 260-308. 

Lande, R. 1988. Genetics and demography in biological conservation. Science 241: 1455-1460. 

Lande, R. 1995. Mutation and conservation. Conservation Biology 9: 782-791. 

Larkin, G. A. and P. A. Slaney. 1996. Trends in marine-derived nutrient sources to south coastal 

British Columbia streams: impending implications to salmonid production. Province of British 

Columbia, Ministry of Environment, Lands and Parks, and Ministry of Forests. Watershed 

Restoration Project Report No. 3: 56p. 

Larkin, G. and P. A. Slaney. 1997. Implications of trends in marine-derived nutrient influx to south 

coastal British Columbia salmonid production. Fisheries 22(11): 16-24. 

Larmoyeux, J.D., and R.G. Piper. 1971. Reducing eroded fin condition in hatchery trout. U.S. Trout 

News. 1971(5):8-9. 

Larsen D.A., B.R. Beckman, K.A. Cooper, D. Barrett, M. Johnston, P. Swanson, and W.W. Dickhoff. 

Assessment of high rates of precocious male maturation in a spring Chinook salmon 

supplementation hatchery program. Transactions of The American Fisheries Society. 133 (1): 

98-120. 

Larsen, D.A. and six coauthors. 2004. Assessment of high rates of precocious male maturation in a 

spring Chinoook salmon supplementation hatchery program. Trans. Am. Fish. Soc. 133:98-

120. 
Scientific Framework – Sources and References A-75 

Larsen, D.A., B.R. Beckman, K.A. Cooper, P. Swanson, and W.W. Dickhoff. 2004. Assessment of 

high rates of precocious male maturation in a spring Chinook salmon supplementation 

hatchery program. Trans. Am. Fish. Soc. 133:98-120. 

Leider, S. A., P. L. Hulett, J. J. Loch, and M. W. Chilcote. 1990. Electrophoretic comparison of the 

reproductive success of naturally spawning transplanted and wild steelhead trout through the 

returning adult stage. Aquaculture 88: 239-252. 

Leon, K. A. and W. A. Bonney. 1979. Effects of artificial substrate and covering on growth and 

survival of hatchery-reared coho salmon. Aquaculture 41: 20-25. 

Lestelle, L. C., L. E. Mobrand, J. A. Lichatowich, and T. S. Vogel. 1996. Applied ecosystem analysis - 

a primer, EDT: the ecosystem diagnosis and treatment method, Bonneville Power 

Administration, Portland, Oregon. 

Levin, P.S., R.W. Zabel and J.G. Williams. 2001. The road to extinction is paved with good intentions: 

negative association of fish hatcheries with threatened salmon. Proceedings of the Royal 

Society of London B (268), 1-6. 

Li, M.H., and R.W. Hardy. 2000. Protein sources for feeds. In: The Encyclopedia of Aquaculture, R.R. 

Stickney (Ed.), John Wiley and Sons, Inc., New York, pp.688-695. 

Lichatowich, J. 1999. Salmon Without Rivers- A History of the Pacific Salmon Crisis. Island Press. 

Covelo, CA. 

Lichatowich, J., L. E. Mobrand, L. Lestelle, and T. Vogel. 1995. An approach to the diagnosis and 

treatment of depleted Pacific salmon populations in freshwater ecosystems. Fisheries 20: 10-

18. 

Lichatowich, J., T. Quinn, W. Hershberger, and A. Kapuscinski. 1994. Written reviews of IHOT 

Policy as requested by BPA. Mobrand Biometrics Inc., compiler. Development of procedures 

for integrating genetic risks and benefits into the planning processes. Vashon, Washington: 

Mobrand Biometrics, Inc. 

Lichatowich, J.A. 1993. Ocean carrying capacity. Technical Report No. 6, Recovery issues for 

threatened and endangered Snake River salmon. Prepared for Bonneville Power 

Administration, Portland, OR. 

Lynch, M. 1991. The genetic interpretation of inbreeding depression and outbreeding depression. 

Evolution 45: 622-629. 

Lynch, M. 1996. A quantitative-genetic perspective on conservation issues. Pages 471-501 in J. C. 

Avise and J. L. Hamrick, editors. Conservation genetics: case histories from nature. Chapman 

& Hall, New York, NY. 
A-76 Scientific Framework – Sources and References 

Lynch, M. 1997. Inbreeding depression and outbreeding depression. Pages 59-70 in W. S. Grant, 

editor. Genetic effects of straying on non-native hatchery fish into natural populations: 

Proceedings of the workshop. W. S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSDC30, 130 p. 

Lynch, M., and M. O'Hely. 2001. Supplementation and the genetic fitness of natural populations. 

Conservation Genetics 2: 363-378. 

Mackey, G., McLean, J.E., and Quinn, T.P. 2001. Comparisons of run timing, spatial distribution, and 

length of wild and newly established hatchery populations of steelhead in Forks Creek, 

Washington. North Am. J. Fisheries Management 21: 717-724. 

Maheshkumar, S., S. M. Goyal, and P. P. Economon. 1992. Evaluation of a concentration procedure to 

detect infectious pancreatic necrosis in water. J. Aquat. Health 4: 58-62. 

Mahnken, C.V.W., G.T. Ruggerone, F.W. Waknitz, and T. A. Flagg. 1998. A historical perspective on 

salmonid production from Pacific Rim hatcheries. N. Pac. Anadr. Fish. Comm. Bull. 1:38-53. 

Mason, J. C. and D. W. Chapman. 1965. Significance of early emergence, environmental rearing 

capacity, and behavioral ecology of juvenile coho salmon in stream channels. J. Fish. Res. 

Board Can. 22: 172-190. 

Mathisen, O.A., P.L. Parker, J.J. Goering, T.C. Kline, P.H. Poe and R.S. Scalan. 1988. Recycling of 

marine elements transported into freshwater systems by anadromous salmon. Verb. Internal. 

Verein. Limnol. 23:2,249-258. 

Maynard, D. J. 1987. Status signaling and the social structure of juvenile coho salmon. University 

Microfilms, Ann Arbor, MI., 226 p. 

Maynard, D. J., T. A. Flagg, and C. V. W. Mahnken. 1995. A review of innovative culture strategies 

for enhancing the post-release survival of anadromous salmonids. Am. Fish. Soc. Symp. 

15:307-314. 

Maynard, D. J., T. A. Flagg, and C. V. W. Mahnken. 1995. A review of innovative culture strategies 

for enhancing the post-release survival of anadromous salmonids. Pages 307-314 in H. L. 

Schramm, Jr. and R. G. Piper, editors. Uses and effects of cultured fishes in aquatic 

ecosystems. American Fisheries Society Symposium 15, Bethesda, MD. 

Maynard, D. J., T. A. Flagg, C. V. W. Mahnken, and S. L. Schroder. 1996. Natural rearing 

technologies for increasing postrelease survival of hatchery-reared salmon. Bull. Nat. Res. 

Inst. Aqua., Supp. 2:71-77. 

Maynard, D. J., T. A. Flagg, C. V. W. Mahnken, and S. L. Schroder. 1996. Natural rearing 

technologies for increasing post-release survival of hatchery-reared salmon. Bull. Natl. Res. 

Inst. Aquacult., Supplement 2: 71-77. 
Scientific Framework – Sources and References A-77 

Mazur, C. F., D. Tillapaugh, and G. K. Iwama. 1993. The effects of feeding level and rearing density 

on the prevalence of Renibacterium salmoninarum in Chinook salmon (Oncorhynchus 

tshawytscha) reared in salt water. Aquaculture 117: 141-147. 

McAllister, K. W. and P. E. McAllister. 1988. Transmission of infectious pancreatic necrosis virus 

from carrier striped bass to trout. Dis. Aquat. Org. 4: 101-104. 

McCubbing, D. J. F. and B. R. Ward. 2000. Stream rehabilitation in British Columbia's Watershed 

Restoration Program: juvenile salmonid response in the Keogh and Waukwaas rivers, 1998. 

Province of British Columbia, Ministry of Environment, Lands and Parks, and Ministry of 

Forests. Watershed Restoration Project Report No. 12: 22. 

McElhany, P., M.H. Ruckleshaus, M.J. Ford, T.C. Wainwright, and E.P. Bjorkstedt. 2000. Viable 

salmonid populations and the recovery of evolutionarily significant units. U.S. Department of 

Commerce, Seattle, Washington. 

McGinnity, P., C. Stone, J. B. Taggart, D. Cooke, D. Cotter, R. Hynes, C. McCamley, T. Cross, and 

A. Ferguson. 1997. Genetic impact of escaped farmed Atlantic salmon (Salmo salar L.) on 

native populations: use of DNA profiling to assess freshwater performance of wild, farmed 

and hybrid progeny in a natural river environment. ICES Journal of Marine Science 54: 998-

1008. 

McGregor, A. J., S. Lane, M. A. Thomason, L. A. Zhivotovsky, W. W. Smoker, and A. J. Gharrett. 

1998. Migration timing, a life history trait important in the genetic structure of pink salmon. 

North Pacific Anadromous Fish Commission Bulletin 1: 262-273. 

McIsaac, D. O. and T. P. Quinn. 1988. Evidence for a hereditary component in homing behavior of 

Chinook salmon (Oncorhynchus tshawytscha). Can, J. Fish. Aquat. Sci. 45: 2201-2205. 

McKibben, C. L. and R. J. Pascho. 1999. Shedding of Renibacterium salmoninarum by infected 

Chinook salmon Oncorhynchus tshawytscha. Dis. Aquat. Org. 38: 75-79. 

McMichael, G. A., T. N. Pearsons, and S. A. Leider. 1999. Minimizing ecological impacts of hatchery 

reared juvenile steelhead trout on wild salmonids in a Yakima basin watershed. Pages 365-380 

in E. E. Knudsen and others, editors. Sustainable fisheries management: balancing the 

conservation, and use of Pacific salmon. CRC Press, Boca Raton, Florida . 

McNicol, R. E. and D. L. G. Noakes. 1984. Environmental influences on territoriality of juvenile 

brook char, Salvelinus fontinalis, in a stream environment. Environmental Biology of Fishes 

10: 29-42 

Meade, J. 1989. Aquaculture Management. Van Nostrand Reinhold. New York. 

Metcalfe, N. B. 1986. Intraspecific variation in competitive ability and food intake in salmonids: 

consequences for energy budgets and growth rates. J. Fish Biol. 28: 525-531. 
A-78 Scientific Framework – Sources and References 

Mighell, J. L. 1981. Culture of Atlantic salmon, Salmo salar, in Puget Sound. Mar. Fish. Rev. 43: 1-8. 

Miller, R. B. 1952. Survival of hatchery-reared cutthroat trout in an Alberta stream. Transactions of 

the American Fisheries Society 81: 35-42. 

Mjolnerod, I. B., I. A. Fleming, U. H. Refseth, and K. Hindar. 1998. Mate and sperm-competition 

during multiple-male spawnings of Atlantic salmon. Can. J. Zool. 76: 70-75. 

Mobrand, L. E., J. A. Lichatowich, L. C. Lestelle, and T. S. Vogel. 1997. An approach to describing 

ecosystem performance "through the eyes of salmon". Canadian Journal of Fisheries and 

Aquatic Sciences 54: 2964-2973. 

Modin, J. 1998. Whirling disease in California: a review of its history, distribution, and impacts, 1965-

1997. Aquat. J. Anim. Health 10: 132-142. 

Moyle, P. B. 1969. Comparative behavior of young brook trout of domestic and wild origin. Prog. 

Fish-Cult. 31: 51-59. 

Mulcahy, D., R. J. Pascho, and C. K. Jenes. 1983. Detection of infectious haematopoietic necrosis 

virus in river water and demonstration of water-borne transmission. J. Fish. Dis. 6: 321-330. 

Mundie, J. H., K. S. Simpson, and C. J. Perrin. 1991. Responses of stream periphyton and benthic 

insects to increases in dissolved inorganic phosphorus in a mesocosm. Can. J. Fish. Aquat. 

Sci. 48: 2061-2072. 

Mundie, J. H., S. M. McKinell, and R. E. Traber. 1983. Responses of stream zoobenthos to enrichment 

of gravel substrates with cereal grain and soybean. Can. J. Fish. Aquat. Sci. 40: 1702-1712. 

Murray, C. B. and T. D. Beacham. 1986. Effect of incubation density and substrate on the 

development of chum salmon eggs and alevins. Progressive Fish-Culturist 48: 242-249. 

Nickelson, T. E. 1986. A model for determining factors limiting abundance, and thereby carrying 

capacity of fishes in stream systems. Pages 13-17 in J. W. Buell, editor. Stream habitat 

enhancement evaluation workshop: level I. Project 86-107. U.S. Department of Energy, 

Bonneville Power Administration, Portland, OR. 

Nickelson, T.E., M.F. Solazzi, and S.L. Johnson. 1986. Use of hatchery coho salmon (Oncorhynchus 

kisutch) pre-smolts to rebuild wild populations in Oregon coastal streams. Can. J. Fish. Aquat. 

Sci. 43: 2443-2449. 

Nickelson, T.E., M.F. Solazzi, S.L. Johnson, and J.D. Rodgers. 1993. An approach to determining 

stream carrying capacity and limiting habitat for coho salmon (Oncorhynchus kisutch). Pages 

251-260 in L. Berg and P. W. Delaney, editors. Proceeding of the Coho Workshop, Nanaimo, 

B. C., May 26-28, 1992. 
Scientific Framework – Sources and References A-79 

Nielsen, J.L. 1994. Invasive cohorts-impacts of hatchery-reared coho salmon on the trophic, 

developmental, and genetic ecology of wild stocks. Pages 361-385 in Theory and Application 

in the Fish Feeding Ecology. The Belle Baruch Library in Marine Science, University of 

South Carolina, Columbia. 

Noakes, D. L. G. 1980. Social behavior in young charrs. Pages 383-702 in E. K. Balon, editor. Charrs, 

salmonid fishes of the genus Salvelinus. Junk Publishers, The Hague. 

Norton, B. G. 1994. Thoreau and Leopold on science and values. Pages 31-46 in K. C. Kim and R. D. 

Weaver, editors. Biodiversity and landscapes. Cambridge University Press, New York. 

NRC (National Research Council, US). 1993. Nutrient Requirements of Fish, National Academy 

Press, Washington, DC, 114 p. 

Olla, B. L., M. W. Davis, and C. H. Ryer. 1988. Understanding how the hatchery environment 

represses or promotes the development of behavioral survival skills. Bull. Mar. Sci. 62: 531-

550. 

Olla, B. L., M. W. Davis, and C. H. Ryer. 1990. Foraging and predator avoidance in hatchery-reared 

Pacific salmon: achievement of behavioral potential. Pages 5-12 in J. E. Thorpe and F. A. 

Huntingford, editors. The importance of feeding behavior for the efficient culture of salmonid 

fishes. World Aquaculture Society, Baton Rouge, LA. 

Olsen, D. and J. Richards. 1994. Inter-basin comparison study: Columbia River salmon production 

compared to other west coast production areas, Phase II analysis. Report to the Army Corps of 

Engineers, Portland, OR. 29 p. 

Pascual, M. A., Quinn, T. P., and Fuss, H. 1995. Factors affecting the homing of fall Chinook salmon 

from Columbia River hatcheries. Transactions of the American Fisheries Society 124: 308-

320. 

Pearce, R.O., and R. T. Lee. 1991. Some design considerations for approach velocities at juvenile 

screening facilities. In J. Colt and R. White, Editors. Fisheries Bioengineering Symposium. 

American Fisheries Society Symposium 10:237-248. 

Pennell, W. and B. A. Barton. 1996. Principles of Salmonid Culture. Elsevier Science. B. V., 

Amsterdam, The Netherlands. 

Perez, M. J., A. I. G. Fernandez, L. A. Rodriguez, and T. P. Nieto. 1996. Differential susceptibility to 

furunculosis of turbot and rainbow trout and release of the furunculosis agent from 

furunculosis-affected fish. Dis. Aquat. Org. 26: 133-137. 

Perry, E. A. 1995. Salmon stock restoration and enhancement: strategies and experiences in British 

Columbia. American Fisheries Society Symposium 15: 152-160. 
A-80 Scientific Framework – Sources and References 

Peterman, R. M. and M. Gatto. 1978. Estimation of functional responses of predators on juvenile 

salmon. J. Fish. Res. Board Can. 35: 797-808. 

Petersen, J. H. and D. L. DeAngelis. 1992. Functional response and capture timing in an individualbased model: predation by northern squawfish (Ptychocheilus oregonensis) on juvenile 

salmonids in the Columbia River. Can. J. Fish. Aquat. Sci. 49: 2551-2565. 

Phelps, S. R., L. L. Leclair, S. Young, and H. L. Blankenship. 1994. Genetic diversity patterns of 

chum salmon in the Pacific Northwest. Canadian Journal of Fisheries and Aquatic Sciences 

51: 65-83. 

Piper, R. G., I. B. McElwain, L. E. Orme, J. P. McCraren, L. G. Fowler, and J. R. Leonard. 1992. Fish 

Hatchery Management, 5th edition. U. S. Fish and Wildlife Service. Washington D. C. 

Poe, T. P., H. C. Hansel, S. Vigg, D. E. Palmer, and L. A. Prendergast. 1991. Feeding of predaceous 

fishes on out-migrating juvenile salmonids in John Day Reservoir, Columbia River. 

Transactions of the American Fisheries Society 120: 405-420. 

Poon, D. C. 1977. Quality of salmon fry from gravel incubators. Ph.D. Thesis, Oregon State Univ. 

Corvallis. 

Quinn, T. 1997. Homing, straying, and colonization. Pages 73-85 in W. S. Grant, editor. Genetic 

effects of straying on non-native hatchery fish into natural populations: Proceedings of the 

workshop. U. S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSDC-30, 130 p. 

Quinn, T. P. 1993. A review of homing and straying of wild and hatchery-produced salmon. Fisheries 

Research 18: 29-44. 

Quinn, T. P. and C. J. Foote. 1994. The effect of body size and sexual dimorphisms on the 

reproductive behavior of sockeye salmon, Oncorhynchus nerka. Anim. Behav. 48: 751-761. 

Raleigh, R. F. 1967. Genetic control in the lakeward migrations of sockeye salmon (Oncorhynchus 

nerka) fry. J. Fish. Res. Board Can. 24: 2613-2622. 

Raleigh, R. F. 1971. Innate control of migrations of salmon and trout fry from natal gravels to rearing 

areas. Ecology 52: 291-297. 

RASP. 1992. Supplementation in the Columbia Basin: summary report series. Final Report, Project 

No. 85-62, Bonneville Power Administration, Portland 

OR. 

Reeves, G. H., J. D. Hall, T. D. Roelofs, T. L. Hickman, and C. O. Baker. 1991. Rehabilitating and 

Modifying Stream Habitats. Pages 519-557 in W. R. Meehan, editor. Influences of forest and 

rangeland management on salmonid fishes and their habitats, American Fisheries Society 

Special Publication 19. American Fisheries Society, Bethesda, Maryland. 
Scientific Framework – Sources and References A-81 

Reimchen, T.E. 1994. Further studies of predator and scavenger use of chum salmon in stream and 

estuarine habitats at Bag Harbour, Gwaii Haanas. Technical report prepared for Canadian 

Parks Service. Queen Charlotte City, British Columbia, Canada. 

Reimers, N. 1963. Body condition, water temperature, and over-winter survival of hatchery-reared 

trout in Convict Creek, California. Transactions of the American Fisheries Society 92: 39-46. 

Reisenbichler, R. R. 1997. Genetic factors contributing to declines of anadromous salmonids in the 

Pacific Northwest. Pages 223-244 in Pacific salmon and their ecosystems. Chapman Hall, 

Inc.. 

Reisenbichler, R. R. and S. P. Rubin. 1999. Genetic changes from artificial propagation of Pacific 

salmon affect the productivity and viability of supplemented populations. ICES Journal of 

Marine Science 56: 459-466. 

Rhodes, J. S. and T. P. Quinn. 1998. Factors affecting the outcome of territorial contests between 

hatchery and naturally reared coho salmon parr in the laboratory. J. Fish. Biol. 53: 1220-1230. 

Ricker, W. E. 1972. Hereditary and environmental factors affecting certain salmonid populations. 

Pages 19-160 in R. C. Simon and P. A. Larkin, editors. The stock concept in Pacific salmon. 

H.R. MacMillan Lectures in Fisheries, Institute of Animal Resource Ecology, University of 

British Columbia. 

Riddell, B. E. and D. P. Swain. 1991. Competition between hatchery and wild coho salmon 

(Oncorhynchus kisutch): genetic variation for agonistic behavior in newly emerged wild fry. 

Aquaculture 98: 161-172. 

Rieman, B. E., R. C. Beamesderfer, S. Vigg, and T. P. Poe. 1991. Estimated loss of juvenile salmonids 

to predation by northern squawfish, walleyes, and smallmouth bass in John Day Reservoir, 

Columbia River. Transactions of the American Fisheries Society 120: 448-458. 

Rose, A. S., A. E. Ellis, and A. L. S. Munro. 1989. The infectivity by different routes of exposure and 

shedding rates of Aeromonas salmonicida subsp. salmonicida in Atlantic salmon, Salmo salar 

L., held in sea water. J. Fish. Dis. 12: 573-578. 

Ruggerone, G. T. and D. E. Rogers. 1984. Arctic char predation an sockeye salmon smolts at Little 

Togiak River, Alaska. Fish. Bull. 82: 401-410. 

Ryman, N. and L. Laikre. 1991. Effects of supportive breeding on the genetically effective population 

size. Conservation Biology 5: 325-3329. 

Ryman, N., Jorde, P. E., and Laikre, L. 1995. Supportive breeding and variance effective population 

size. Conservation Biology 9: 1619-1628. 
A-82 Scientific Framework – Sources and References 

Sakamoto, T. and T. Hirano. 1993. Expression of insulin-like growth factor I gene in osmoregulatory 

organs during seawater adaptation of the salmonid fish: Possible mode of osmoregulatory 

action of growth hormone . Proc. Natl. Acad. Sci. USA 90: 1912-1916. 

Salo, E. O. and W. H. Bayliff. 1958. Artificial and natural production of silver salmon, Oncorhynchus 

kisutch, at Minter Creek, Washington. Wash. Dep. Fish. Res. Bull. 4. 

Sandercock, F. K. 1991. Life history of coho salmon (Oncorhynchus kisutch) . Pages 397-445 in C. 

Groot and L. Margolis, editors. Pacific salmon life histories. University of British Columbia 

Press, Vancouver, B. C., Canada. 

Schiewe, M. H., Flagg, T. A., and Berejikian, B. A. 1997. The use of captive broodstocks for gene 

conservation of salmon in the western United States. Bull. Natl. Res. Inst. Aquacult. Suppl. 3: 

29-34. 

Schreck, C. B. 1996. Immunomodulation: endogenous factors. Pages 311-337 in G. Iwama and T. 

Nakanishi, editors. The fish immune system: organism, pathogen, and environment. Academic 

Press, San Diego. 

Schroder, S. L. 1981. The role of sexual selection in determining the overall mating patterns and mate 

choice in chum salmon. Ph.D. dissertation, University of Washington, Seattle, 241 p. 

Schroder, S. L. 1982. The influence of intrasexual competition on the distribution of chum salmon in 

an experimental stream. Pages 275-285 in E. L. Brannon and E. O. Salo, editors. Salmon and 

trout migratory behavior. University of Washington Press, Seattle. 

Seeb, L. W., J. E. Seeb, R. L. Allen, and W. K. Hershberger. 1990. Evaluation of adult returns of 

genetically marked chum salmon, with suggested future applications. Pages 418-425 in N. C. 

Parker and others, editors. Fish-marking techniques, American Fisheries Society Symposium 

7. 

Shepherd, B. G. 1991. On choosing well: bioengineering reconnaissance of new hatchery sites. In J. 

Colt and R. White, Editors. Fisheries Bioengineering Symposium. American Fisheries Society 

Symposium 10:354-364. 

Sheridan, W. L. 1962. Relation of stream temperatures to timing of pink salmon escapements in 

southeast Alaska. Pages 87-102 in N. J. Wilimovsky, editor. Symposium on Pink Salmon. H. 

R. Mac Millan Lectures in Fisheries. Institute of Fisheries, University of British Columbia , 

Vancouver, BC. 

Shively, R. S., T. P. Poe, and S. T. Sauter. 1996. Feeding response by northern squawfish to a hatchery 

release of juvenile salmonids in the Clearwater River, Idaho. Transactions of the American 

Fisheries Society 125: 230-236. 

Siitonen, L. and G. A. E. Gall. 1989. Response to selection for early spawn date in rainbow trout 

Salmo gairdneri. Aquaculture 78: 153-161. 
Scientific Framework – Sources and References A-83 

Silverstein, J. T. and W. K. Hershberger. 1992. Precocious maturation in coho salmon (Oncorhynchus 

kisutch): Estimation of heritability. Proceedings, 1992 Meeting of the Aquaculture 

Association of Canada, 1-3 June, 1992, University of British Columbia, Vancouver, BC. Bull. 

Aquacult. Assoc. Can. 92: 34-36. 

Silverstein, J.T., K.D. Shearer, W.W. Dickhoff and E.M. Plisetskaya. 1998. The effects of growth and 

fatness on sexual development of chinook salmon (Oncorhynchus tshawytscha) parr. Can. J. 

Fish. Aquat. Sci. 55:2376-2382. 

Simberloff, D. 1988. The contribution of population and community biology to conservation science. 

Annual Review of Ecology and Systematics 19: 473-511. 

Simon, R. C., J. D. McIntyre, and A. R. Hemmingsen. 1986. Family size and effective population size 

in a hatchery stock of coho salmon (Oncorhynchus kisutch). Can. J. Fish. Aquat. Sci 43: 2434-

2443. 

Smoker, W. W., A. J. Gharrett, and M. S. Stekoll. 1998. Genetic variation of return date in a 

population of pink salmon: a consequence of fluctuating environment and dispersive 

selection? Alaska Fishery Research Bulletin 5: 46-54. 

Smoker, W. W., A. J. Gharrett, M. S. Stekoll, and J. E. Joyce. 1994. Genetic analysis of size in an 

anadromous population of pink salmon. Canadian Journal of Fisheries and Aquatic Sciences 

51 (Suppl. 1): 9-15. 

Smoker, W. W., and F. P. Thrower. 1995. Homing propensity in transplanted and native chum salmon. 

Pages 575-576 in H. L. Schramm, Jr. and R. G. Piper, editors. Effects and Uses of Cultured 

Fishes in Aquatic Ecosystems. Special Symposium. American Fisheries Society Symposium 

15. 

Soule, M. E. 1980. Thresholds for survival: Maintaining fitness and evolutionary potential. Pages 151-

169 in M. E. Soule and B. A. Wilcox, editors. Conservation biology: An evolutionaryecological perspective. Sinauer Assoc., Sunderland, MA. 

Stalnaker, C.B., B.L. Lamb, J. Henriksen, K. Bovee, and J. Bartholow. 1995. The instream flow 

incremental methodology: a primer for IFIM. Biological Report 29. U.S. Department of the 

Interior, U.S. Geological Survey. Fort Collins, Colorado. 

Stockner, J. G. and K. R. S. Shortreed. 1978. Enhancement of autotrophic production by nutrient 

addition in a coastal rainforest stream on Vancouver Island. J. Fish. Res. Board Can. 35: 28-

34. 

Su, G.-S., L.-E. Liljedahl, and G. A. E. Gall. 1996. Genetic and environmental variation of body 

weight in rainbow trout (Oncorhynchus mykiss). Aquaculture 144: 71-80. 

Su, G.-S., L.-E. Liljedahl, and G. A. E. Gall. 1997. Genetic and environmental variation of female 

reproductive traits in rainbow trout (Oncorhynchus mykiss) . Aquaculture 154: 113-122. 
A-84 Scientific Framework – Sources and References 

Su, G.-S., L.-E. Liljedahl, and G. A. E. Gall. 1999. Estimates of phenotypic and genetic parameters for 

within-season, date and age at spawning of female rainbow trout. Aquaculture 171: 209-220. 

Swain, D. P. and B. E. Riddell. 1990. Variation in agonistic behavior between newly emerged 

juveniles from hatchery and wild populations of coho salmon, Oncorhynchus kisutch. Can. J. 

Fish. Aquat. Sci. 47: 565-571. 

Swain, D. P., B. E. Riddell, and C. B. Murray. 1991. Morphological differences between hatchery and 

wild populations of coho salmon (Oncorhynchus kisutch): environmental versus genetic 

origin. Can. J. Fish. Aquat. Sci. 48: 1783-1791. 

Symons, P. E. K. 1968. Increase in aggression and in strength of the social hierarchy among juvenile 

Atlantic salmon deprived of food. J. Fish. Res. Board Can. 25: 2387-2401. 

Tallman, R. F. and M. C. Healey. 1994. Homing, straying, and gene flow among seasonally separated 

populations of chum salmon (Oncorhynchus keta). Can. J. Fish. Aquat. Sci. 51: 577-588. 

Taylor, E. B. 1991. A review of local adaptation in Salmonidae with particular reference to Pacific and 

Atlantic salmon. Aquaculture 98: 185-207. 

Taylor, E. B., and J. D. McPhail. 1985. Variation in burst and prolonged swimming performance 

among British Columbia populations of coho salmon, Oncorhynchus kisutch. Can. J. Fish. 

Aquat. Sci. 42:2029-2033. 

Taylor, E.B. and J.D. McPhail. 1985. Variation in burst and prolonged swimming performance among 

british-columbia populations of coho salmon, oncorhynchus-kisutch. Canadian Journal Of 

Fisheries And Aquatic Sciences. 42 (12): 2029-2033. 

Taylor, E.B., and P.A. Larken. 1986. Current response and agonistic behavior in newly emerged fry of 

chinook salmon, oncorhynchus-tshawytscha, from ocean-type and stream-type populations. 

Canadian Journal Of Fisheries And Aquatic Sciences. 43 (3): 565-573. 

Templeton, A. 1986. Coadaptation and outbreeding depression. Pages 105-116 in M. E. Soule, editor. 

Conservation Biology: The Science of Scarcity and Diversity. Sinauer, Sunderland, MA. 

Tipping, J. M. 1997. Effect of smolt length at release on adult returns of hatchery-reared winter 

steelhead. Progressive Fish-Culturist 59: 310-311. 

Tipping, J. M. and H. L. Blankenship. 1993. Effect of condition factor at release on smolt-to-adult 

survival of hatchery sea-run cutthroat trout. Progressive Fish-Culturist 55: 184-186. 

Uchida, K., K. Tsukamotot, S. Ishii, R. Ishida, and T. Kajihara. 1989. Larval competition for food 

between wild and hatchery-reared ayu (Plecoglossus altivelis) in culture ponds. Journal of 

Fish Biology 34:399-407. 
Scientific Framework – Sources and References A-85 

USFWS. 1992. Biological assessment of proposed 1992 LSRCP steelhead and rainbow trout releases. 

USFWS, 4696 Overland Rd, Boise ID 83702. 

Vander Haegen, G. and D. Doty. 1995. Homing of coho and fall Chinook salmon in Washington. 

Washington State Department of Fish and Wildlife Technical Report H95-08. 

Vander Haegen, G., and D. Doty. 1995. Homing of coho and fall chinook salmon in Washington. 

Washington Department of Fish and Wildlife #H95-08. Olympia. 

Varnavsky, V.S., T. Sakamoto, And T. Hirano. 1992. Stunting of wild coho salmon (oncorhynchuskisutch) in seawater - patterns of plasma thyroid-hormones, cortisol, and growth-hormone. 

Canadian Journal Of Fisheries And Aquatic Sciences. 49 (3): 458-461. 

Vincent, R. E. 1960. Some influences of domestication upon three stocks of brook trout (Salvelinus 

fontinalis Mitchill). Transactions of the American Fisheries Society 89: 35-52. 

Wade, M. 1986. The relative effects of Ceratomyxa shasta on crosses of resistant and susceptible 

stocks of summer steelhead. M.S. Thesis, Oregon State University, Corvallis, Oregon. 

Wagner, H.H., F.P. Conte, and J.L. Fessler. 1969. Development of osmotic and ionic regulation in two 

races of chinook salmon Oncorhynchus tshawytscha. Comparitive Biochemistry and 

Physiology 29: 325-341. 

Wahl, D. H., R. A. Stein, and D. R. DeVries. 1995. An ecological framework for evaluating the 

success and effects of stocked fishes. Pages 176-189 in H. L. Schramm, Jr. and R. G. Piper, 

editors. Uses and effects of cultured fishes in aquatic ecosystems. American Fisheries Society 

Symposium 15. 

Waples, R. S. 1989. A generalized approach for estimating effective population size from temporal 

changes in allele frequency. Genetics 121: 379-391. 

Waples, R. S. 1990a. Conservation genetics of Pacific salmon II. Effective population size and the rate 

of loss of genetic variability. J. Hered. 81: 267-276. 

Waples, R. S. 1990b. Conservation genetics of Pacific salmon .III. Estimating effective population 

size. J. Hered. 81: 277-289. 

Waples, R. S. and D. J. Teel. 1990. Conservation genetics of Pacific salmon I. Temporal changes in 

allele frequency. Cons. Biol. 4: 144-156. 

Waples, R. S., R. P. Jones Jr., B. R. Beckman, and G. A. Swan. 1991. Status review for Snake River 

fall Chinook salmon. NOAA (National Oceanic and Atmospheric Administration ) Technical 

Memorandum NMFS (National Marine Fisheries Service) F/NWC-201, Northwest Fisheries 

Science Center, Seattle. 
A-86 Scientific Framework – Sources and References 

Waples. R. S. and C. Do. 1994. Genetic risk associated with supplementation of Pacific salmonids: 

captive broodstock programs. Canadian Journal of Fisheries and Aquatic Sciences 51: 310-

329. 

Warren, J. W. 1991. Diseases of hatchery fish. U.S. Fish and Wildlife Service Publication. 90p. 

Washington Department of Ecology. 2002. A guide to instream flow setting in Washington state. 

Olympia 

Washington Department of Fish and Wildlife. 1997. Fish Health Manual of the Washington 

Department of Fish and Wildlife. 

Washington Department of Fish and Wildlife. 2000. Fish passage barrier and surface water diversion 

screening assessment and prioritization manual. Environmental restoration division, Habitat 

program, Washington Department of Fish and Wildlife. Olympia. 

Washington Fish and Wildlife Commission. 1997a. Policy of Washington Department of Fish and 

Wildlife and Western Washington Treaty Tribes concerning wild salmonids. Olympia, WA. 

46p. 

Washington Fish and Wildlife Commission. 1997b. Additional policy guidance on deferred issues 

concerning wild samonid policy. Olympia, WA. 21p. 

Wedemeyer, G. A. 1996. Physiology of fish in intensive culture systems. Chapman and Hall. New 

York. 

Williams, R. N., J. A. Lichatowich, P. R. Mundy, and M. Powell. 2003. Integratingartificial 

production with salmonid life history, genetic, and ecosystem diversity: a landscape 

perspective. Issue Paper for Trout Unlimited, West Coast Conservation Office, Portland. 

Willoughby, H., H.N. Larsen, and J.T. Bowen. 1972. The pollutional effect of fish hatcheries. 

American Fishes and US Trout News 17(3):6-7, 20-21. 

Winfree, R.A., G.A. Kindschi, and H.T. Shaw. 1998. Elevated water temperature, crowding, and food 

deprivation accelerate fin erosion in juvenile steelhead. Prog. Fish. Cult. 60:192-199. 

Winfree, R.A., G.A. Kindschi, H.T. Shaw. 1998. Elevated water temperature, crowding, and food 

deprivation accelerate fin erosion in juvenile steelhead. Progressive Fish-Culturist. 60 (3): 

192-199. 

Winter, G. W., C. B. Schreck, and J. D. McIntyre. 1980. Resistance of different stocks and transferring 

genotypes of coho salmon, Oncorhynchus kisutch, and steelhead trout, Salmo gairdneri, to 

bacterial kidney disease and vibriosis. Fish. Bull 77: 795-802. 

Wishard, L. N., J. E. Seeb, F. M. Utter, and D. Stefan. 1984. A genetic investigation of suspected 

redband trout populations. Copeia 1984(1): 120-132. 
Scientific Framework – Sources and References A-87 

Withler, F. C. 1982. Transplanting Pacific salmon. Can. Tech. Rep. Fish. Aquat. Sci. 1079: 27. 

Withler, R. 1997. Conclusions of panel. Pages 117-130 in W. S. Grant, editor. Genetic effects of 

straying on non-native hatchery fish into natural populations: Proceedings of the workshop. U. 

S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSDC-30, 130 p. 

Withler, R. E. 1988. Genetic consequences of fertilizing Chinook salmon (Oncorhynchus tshawytscha) 

eggs with pooled milt. Aquaculture 68: 15-25. 

Withler, R. E. and T. D. Beacham. 1994. Genetic consequences of the simultaneous or sequential 

addition of semen from multiple males during hatchery spawning of Chinook salmon 

(Oncorhynchus tshawytscha). Aquaculture 126: 11-23. 

Wolf, L.E. 1938. Effect of amount of food on fin condition of fingerling trout. Prog. Fish. Cult. 39:16-

18. 

Wright, A. 1936. A report of four years experience with fin rot and some remarks on octomitiasis. 

Prog. Fish. Cult. 24:1-26. 

Zhang, Y. and J. L. Congleton. 1994. Detection of infectious hematopoietic necrosis (IHN) virus in 

rearing units for steelhead before and during IHN epizootics. J. Aquat. Anim. Health 6: 281-

287. 

Emerging Issues - Contents and Overview B-1 

B. Emerging Issues in Hatchery Reform 

CONTENTS

MANAGEMENT GOALS FOR HATCHERY BROODSTOCKS: GENETIC INTEGRATION VERSUS 

SEGREGATION ........................................................................................................................................B-3

USING HATCHERY SALMON CARCASSES FOR NUTRIFICATION OF FRESHWATER ECOSYSTEMS WHILE 

REDUCING ASSOCIATED FISH HEALTH RISKS. ...................................................................................B-28

HATCHERY SMOLT QUALITY AND ACHIEVING THE WILD SALMON TEMPLATE ..............................B-30

BENEFITS OF HATCHERY FISH AS A SOURCE OF FOOD.......................................................................B-39

MARINE CARRYING CAPACITY ...........................................................................................................B-41

OUTPLANTING AND NET PEN RELEASE OF HATCHERY-ORIGIN FISH................................................B-44

ASSESSING THE POTENTIAL FOR PREDATION ON WILD SALMONID FRY BY HATCHERY-REARED 

SALMONIDS IN WASHINGTON..............................................................................................................B-51

USING ACCLIMATION PONDS IN THE REARING OF SALMON..............................................................B-68
B-2 Emerging Issues – Contents and Overview 

 

OVERVIEW

The HSRG—recognizing that the scientific framework needs to be a “living document” that is 

regularly updated to include new information and issues not identified in its original drafting—decided 

that significant revisions to the scientific framework should be derived – not just from new published 

scientific literature – but also from “emerging issue” papers authored by the HSRG or its individuals 

members. These papers can be as simple as a few paragraphs or as detailed as an essay for a peerreviewed journal. The HSRG welcomes feedback on these “emerging issues.” They are incorporated 

into the framework once they have been reviewed and refined. Several that have been incorporated to 

date remain in this chapter as well, to highlight their importance. 

These emerging issues papers also relate to two other key elements of the Hatchery Reform Project. 

They are tied to the hatchery reform research program52 because they discuss topics that reflect 

recently available scientific information or an emerging principle derived from the collation of old and 

new information. In addition, they are tied to the three principles of hatchery reform53 because 

developing scientific knowledge in these areas will support successful hatchery operation and 

management in the context of well-defined goals, scientifically defensible programs, and informed 

decision making. 

In keeping with their status as “emerging issues,” it is important to keep in mind that all of these 

papers are “works in progress,” to be revised as new information comes to light on the issues at hand. 

They are not to be considered definitive, exhaustive and/or final statements on their respective topics, 

although some of them may form the basis for publications in the scientific literature if they so 

warrant. 

52 See Research Program in Applied Hatchery Reform chapter. 

53 See Principles and System-Wide Recommendations in Applied Hatchery Reform chapter. 
Emerging Issues - Genetic Integration versus Segregation B-3 

MANAGEMENT GOALS FOR HATCHERY BROODSTOCKS:

GENETIC INTEGRATION VERSUS SEGREGATION

Background

More than 200 hatcheries and satellite facilities propagate Pacific salmon (Oncorhynchus spp.) 

and steelhead (O. mykiss) throughout the Pacific Northwest. More than 100 of these facilities exist 

in Washington state alone. This extensive hatchery system was developed over a 100-year period 

with a principal goal of producing fish for harvest, largely to mitigate for the effects of 

overfishing, land-use practices, hydropower development, and losses of freshwater habitats (see 

Lichatowich 1999 for a historical review). In general, hatcheries have been very successful at 

providing fish for harvest. Hatchery-origin fish support nearly all commercial, tribal and 

recreational salmon fisheries in Washington, and they also contribute to salmon fisheries in British 

Columbia and Alaska. 

A new conservation role for salmon hatcheries has been emerging in the Pacific Northwest in 

recent years. This new role has been motivated by significant declines in the abundance of 

naturally-spawning salmon and steelhead since the mid-1970s. These declines culminated in the 

listing of 26 Evolutionarily Significant Units, or ESUs (Waples 1995), of Pacific salmon and 

steelhead under the U.S. Endangered Species Act (ESA; see www.nwr.noaa.gov). Hatchery 

programs with conservation goals include captive rearing of endangered species (Schiewe et al. 

1997), maintenance propagation of imperiled populations (Bugert et al. 1995), and 

supplementation, natural spawning by hatchery-origin adults (Carmichael and Messmer 1995; 

Hedrick et al. 2000). Several hatchery programs with conservation goals exist in western 

Washington, including programs for genetically distinct populations of Chinook salmon (O. 

tshawytscha) on the Elwha, Dungeness and White rivers, and summer chum salmon (O. keta) in 

the Hood Canal region of Puget Sound. 

Concerns regarding potential genetic and ecological impacts of hatchery-origin fish on naturally 

spawning populations have raised questions regarding the future role of salmon and steelhead 

hatcheries in the Pacific Northwest (Hindar et al. 1991; Waples 1991; Hilborn 1992; Busack and 

Currens 1995; Campton 1995; Currens and Busack 1995; Reisenbichler and Rubin 1999; Levin et 

al. 2001). These concerns began in the mid-1970s (e.g. Reisenbichler and McIntyre 1977) and 

reached a peak of criticism in the early 1990s (e.g. Meffe 1992). In response, hatchery programs 

are currently undergoing reform measures to reduce genetic and ecological risks to naturally 

spawning populations, while continuing to provide harvest and conservation benefits (Maynard et 

al. 1995; Flagg and Nash 1999; see also www.hatcheryreform.org). 

The mandates of hatchery reform and the need to recover ESA listed populations have motivated a 

fundamental reevaluation of the basic biological premises under which hatchery programs are 

designed, managed and operated. This reevaluation requires that each hatchery program operate in 

a manner consistent with fundamental biological principles, including the constraints imposed by 

the aquatic ecosystems within which those programs occur. This reevaluation requires that each 
B-4 Emerging Issues – Genetic Integration versus Segregation 

 

program explicitly state: 1) the specific purpose and desired benefits to be derived from hatcheryorigin fish; and 2) the genetic management goals of each hatchery broodstock relative to naturally 

spawning populations. In the past, these purposes and goals have not always been clearly defined, 

quantified or distinguished. 

Here we describe two distinct types of hatchery programs that reflect fundamentally different 

genetic management goals for hatchery broodstocks. We refer to these two types of programs as 

“integrated” and “segregated.” Hatchery programs are classified as integrated if the principal goal 

is to manage the broodstock as an artificially propagated component of a naturally spawning 

population or gene pool. An implicit goal of an integrated program is to artificially increase the 

demographic size or productivity of a population, while preventing genetic divergence between 

the hatchery and naturally-spawning components. Conversely, hatchery programs are classified as 

segregated if the principal goal is to develop and manage a broodstock as a genetically discrete or 

segregated population relative to naturally spawning populations. Segregated broodstocks are 

managed as if they are distinct populations or species relative to natural populations; no explicit 

genetic constraints are placed on segregated broodstocks except those necessary to achieve desired 

benefits while minimizing genetic and ecological risks to naturally spawning populations. In 

practice, all hatchery programs must fall into one of the two categories; “intermediate” programs 

cannot exist without imposing significant risks to natural populations because of fundamental 

differences in the biological principles underlying the two types of programs. 

Terms similar to integrated and segregated (e.g. “integrated” and “isolated”) have been used 

elsewhere to describe hatchery programs in the Pacific Northwest; however, those other 

definitions are based primarily on the presence and absence, respectively, of natural spawning by 

hatchery-origin fish54. Such definitions only reflect past or hypothesized consequences of hatchery 

programs on natural populations and do not provide genetic management goals or future guidance 

for hatchery programs or their broodstocks. In contrast, the definitions presented here for 

integrated and segregated refer explicitly to the genetic management goals for hatchery 

broodstocks relative to naturally spawning populations, irrespective of the presence or absence of 

natural spawning by hatchery-origin fish. For example, “integrated” programs do not imply that 

natural spawning by hatchery-origin fish has occurred or is desired. Similarly, segregated 

programs do not imply that released hatchery-origin fish do not spawn naturally or interact 

biologically with natural-origin fish. 

In our descriptions below, we first describe the general concepts, goals, and operational 

constraints for each of the two types of programs. We then provide operational guidelines and 

specific recommendations for their implementation. The major emphasis here is on integrated 

programs, because they represent a relatively new conceptual approach to hatchery management in 

Puget Sound and coastal Washington. 

54 Those other definitions may have developed as a misinterpretation of the concepts and definitions described here when these latter 

definitions were first conveyed orally to the comanaging agencies. 
Emerging Issues - Genetic Integration versus Segregation B-5 

Integrated Hatchery Programs

General concepts and goals 

A fundamental goal of an integrated hatchery program is to minimize genetic divergence of a 

hatchery broodstock from a naturally spawning population in areas where fish are released and/or 

collected for broodstock. The long-term goal of an integrated program is to maintain genetic 

characteristics of a local, natural population among hatchery-origin fish by minimizing the genetic 

effects of potential domestication. Another goal is to reduce the genetic risks that hatchery-origin 

fish may pose to naturally spawning populations. In an idealized integrated program, naturalorigin and hatchery-origin fish represent two genetically equal components of a single gene pool. 

A hatchery supporting an integrated program can be viewed conceptually as an artificial extension 

of the natural environment such that the population as a whole (hatchery plus natural) is sustained 

at a higher level of abundance than the level sustainable by the natural habitat without a hatchery. 

A properly-managed, integrated broodstock can potentially serve as a genetic repository for a 

natural population in the event of a major decline in the abundance of natural-origin fish (e.g. due 

to a catastrophic event, change in marine survival, etc.). 

As noted previously, integrated programs do not imply that natural spawning of hatchery-origin 

fish is desired or necessarily occurs. Natural spawning and reproduction by hatchery-origin fish 

does not make a hatchery broodstock genetically integrated with a natural population. A principal 

goal of an integrated program is to maintain the genetic characteristics of a natural population 

among hatchery-origin fish, not vice-versa. 

Integrated programs may be most appropriate when: a) conservation is one of the programmatic 

goals; or b) significant genetic and ecological risks cannot be avoided. For example, if genetic 

divergence between hatchery- and natural-origin fish within a watershed is minimized, then the 

genetic risks to natural populations imposed by naturally-spawning hatchery fish may also be 

minimized. Ecological risks may also be reduced relative to segregated programs (see below) 

because competition or predation between hatchery- and natural-origin components of a single 

gene pool is conceptually equivalent to the same interactions resulting from increased abundance 

of individuals within a single natural population. 

Operational constraints 

Explicit hatchery practices are needed to achieve an integrated broodstock that achieves the 

desired genetic management goals. These practices include the following: a) incorporation of 

sufficient numbers of natural-origin adults into the broodstock each year to overcome the potential 

effects of random genetic drift, domestication and divergent natural selection in the two 

environments (Ford 2002); b) strict protocols for trapping and spawning adults such that the 

means and variances of phenotypic characters related to fitness (e.g., run timing) equal those of 

the parental natural population; and c) efforts be made to minimize natural selection and other 

domestication effects in the hatchery. For example, it may be desirable to implement spawning 

protocols that tend to equalize parental genetic contributions, to reduce the potential effects of 
B-6 Emerging Issues – Genetic Integration versus Segregation 

domestication selection (Allendorf 1993; Hedrick et al. 2000; Heath et al. 2003; Campton 2004). It 

may also be desirable to modify hatchery rearing conditions to reduce the selection effects of 

hatchery environments (Zydlewski et al. 2003). Integrated programs will invariably represent 

trade-offs between ease of culture and achievement of genetic management goals. 

A major biological uncertainty for integrated programs is the proportion of a hatchery broodstock 

that needs to be composed each year of natural-origin adults to overcome the potential effects of 

genetic drift, domestication selection, and divergent natural selection in the two environments. 

Theoretical models indicate that one-way gene flow is a powerful force that can minimize the 

divergent effects of natural selection in two different environments (Appendix 1). Those models 

indicate that 10–20% of a population derived genetically from another population each generation 

can largely overcome the divergent effects of genetic drift and natural selection. However, gene 

flow in the opposite direction (i.e., hatchery to wild) needs to be restricted to allow the natural 

environment to dominate the natural selection process for the population as a whole. The major 

obstacles for developing operational guidelines from those models are scientific unknowns 

regarding the magnitude of the difference in mean phenotypic values for the integrated population 

that optimize fitness in the hatchery and natural environments, respectively. 

Another general conclusion emerging from those theoretical models (Appendix 1) is that the rate 

of gene flow from the natural environment to the hatchery environment must exceed the reverse 

rate of gene flow for the mean fitness of hatchery-origin fish, and the population as a whole, to be 

closer to the optimum fitness for the natural environment than to the optimum fitness for the 

hatchery environment. In other words, the proportion of a hatchery broodstock composed of 

natural-origin fish must exceed the proportional genetic contribution of hatchery-origin fish to the 

naturally spawning population if selection regimes in the natural environment are to dominate the 

mean fitness of the population as a whole. For example, if natural-origin adults constitute—on 

average—20% of a hatchery broodstock each year, then the genetic contribution of hatcheryorigin fish to the naturally spawning component must be less than 20% per year. By controlling 

gene flow in both directions (i.e., by ensuring sufficient gene flow into the hatchery and 

controlling natural spawning of hatchery-origin adults), the genetic risks imposed by an integrated 

hatchery program to a naturally spawning population can be substantially less than the risks posed 

by a segregated program of equal size (see segregated hatchery programs below). 

Further guidelines and constraints for integrated hatchery programs can be gleaned from several 

pseudo-examples (Appendix 3). For example, the number of adult spawners in the hatchery must 

be less than the number of natural-origin adults returning to the watershed where adults are 

trapped for broodstock if integrated programs are to meet their genetic management goals. Indeed, 

integrated hatchery programs have the greatest likelihood of achieving their goals if the number of 

returning natural-origin adults is at least twice the number of adults required for broodstock. 

Clearly, naturally spawning populations must be viable and largely self-sustaining if they are to 

support successful, integrated programs that, in turn, can provide excess adults for harvest or other 

purposes. 

Many hatchery programs are designed to rebuild or restore naturally spawning populations by 

purposefully allowing hatchery-origin fish to spawn naturally. In such situations, demographic 

goals will initially outweigh genetic management goals, and 50% or more of the natural spawners 
Emerging Issues - Genetic Integration versus Segregation B-7 

may be composed of hatchery-origin fish. However, as the number of natural-origin fish returning 

to a watershed increases over time (i.e. assuming that population restoration is successful), then 

the number of hatchery-origin adults allowed to spawn naturally would have to be reduced for 

selection regimes in the natural environment to dominate natural selection in the hatchery 

environment. An example of this latter situation is given in Appendix 4. 

Operational guidelines 

• Naturally spawning populations must be viable and self-sustaining for hatchery 

broodstocks to be genetically integrated with a naturally spawning component. The longterm goal is to make the natural environment drive the fitness of the population as a 

whole, not vice versa. Such requirements underscore the need to maintain healthy habitat 

conditions necessary for viable, self-sustaining natural populations. 

• The maximum size of hatchery broodstocks is restricted by the size of the naturally 

spawning component. At equilibrium, the number of spawners in a hatchery must be less 

than the number of natural-origin fish returning to a watershed. The ability of integrated 

hatchery programs to achieve their genetic management goals will be optimized if the 

number of natural-origin adults returning to a watershed is at least twice the total number 

of adults (hatchery plus natural) needed for broodstock. 

• Although genetic integration may be a long-term goal of a hatchery program, low 

abundance or viability of a natural population may preclude short-term achievement of 

genetic integration goals. In such situations, rebuilding of a natural population may be 

necessary before complete genetic integration is possible (see Appendix 4). 

Recommendations for integrated hatchery programs 

• Develop a detailed, genetic management plan for the hatchery broodstock and the 

naturally spawning population in the watershed where adults are trapped for broodstock. 

• Ensure that an average of 10–20% of the hatchery broodstock is composed of naturalorigin adults each year. A sliding scale can be developed that reduces the desired 

percentage in low-return years but increases this percentage in high return years. 

• Collect and spawn adults randomly with respect to time of return, time of spawning, size 

and other characteristics related to fitness. 

• Impose hatchery management practices that minimize the potential domestication effects 

of the hatchery environment. This may include spawning more hatchery-origin adults than 

required, but then culling each full-sib family to a predetermined number of eyed eggs. It 

may also include modified hatchery environments (e.g., raceway covers, underwater 

feeders, etc.) that reduce potential domestication effects and natural selection differences 

between the two environments. 

• Mark or tag all hatchery-released fish so that the proportions of natural- and hatcheryorigin fish among natural spawners and in the broodstock can be monitored and 

controlled. 
B-8 Emerging Issues – Genetic Integration versus Segregation 

• Monitor and control natural spawning by hatchery-origin adults so that the percentage of 

natural spawners composed of hatchery-origin fish is less than the percentage of the 

hatchery broodstock derived from natural-origin fish. In most cases, hatchery-origin adults 

are expected to have a lower natural reproductive success than natural-origin adults 

(irrespective of any genetic factors), so the actual genetic contribution of hatchery origin 

fish to natural reproduction is expected to be less than their relative proportion on the 

spawning grounds. A maximum risk limit of 30% hatchery-origin adults among natural 

spawners (minimum two-to-one ratio of natural:hatchery fish) is thus recommended in all 

cases except in restoration supplementation programs where natural spawning by 

hatchery-origin adults is an intended purpose of the hatchery program. 

• Adjust the size of integrated hatchery programs relative to the size of the naturally 

spawning population, so that the number of adults used for broodstock is less than the 

number of natural-origin adults spawning naturally in the same watershed. The number of 

natural-origin adults returning to a watershed should be at least twice the number of adults 

used for broodstock in integrated programs that have achieved genetic equilibrium with 

their naturally spawning components. In some cases, natural populations will need to be 

restored or rebuilt to a higher level of abundance before the number of natural-origin 

adults returning to a watershed is sufficient to achieve the genetic management goals of a 

genetically-integrated hatchery program. 

Segregated Hatchery Programs

General concepts and goals 

The principal goal of a segregated hatchery program is to maintain the hatchery broodstock as a 

reproductively distinct or genetically segregated population. Once such programs are established, 

the broodstock is derived exclusively from returning hatchery-origin fish. Hence, little or no gene 

flow occurs, or is intended to occur, from a natural population to the broodstock. In a segregated 

program, the hatchery population is managed as a distinct gene pool and is expected to diverge 

genetically from the founding natural population due to genetic adaptation to the hatchery 

environment, domestication and genetic drift. Many, if not most, hatchery programs for Pacific 

salmon and steelhead historically followed this segregated approach, either purposefully or 

inadvertently (e.g. Waples and Teel 1990). Segregated programs are usually intended to achieve 

harvest goals in the most efficient manner possible; consequently, this segregated approach can 

result in significant genetic change in a hatchery population after several generations (Campton 

1995). 

Segregated hatchery programs may have conservation goals under some circumstances. For 

example, hatcheries often propagate native populations for which spawning habitat is no longer 

available because a dam blocks upstream migration to historical spawning areas. Genetic 

maintenance of a native population is often a long-term goal of such programs. In addition, fish 

from a segregated hatchery population may be introduced into a watershed where the native 

population has been extirpated. The long-term goal of these latter programs is for hatchery-origin 

fish to spawn successfully and initiate restoration of a natural population. In this latter situation, 
Emerging Issues - Genetic Integration versus Segregation B-9 

the hatchery program would initially be classified as “segregated,” because no naturally spawning 

population may be associated genetically with the hatchery broodstock. Over time, however, such 

a program could evolve into an integrated program if hatchery-origin fish spawn successfully and 

returning, natural-origin adults are subsequently included in the broodstock in a prescribed, 

systematic manner (Appendix 4). A new, locally-adapted broodstock integrated genetically with a 

naturally spawning population would, in theory, evolve. Many restoration programs for Pacific 

salmon may attempt this latter approach as dams are removed and/or other natural habitats are 

restored. Intense genetic and ecological monitoring will be necessary to scientifically evaluate the 

efficacy of such programs. 

Operational constraints 

Segregated programs, particularly those with only harvest goals, typically have few operational 

constraints. Segregated hatchery broodstocks may be bred selectively for particular traits (e.g. 

early run-timing), to facilitate ease of culture and/or to help achieve desired benefits (e.g., 

harvest). In general, segregated programs are managed in a way that maximizes productivity (i.e., 

recruit per spawner) or efficiency of a hatchery irrespective of the ability of returning adults to 

reproduce naturally or confer any benefits to naturally spawning populations. Indeed, hatcheryorigin fish from a genetically segregated program can impose unacceptable genetic and ecological 

risks to natural populations (Busack and Currens 1995). As a result, segregated programs often 

represent major trade-offs between minimizing biological risks to naturally spawning populations 

and maximizing efficiency and harvest benefits of the hatchery program. 

Many segregated hatchery programs have selectively bred adults, either purposefully or 

inadvertently, for “early” spawn or run timing, primarily by excluding late-returning adults from 

broodstocks. Many hatchery stocks of salmon and steelhead now return and spawn several weeks 

earlier than their natural-origin counterparts. Differences in return timing between natural- and 

hatchery-origin adults can be used as a management tool to focus fisheries on “early-returning 

hatchery fish,” while protecting “late-returning natural fish”. This approach can facilitate fisheries 

management from an agency perspective. However, if non-harvested fish spawn naturally, then 

these segregated programs can impose significant genetic risks to naturally spawning populations. 

Indeed, any natural spawning by fish from these broodstocks may be considered unacceptable 

because of the potential genetic impacts on natural populations. Proponents of such “segregated” 

programs argue that “early-returning” hatchery fish are mis-timed biologically to stream flows and 

water temperatures and, thus, fail to reproduce successfully even if they do spawn in nature. 

However, empirical and experimental evidence indicates that such “early-returning” hatchery fish 

do indeed reproduce successfully, albeit at a reduced rate relative to natural-origin fish (Chilcote et 

al. 1986; Campton et al. 1991; Mackey et al. 2001). Although these hatchery-origin fish have a 

lower reproductive success relative to their natural-origin counterparts, their overall genetic 

contributions can be substantial if hatchery-origin fish outnumber natural-origin spawners 

(Chilcote et al. 1986; Leider et al. 1990). 

Clearly, the degree to which segregated hatchery programs are successful depends significantly on 

the degree to which genetic and ecological risks to natural populations can be minimized. Most 

hatchery programs for Pacific salmon and steelhead have historically been managed as segregated 
B-10 Emerging Issues – Genetic Integration versus Segregation 

broodstocks with no concerted effort to include natural-origin fish in the broodstocks or to control 

natural spawning by hatchery-origin fish within a watershed. Such programs essentially treat 

hatcheries as “fish farms,” or ocean ranching operations where a small proportion of fish surviving 

to adulthood are recaptured for broodstock each year to propagate the stock and maintain the 

program over time. Although this approach can maximize the efficiency of a salmon hatchery for 

achieving fishery benefits, it also overlooks the ecological and genetic risks that these hatchery 

stocks may pose to naturally spawning populations. After several generations of artificial 

propagation, segregated hatchery broodstocks may pose genetic and ecological risks to naturally 

spawning populations that are not unlike those imposed by exotic or introduced species. Many 

segregated hatchery broodstocks also represent the genetic products of historical stock transfers 

among facilities or regions, thus further confounding the genetic and ecological risks that those 

programs may impose on naturally spawning populations. To minimize these risks, segregated 

hatchery programs need to be located in areas where virtually all returning adults can be harvested 

or recaptured, or where natural spawning or ecological interactions with natural-origin fish are 

considered minimal or inconsequential. Outplanting from such programs should also be 

discontinued (see emerging issue paper on this topic). 

Operational guidelines 

• Segregated hatchery programs are most appropriate where nearly all returning hatcheryorigin adults can be harvested or recaptured, or where the habitat or natural environment 

cannot support natural populations of salmon or steelhead. Segregated programs may also 

be most appropriate where: a) the only goal of the program is harvest; and b) the potential 

for genetic and ecological interactions between hatchery- and natural-origin fish is 

minimal, or the biological effects of those interactions are considered inconsequential. 

• The size of segregated hatchery programs must not exceed thresholds above which natural 

stray rates would pose significant genetic or ecological risks to natural populations. Stray 

rates as low as one to two percent for a large, segregated hatchery program may pose 

unacceptable biological risks to natural populations. 

Recommendations for segregated hatchery programs 

• Release fish in areas that minimize potential straying and natural spawning, and where 

opportunities to recapture non-harvested adults are maximized. 

• Mark all released hatchery-origin fish to maximize potential harvest, and to assess stray 

rates and genetic risks to naturally spawning populations. 

• Release fish in a manner and/or at locations that ensure hatchery-origin adults constitute 

no more one to five percent of natural spawners in a watershed. 

• Adjust the size of segregated hatchery programs as environmental conditions change to 

maintain total adult returns and potential stray rates within biologically-accepted limits. 

• Avoid trapping natural-origin adults and exclude them from the broodstock. 
Emerging Issues - Genetic Integration versus Segregation B-11 

Summary and Conclusions

Every hatchery program must be identified as either integrated or segregated, with operational 

procedures and facilities designed to achieve the specific goals for one of those two types of 

programs. In this context, “intermediate” programs cannot exist because the operational 

procedures and underlying biological constraints differ substantially between the two types of 

programs. 

Integrated hatchery programs are intended to minimize genetic risks to naturally spawning 

populations, while also achieving harvest and/or conservation objectives; however, they also 

represent potential trade-offs between ease of culture and attainment of genetic management goals. 

Segregated programs are usually intended to provide only harvest benefits in the most efficient 

manner possible. Consequently, they must be operated in a manner that prevents returning adults 

from interbreeding with naturally spawning populations. 

In contrast to most segregated programs, properly-developed (or idealized) integrated programs 

can potentially confer genetic and/or demographic benefits to naturally spawning populations 

because such programs are designed to increase the total number of spawners and the effective 

number of breeders (Appendix 2) for those natural populations. However, regardless of the degree 

of genetic integration, significant phenotypic differences between natural- and hatchery-origin fish 

can still arise due to single-generation environmental effects associated with early rearing in a 

hatchery environment. Nevertheless, integrated programs do provide a conceptual mechanism for 

hatcheries to achieve both harvest and conservation objectives under the legal and legislative 

mandates of fishery compensation (i.e., harvest opportunities) and natural resource protection 

(e.g., ESA). The key to the success of an integrated hatchery program is the ability to distinguish 

natural- and hatchery-origin fish as returning adults so that separate management strategies can be 

applied to the two gene pool components (hatchery and natural) in accordance with their different 

population dynamic parameters and natural selection regimes. Segregated hatchery programs are 

inherently simpler to operate, but they can also inhibit recovery of naturally spawning populations 

if hatchery-origin fish interact ecologically or genetically with depressed natural populations. 

Recognizing the fundamental distinction between genetically integrated and genetically segregated 

hatchery programs is the critical first-step towards reforming salmon hatcheries in the Pacific 

Northwest. This first step is not a facility- or hardware-driven goal, but is rather a conceptual or 

philosophical goal associated with recognizing the biological constraints and consequences of 

hatchery programs. This first step is also intended to improve hatchery management practices in a 

scientifically-defensible manner to achieve desired benefits while reducing risks to natural 

populations (see Busack and Currens 1995). In the past, most fish were released from hatcheries 

unmarked or untagged, and the relative proportions of hatchery- and natural-origin fish in 

broodstocks and on natural spawning grounds was largely unknown. Both integrated and 

segregated hatchery programs clearly require that hatchery- and natural-origin adults are readily 

distinguishable to (a) hatchery workers who are spawning fish and (b) field fishery biologists who 

are monitoring stray rates and potential natural spawning. Understanding the distinction between 

integrated and segregated programs and adhering to their respective operational constraints, 

including monitoring of harvest contributions and natural spawning escapements, is the underlying 

foundation of hatchery reform in Washington state. 
B-12 Emerging Issues – Genetic Integration versus Segregation 

References

Allendorf, F. W. 1993. Delay of Adaptation to Captive Breeding by Equalizing Family Size. 

Conservation Biology 7: 416-419. 

Allendorf, F. W. 1983. Isolation, gene flow, and genetic differentiation among populations 

(Chapter 3). Pages 51-65 in C. M. Schonewald-Cox, S. M. Chambers, B. MacBryde, and 

W. L. Thomas, editors. Genetics and Conservation: A Reference for Managing Wild 

Animal and Plant Populations. The Benjamin Cummings Publishing Company, Inc., 

Menlo Park, California. 

Berejikian, B. A., Mathews, S. B., and Quinn, T. P. 1996. Effects of hatchery and wild ancestry 

and rearing environments on the development of agonistic behavior in steelhead trout 

(Oncorhynchus mykiss) fry. Canadian Journal of Fisheries and Aquatic Sciences 53: 

2004-2014. 

Berejikian, B. A., Tezak, E. P., Flagg, T. A., LaRae, A. L., Kummerow, E., and Mahnken, C. V. 

W. 2000. Social dominance, growth, and habitat use of age-0 steelhead (Oncorhynchus 

mykiss) grown in enriched and conventional hatchery rearing environments. Can. J. Fish. 

Aquatic Sci. 57: 628-636. 

Brannon, E. L. and plus 6 coauthors. 1999. Review of artificial production of anadromous and 

resident fish the Columbia River Basin, Part I: A scientific basis for Columbia River 

production programs. Council Document 99-4, ed. Northwest Power Planning Council. 

Portland, OR. 

Bugert, R. M., Hopley, C. W., Busack, C. A., and Mendel, G. W. 1995. Maintenance of stock 

integrity in Snake River Fall Chinook Salmon. Am. Fish. Soc. Symp. 15: 267-276. 

Busack, C. A. and Currens, K. P. 1995. Genetic risks and hazards in hatchery operations: 

fundamental concepts and issues. Am. Fish. Soc. Symp. 15: 71-80. 

Campton, D. E. 1995. Genetic effects of hatchery fish on wild populations of Pacific salmon and 

steelhead: What do we really know? Pages 337-353 in H. L. Jr. Schramm and R. G. Piper, 

editors. American Fisheries Society, Bethesda, Maryland. 

Campton, D.E. 2004. Sperm competition in salmon hatcheries: the need to institutionalize 

genetically-benign spawning protocols. Transactions of the American Fisheries Society 

133: in press. 

Campton, D. E., Allendorf, F. W., Behnke, R. J., Utter, F. M., Chilcote, M. W., Leider, S. A., and 

Loch, J. J. 1991. Reproductive success of hatchery and wild steelhead. Transactions of the 

American Fisheries Society 120: 816-827. 
Emerging Issues - Genetic Integration versus Segregation B-13 

Campton, D. E. and Johnston, J. M. 1985. Electrophoretic evidence for a genetic admixture of 

native and nonnative rainbow trout in the Yakima River, Washington. Transactions of the 

American Fisheries Society 114: 782-793. 

Carmichael, R. W. and Messmer, R. T. 1995. Status of supplementing chinook salmon natural 

populations in the Imnaha River Basin. Am. Fish. Soc. Symp. 15: 284-291. 

Chilcote, M. W., Leider, S. A., and Loch, J. J. 1986. Differential reproductive success of hatchery 

and wild summer-run steelhead under natural conditions. Transactions of the American 

Fisheries Society 115: 726-735. 

Cobb, J. N. 1930. Pacific salmon fisheries, Document No. 1092, ed. U.S. Bureau of Fisheries. 

Washington, DC. 

Currens, K. P. and Busack, C. A. 1995. A framework for assessing genetic vulnerability. Fisheries 

20: 24-31. 

Dickhoff, W. W. and plus 6 coauthors. 1995. Quality assessment of hatchery-reared spring 

chinook salmon smolts in the Columbia River Basin. Pages 292-302 in H. L. Jr. Schramm 

and R. G. Piper, editors. Uses and Effects of Cultured Fishes in Aquatic Ecosystems, 

American Fisheries Society Symposium 15. American Fisheries Society, Bethesda, MD. 

Flagg, T. A. and Nash, C. F. 1999. A Conceptual Framework for Conservation Hatchery Strategies 

for Pacific Salmonids. NOAA Tech. Mem. NMFS-NWFSC-38., ed. U.S. Dept. of 

Commerce, National Marine Fisheries Service. Seattle, WA. 

Flagg, T. A., Waknitz, F. W., Maynard, D. J., Milner, G. B., and Mahnken, C. V. W. 1995. The 

effect of hatcheries on native coho salmon populations in the lower Columbia River. Am. 

Fish. Soc. Symp. 15: 366-375. 

Ford, M.J. 2002. Selection in captivity during supportive breeding may reduce fitness in the wild. 

Conservation Biology 16: 815-825. 

Ham, K. D. and Pearsons, T. N. 2001. A practical approach for containing ecological risks 

associated with fish stocking programs. Fisheries (Am. Fish. Soc.) 26: 15-23. 

Hare, S. R., Mantua, N. J., and Francis, R. C. 1999. Inverse production regimes: Alaska and west 

coast Pacific salmon. Fisheries (Am. Fish. Soc.) 24: 6-14. 

Hatch, D.R., M. Schwartzberg, and P.R. Mundy. 1994. Estimation of pacific salmon escapement 

with a time-lapse video recording technique. North American Journal of Fisheries 

Management 14:626-635. 

Heath, D.D., Heath, J.W., Bryden, C.A., Johnson, R.M., Fox, C.W. 2003. Rapid evolution of egg 

size in captive salmon. Science 299:1738-1740. 
B-14 Emerging Issues – Genetic Integration versus Segregation 

Hedrick, P. W., Hedgecock, D., Hamelberg, S., and Croci, S. J. 2000. The impact of 

supplementation in winter-run chinook salmon on effective population size. J. Heredity 

91: 112-116. 

Hilborn, R. 1992. Hatcheries and the future of salmon in the northwest. Fisheries 17: 5-8. 

Hindar, K., Ryman, N., and Utter, F. 1991. Genetic Effects of cultured fish on natural fish 

populations. Canadian Journal of Fisheries and Aquatic Sciences 48: 945-957. 

Krueger, C. C. and May, B. 1991. Ecological and genetic effects of salmonid introductions in 

North America. Can. J. Fish. Aquat. Sci. 48(Suppl. 1): 66-77. 

Leider, S. A., P. L. Hulett, J. J. Loch, and M. W. Chilcote. 1990. Electrophoretic comparison of 

the reproductive success of naturally spawning transplanted and wild steelhead trout 

through the returning adult stage. Aquaculture 88: 239-252. 

Levin, P. S., Zabel, R. W., and Williams, J. G. 2001. The road to extinction is paved with good 

intentions: negative association of fish hatcheries with threatened salmon . Proc. R. So. 

Lond. B 268: 1153-1158. 

Lichatowich, J. 1999. Salmon without rivers. Island Press. Washington, DC. 

Mackey, G., McLean, J. E., and Quinn, T. P. 2001. Comparisons of run timing, spatial 

distribution, and length of wild and newly established hatchery populations of steelhead in 

Forks Creek, Washington. North Am. J. Fisheries Management 21: 717-724. 

Mantua, N. J., Hare, S. R., Zhang, Y., Wallace, J. M., and Francis, R. C. 1997. A Pacific 

interdecadal climate oscillation with impacts on salmon production. Bull. Am. Meterol. 

Soc. 78: 1069-1079. 

Maynard, D. J., Flagg, T. A., and Mahnken, C. V. W. 1995. A review of seminatural culture 

strategies for enhancing the postrelease survival of anadromous salmonids. Am. Fish. Soc. 

Symp. 15: 307-314. 

Meffe, G. K. 1992. Techno-Arrogance and Halfway Technologies - Salmon Hatcheries on the 

Pacific Coast of North America. Conservation Biology 6: 350-354. 

Mills, L. S. and Allendorf, F. W. 1996. The one-migrant-per-generation rule in conservation and 

management. Conservation Biology 10: 1509-1518. 

Olson, D. E., Cates, B. C., and Diggs, D. H. 1995. Use of a national fish hatchery to complement 

wild salmon and steelhead production in an Oregon stream. Am. Fish. Soc. Symp. 15: 

317-328. 
Emerging Issues - Genetic Integration versus Segregation B-15 

Reisenbichler, R. R. and McIntyre, J. D. 1977. Genetic differences in growth and survival of 

juvenile hatchery and wild steelhead trout. Journal of the Fisheries Research Board of 

Canada 34: 123-128. 

Reisenbichler, R. R. and Rubin, S. P. 1999. Genetic changes from artificial propagation of Pacific 

salmon affect the productivity and viability of supplemented populations. ICES J. Marine 

Sci. 56: 459-466. 

Schiewe, M. H., Flagg, T. A., and Berejikian, B. A. 1997. The use of captive broodstocks for gene 

conservation of salmon in the western United States. Bull. Natl. Res. Inst. Aquacult. 

Suppl. 3: 29-34. 

Schwiebert, E. (ed.) 1977. Columbia River salmon and steelhead. Special Publication No. 10, 

American Fisheries Society, Washington, DC. 

Waples, R.S. 1990. Conservation genetics of Pacific salmon. II. Effective population size and the 

rate of loss of genetic variability. Journal of Heredity 81:267-276. 

Waples, R. S. 1991. Genetic interactions between hatchery and wild salmonids: lessons from the 

Pacific Northwest. Canadian Journal of Fisheries and Aquatic Sciences 48: 124-133. 

Waples, R. S. 1995. Evolutionarily significant units and the conservation of biological diversity 

under the Endangered Species Act. Pages 8-27 in J. L. Nielsen, editor. Evolution and the 

Aquatic Ecosystem: Defining Unique Units in Population Conservation. American 

Fisheries Society, Bethesda, Maryland. 

Wright, S. 1940. Breeding structure of populations in relation to speciation . Am. Nat. 74: 232-

248. 

Wright, S. 1969. Evolution and the Genetics of Populations. Vol 2. The Theory of Gene 

Frequencies, ed. University of Chicago Press. Chicago, IL. 

Zydlewski, G.B., J.S. Foott, K. Nichols, S. Hamelberg, J. Zydlewski, and B.T. Björnsson. 2003. 

Enhanced smolt characteristics of steelhead trout exposed to alternative hatchery 

conditions during the final months of rearing. Aquaculture 222: 101-117 

.
B-16 Emerging Issues – Genetic Integration versus Segregation 

 

Appendix 1. Theoretical population genetic 

foundations for recommended gene flow rates 

between natural and hatchery components for 

integrated hatchery programs. 

Genetic drift effects 

The basic principles of population genetics indicate that a relatively small amount of gene flow

between two populations is sufficient to overcome the divergent effects of random genetic drift

alone. The magnitude of this divergence represents a balance between: a) gene flow, which makes 

populations more similar genetically, and b) random genetic drift which makes populations more 

dissimilar genetically. The expected magnitude of this divergence at equilibrium can be quantified 

by the parameter FST

55 according to the well-known expression for a drift-migration, island 

population model (Wright 1969, eq. 12.2): 

 (1-m)2

 FST = —————————— (1) 

 2Ne - (2Ne-1) (1-m)2

 

where m = the migration (gene flow) rate or proportion of a subpopulation derived from migrants 

(i.e. immigrants) from other subpopulations each generation, and Ne = the genetic effective 

population size of each subpopulation (see Appendix 2 for a discussion of effective population 

size). The product Nem is thus the effective number of migrants per generation. Solving for m and 

Nem in equation (1) yields the minimum values of those parameters necessary for achieving a 

maximum desired value of FST (Fig. 1). 

According to the relationship between gene flow and genetic drift (eq. 1), approximately 23–24 

migrants (Nm) per generation are needed to establish an equilibrium FST = 0.01 for effective 

population sizes (Ne) greater than 500 individuals per generation (Fig. 1a). The proportion of 

migrants per generation (m) must similarly be greater than five percent (0.05) to achieve FST = 

0.01 for Ne = 500 (Fig. 1b). Those values of m and Nm would need to be nearly doubled to achieve 

a FST = 0.005 (Figs. 1c, 1d). However, the proportional amount of gene flow (m) necessary to 

achieve a desired value of FST decreases as effective population size increases (Figs 1b, 1d), 

although the required number of migrants remains relatively constant (Figs. 1a, 1c). Hence, 

approximately 50 natural-origin adults would need to be included in a hatchery broodstock each 

generation to overcome the divergent effects of genetic drift alone and achieve an FST = 0.005. 

This latter value of FST is considered the maximum desired value between hatchery and naturalorigin components in integrated hatchery programs. In other words, one goal of integrated 

hatchery programs should be to achieve FST < 0.005. 

55FST, commonly called the fixation index, varies from 0.0 to 1.0 and measures the proportion of the total genetic variation in a

population that is due to allele frequency divergence among subpopulations constituting that population. FST = 0 implies two 

populations have identical allele frequencies. FST = 1.0 implies two populations share no alleles in common. 
Emerging Issues - Genetic Integration versus Segregation B-17 

Natural selection effects 

A major limitation of the preceding calculations and Figure 1 is that they assume no natural 

selection in the two environments occupied by the two populations. One of the principle concerns 

of hatchery programs is the unknown effect and intensity of domestication selection for traits 

directly related to fitness. Mills and Allendorf (1996) noted that natural selection will not have a 

major effect on the distribution of allele frequencies in a subdivided population if the divergent 

selection coefficients (“s” and “t”) in the two environments are less than the migration rate (m) 

between them (Wright 1940). Consequently, a minimum gene flow rate from a natural population 

to a hatchery broodstock of 10% per year is expected to significantly retard the genetic divergence 

between two populations, or gene pool components, if the magnitude of the divergent selection 

coefficients in the two environments is minor to moderate (i.e. s, t < 0.1). Greater selection 

coefficients would necessitate higher levels of gene flow to attain the same desired FST value. 

Ford (2002) has recently modeled potential genetic effects of domestication selection and gene 

flow from a captive hatchery stock to a naturally spawning population where the goal is to 

supplement natural spawning with the progeny of a captively-bred population. By reversing the 

fitness and gene flow parameters of Ford’s (2002) model, one can use his results to interpret the 

genetic effects of gene flow from a “closed” natural population to a hatchery broodstock where the 

goal is to prevent genetic divergence between the hatchery and natural components of a single 

gene pool. As shown in Fig. 2a of Ford (2002), the receiving population (in our case, the hatchery) 

quickly achieves the optimum fitness level of the donor (i.e. natural) population with one-way 

gene flow rates of 10-20% per generation for a wide range of phenotypic differences in optimum 

fitness between the two environments (indicated by θC in Ford 2002). These latter results (Fig. 2a 

of Ford 2002) apply to the situation where hatchery fish are not allowed to spawn naturally. 

However, if hatchery-origin adults constitute 20% of the natural spawners and natural-origin 

adults constitute 20% of the hatchery broodstock each generation, then the mean equilibrium 

fitness of hatchery-produced fish is only slightly greater than 50% of the difference in mean 

optimum fitness of fish in the two different environments (Fig. 2b of Ford 2002). Moreover, if 

20% of the naturally spawning population is comprised of hatchery-origin fish each generation, 

then approximately 40% of the hatchery broodstock needs to be derived from natural-origin fish 

each generation to achieve a fitness level for hatchery fish that is within approximately 25% of the 

fitness optimum in the natural environment (relative to the hatchery environment) over all ranges 

of fitness differences modeled by Ford (2002). In addition, under these quantitative genetic and 

gene flow models where hatchery-origin fish spawn naturally, the maximum fitness achievable by 

the natural population will always be less than its optimum fitness when hatchery-origin fish are 

not allowed to spawn naturally. We are currently using equations adapted from Ford (2002) to 

model these specific situations for integrated hatchery programs (Campton et al., in prep.). In the 

meantime, the equations and graphs of Ford (2002) provide guidance regarding the amount of 

gene flow necessary to overcome divergent natural selection between the hatchery and natural 

environments. Nevertheless, the general conclusion from Ford (2002) is that gene flow from the 

hatchery environment to the natural environment must be restricted for integrated hatchery 

programs to achieve their goals. A conservative rule of thumb is that gene flow from the natural 

environment to the hatchery environment should be approximately twice the rate of gene flow 

from the hatchery environment to the natural environment when the latter parameter exceeds 10%. 
B-18 Emerging Issues – Genetic Integration versus Segregation 

The major conclusion from Ford (2002) is that one-way gene flow is a powerful force that can 

overcome divergent selection pressures to retard genetic divergence of hatchery-origin fish from 

their natural-origin origin counterparts. The major obstacles for developing operational guidelines 

from those models are scientific unknowns regarding the magnitude of the difference in mean 

phenotypic values that optimize fitness for traits under different selection regimes in the two 

environments. 

Conclusions 

The theoretical considerations presented above indicate that a minimum of 10-20% of the hatchery 

spawners need to be composed of natural-origin adults for integrated hatchery broodstocks to meet 

their genetic goals and overcome the divergent effects of natural selection in the two 

environments. In addition, the proportion of natural spawners composed of hatchery origin fish 

must be less than the proportion of a hatchery broodstock composed of natural-origin fish for 

selection regimes in the natural environment to dominate the mean fitness of the population as a 

whole. 
Emerging Issues - Genetic Integration versus Segregation B-19

Effective population size (Ne)

0 500 1000 1500 2000

M

0.0

0.1

0.2

0.3

0.4

FST = 0.005

(d)

Migrant proportion (M)

0 500 1000 1500 2000

M

0.0

0.1

0.2

0.3

FST = 0.01

(b)

Effective population size (Ne)

0 500 1000 1500 2000

Nm

20

30

40

50

FST = 0.005

(c)

No. of migrants (Nm)

0 500 1000 1500 2000

Nm

14

16

18

20

22

24

FST = 0.01

(a)

Figure A1. Theoretical relationship among effective population size (Ne), the proportion of a

population derived from migrants or immigrants (m) each generation, and the number of migrants 

(immigrants) per generation (Nm) at equilibrium to counterbalance the effects of random genetic drift 

to achieve FST = 0.01 (a, b) or FST = 0.005 for the island model of population structure (eq. 12.2,

Wright 1969). 
B-20 Emerging Issues – Genetic Integration versus Segregation 

Appendix 2. Effective population size. 

Effective population size (Ne) is a theoretical parameter that indirectly quantifies the amount of 

genetic variation that can be transmitted from parental to offspring generations within a 

population, either in terms of potential levels of inbreeding or the variance in gene frequencies 

between generations. Ne is highly influenced by sex ratio of spawners and population bottlenecks 

(i.e. major fluctuations in abundance between generations). For example, the genetic effective size 

of a population composed of different numbers of male and female spawners is approximated by 

the following equation: 

 Ne = 4NmNf / (Nm+Nf ), (1) 

where Nm and Nf = the number of male and female spawners, respectively. The preceding 

expression assumes that males and females are randomly mated, although the sex ratio may be 

skewed. 

A single generation of Pacific salmon is composed of several brood years where each brood year 

is produced by independent spawning events. The relationship between effective population size 

(Ne) for a single generation and the effective number of breeders in a single year (Nb) is given by 

the following relationship (Waples 1990): 

 Ne ≈ (Nb)· t, (2) 

where t = the generation time in years, or the mean age of adults at reproduction. For example, the 

genetic effective size of a hatchery population spawning 500 chinook salmon per year, with a 

mean age at spawning of four years, is Ne ≈ 2,000, assuming that multiple brood years contribute 

to the adults spawning in a single year and all adult spawners fertilize an equal number of eggs 

(Campton 2004). 

Equation (2) does not apply to populations in which all the adults in that population spawn in a 

single year. For example, pink salmon have a discrete, two-year life cycle; hence, Ne = Nb because 

the entire population (even or odd) spawns in a single year, every other year. Similarly, Ne = Nb

for hatchery populations of coho salmon in which jacks (2-year old males) are excluded from 

spawning and all other adults return and spawn at three years of age. In this latter situation, the 

hatchery “population” would actually consist of three discrete populations with potentially 

separate effective population sizes that reflect the number of spawners every three years. This 

latter issue for coho salmon has motivated system-wide recommendations for coho salmon that 

require jacks constitute a minimum of 10% of the male spawners in hatchery broodstocks. 
Emerging Issues - Genetic Integration versus Segregation B-21 

Appendix 3: Pseudo-examples of the demographic 

relationships between numbers of adult spawners in 

hatchery broodstocks and the number of natural-origin 

adults returning to a watershed for integrated 

hatchery programs 

The following tables (Tables 1-4) represent a series of pseudo-examples for two sets of situations. 

Tables 1 and 2 examine the demographic consequences and constraints for varying numbers of 

returning, natural-origin (NOR) adults when a hatchery broodstock requirement is 500 and 1,000 

adults, respectively. Tables 1 and 2 also examine the minimum recruit-to-spawner ratio necessary 

among NOR adults for genetic integration to be successful demographically when (a) 10% or (b) 

20% of the hatchery broodstock is derived each year from NOR adults. Conversely, Tables 3 and 

4 examine the demographic consequences and constraints for varying numbers of adult spawners 

in a hatchery broodstock assuming 10% or 20%, respectively, of the broodstock is derived each 

year from 1,000 returning NOR adults. Tables 3 and 4 also examine the maximum number of 

hatchery-origin (HOR) adults and their maximum allowable stray (gene flow) rates to the naturally 

spawning component under the constraint that the percent of natural spawners composed of HORs 

has to be less than the percent of hatchery spawners composed of NORs. This latter constraint is 

necessary for the mean fitness of the population as a whole (hatchery + natural) to be closer to the 

optimum for the natural environment than the hatchery environment. Maximum stray rates are 

also given for HORs constituting a maximum of 33% of the natural spawners, a situation that 

should be considered an upper risk limit for integrated programs except those in which 

supplementation spawning is deliberate to help restore or rebuild a naturally spawning 

populations. R/S is assumed to equal 1.0 for all natural spawners (NORs + HORs) in Tables 3 and 

4 but is assumed to equal 5.0 for hatchery spawners in all four tables (Tables 1-4). 
B-22 Emerging Issues – Genetic Integration versus Segregation 

Table 1. Broodstock and natural spawning escapement guidelines and constraints for integrated

hatchery programs where the goal is to maintain the hatchery broodstock and natural spawners as 

two components of a single gene pool. The table below is based on a broodstock requirement of 

500 adult fish for the hatchery each year. Each row represents a different example based on the 

number of natural-origin adults (spawners) returning to the watershed and potentially intercepted 

by the hatchery. For each row, two scenarios are presented: either 10% or 20% of the broodstock 

is derived from NOR fish; hence, either 50 (10% of 500) or 100 (20% of 500) NOR adults, 

respectively, would be retained for broodstock each year. The column “Minimum. R/S required” 

is the minimum recruit-to-spawner ratio required for the naturally spawning component to replace 

itself each year after adult NOR fish are removed for broodstock and without counting HORs 

among the natural spawners. The hatchery program is assumed to have a R/S = 5.0, thus resulting 

in 2500 HOR adult returns from the spawning of 500 adults. The column “Max. No. of HORs in 

escapement” represents the maximum number and, in parenthesis, the maximum percent of the 

total number of HORs that should be allowed to spawn naturally under each of the two scenarios, 

respectively, under the constraint that the percent of natural spawners composed of HOR adults 

should be less than the percent of the hatchery broodstock composed of NOR adults. 

______________________________________________________________________________ 

Hatchery broodstock requires 500 adults per year 

______________________________________________________________________________ 

10% of hatchery broodstock derived from NORS. 20% of hatchery broodstock derived from 

NORS 

Number of 

NORs 

%ofNORS 

removed 

for 

broodstock 

Number of 

NORs 

passed 

upstream 

Max.No.(%) 

ofHORsin 

escapement 

Minimum 

R/Srequired 

%ofNORS 

removedfor 

broodstock 

Numberof 

NORspassed 

upstream 

Max.No.(%) 

ofHORsin 

nature 

Minimum 

R/Srequired 

100 50.0% 50 6(0.2%) 2.00 100% 0 NA NA 

250 20.0% 200 22(0.9%) 1.25 40% 150 37(1.5%) 1.67 

500 10.0% 450 50(2.0%) 1.11 20% 400 100(4.0%) 1.25 

750 6.7% 700 78(3.1%) 1.07 13% 650 162(6.5%) 1.15 

1,000 5.0% 950 106(4.2%) 1.05 10% 900 225(9.0%) 1.11 

1,500 3.3% 1,450 161(6.4%) 1.03 7% 1,400 350(14.0%) 1.07 

2,000 2.5% 1,950 217(8.7%) 1.02 5% 1,900 500(20.0%) 1.05 
Emerging Issues - Genetic Integration versus Segregation B-23 

Table 2. Same as Table 3 except 1,000 adult fish are required for the hatchery broodstock each 

year. Under the 10% and 20% broodstock scenarios for NORs shown below, either 100 (10% of 

1,000) or 200 (20% of 1,000) NOR adults would be retained for broodstock each year. The 

hatchery program is still assumed to have a R/S = 5.0, thus resulting in 5000 HOR adult returns 

from the spawning of 1000 adults. 

_______________________________________________________________________________

_____________________________________ 

 Hatchery broodstock requires 1,000 adults per year 

_______________________________________________________________________________

_____________________________________ 

10% of hatchery broodstock derived from NORS. 20% of hatchery broodstock derived from 

NORS| 

Numberof 

NORs 

%ofNORS 

removedfor 

broodstock 

Numberof 

NORspassed 

upstream 

Max.No.(%) 

ofHORsin 

escapement 

Minimum 

R/Srequired 

%ofNORS 

removedfor 

broodstock 

Numberof 

NORspassed 

upstream 

Max.No.(%) 

ofHORsin 

nature 

Minimum 

R/Srequired 

200 50% 100 11(0.2%) 2.00 100% 0 NA NA 

250 40% 150 17(0.3%) 1.67 80% 50 12(0.2%) 5.00 

500 20% 400 44(0.9%) 1.25 40% 300 75(1.5%) 1.67 

750 13% 650 72(1.4%) 1.15 27% 550 137(2.7%) 1.36 

1,000 10% 900 100(2.0%) 1.11 20% 800 200(4.0%) 1.25 

1,500 7% 1,400 156(3.1%) 1.07 13% 1,300 325(6.5%) 1.15 

2,000 5% 1,900 211(4.2%) 1.05 10% 1,800 450(9.0%) 1.11 

4,000 2.5% 3,900 433(8.7%) 1.03 5% 3,800 950(19.0%) 1.05 
B-24 Emerging Issues – Genetic Integration versus Segregation 

Table 3. Broodstock and natural spawning escapement guidelines and constraints for integrated 

hatchery programs where the goal is to maintain the hatchery broodstock and natural spawners as 

two components of a single gene pool. The table below is based on an annual return of 1,000 

natural-origin (NOR) adults back to the watershed in which the hatchery is located. The examples 

below assume a recruit-to-spawner ratio of 5.0 for hatchery spawners and 1.0 for natural spawners. 

Each row represents a different example based on the number of adults (spawners) required for the 

broodstock each year (column 1) and the requirement that 10% of the broodstock is composed of 

NOR adults each year (column 3). For each row, two scenarios for the maximum number of HOR 

adults spawning naturally are provided: (1) HOR adults constitute a maximum of 10% (= to the 

proportion of NOR adults in the broodstock) or (2) 33% of the total number of adults on the 

spawning grounds (#NORs : #HORs = 2). 

Hatchery-origin adults Natural-origin adults 10% of natural spawners are HORS 33% of natural 

spawners are HORs 

No.of 

spawners 

inthe 

hatchery 

NoofHO

R 

recruits 

R/S=5.0 

No.of 

NORsin 

broodstoc

k 

10%rule 

%of 

NORSre

movedfr

omwild 

No.ofNO

RS 

leftin 

wild 

Max.No.

ofHORs 

spawning 

naturally 

10%rule 

TotalNo.

of 

natural 

spawners 

Max. 

stray 

rateofHO

Rs 

(%) 

Max.No. 

ofHORs 

spawning 

naturally 

33%rule 

TotalNo. 

of 

natural 

spawners 

Max. 

stray 

rateof 

HORS 

(%) 

100 500 10 1% 990 110 1,100 22% 495 1,485 99% 

200 1,000 20 2% 980 109 1,089 11% 490 1,470 49% 

300 1.500 30 3% 970 108 1,078 7.2% 485 1,455 32% 

400 2,000 40 4% 960 107 1,067 5.4% 480 1,440 24% 

500 2,500 50 5% 950 106 1,056 4.2% 475 1,425 19% 

600 3,000 60 6% 940 104 1,044 3.5% 470 1,410 16% 

700 3,500 70 7% 930 103 1,033 2.9% 465 1,395 13% 

800 4,000 80 8% 920 102 1,022 2.6% 460 1,380 11% 

900 4,500 90 9% 910 101 1,011 2.2% 455 1,365 10% 

1,000 5,000 100 10% 900 100 1,000 2.0% 450 1,350 9.0% 

1,500 7,500 150 15% 850 94 944 1.3% 425 1,275 5.6% 

2,000 10,000 200 20% 800 89 889 0.9% 400 1,200 4.0% 
Emerging Issues - Genetic Integration versus Segregation B-25 

Table 4. Same as Table 1 except that 20% of the broodstock is composed of NOR adults each year 

(column 3) and HOR adults constitute a maximum of 20% or 33% of the total number of adults on 

the spawning grounds. 

Hatchery-origin adults Natural-origin adults 20% of natural spawners are HORS 33% of natural 

spawners are HORs 

No.of 

spawners 

inthe 

hatchery 

NoofHO

R 

recruits 

R/S=5.0 

No.of 

NORsin 

broodstoc

k 

20%rule 

%of 

NORSre

movedfr

omwild 

No.ofNO

RS 

leftin 

wild 

Max.No.

ofHORs 

spawning 

naturally 

20%rule 

TotalNo.

of 

natural 

spawners 

Max. 

stray 

rateofHO

Rs 

(%) 

Max.No. 

ofHORs 

spawning 

naturally 

33%rule 

TotalNo. 

of 

natural 

spawners 

Max. 

stray 

rateof 

HORS 

(%) 

100 500 20 2% 980 245 1,225 49% 490 1,470 98% 

200 1,000 40 4% 960 240 1,200 24% 480 1,440 48% 

300 1.500 60 6% 940 235 1,175 16% 470 1,410 31% 

400 2,000 80 8% 920 230 1,150 12% 460 1,380 23% 

500 2,500 100 10% 900 225 1,125 9.0% 450 1,350 18% 

600 3,000 120 12% 880 220 1,100 7.3% 440 1,320 15% 

700 3,500 140 14% 860 215 1,075 6.1% 430 1,290 12% 

800 4,000 160 16% 840 210 1,050 5.3% 420 1,260 10% 

900 4,500 180 18% 820 205 1,025 4.6% 410 1,230 9.1% 

1,000 5,000 200 20% 800 200 1,000 4.0% 400 1,200 8.0% 

1,500 7,500 300 30% 700 175 875 2.3% 350 1,050 4.7% 

2,000 10,000 400 40% 600 150 750 1.5% 300 900 3.0% 
B-26 Emerging Issues – Genetic Integration versus Segregation 

 

Appendix 4. An example of a plan to restore a 

naturally spawning population of steelhead from an 

established hatchery population with the goal of 

developing a genetically integrated broodstock 

The U.S. Fish and Wildlife Service is proposing to restore a naturally spawning population of 

steelhead in Battle Creek, California, from a native hatchery stock propagated at the Coleman 

National Fish Hatchery (NFH). Battle Creek is a tributary to the upper Sacramento River near 

Anderson, California. Coleman NFH is located on Battle Creek, approximately six miles upstream 

from its confluence with the Sacramento River. 

The hatchery stock was developed during the 1950s from natural-origin adults trapped in the 

mainstem Sacramento River as partial mitigation for construction and operation of Shasta Dam, a 

mainstem barrier to upstream migration. Several small diversion dams used by a private utility for 

hydropower generation on Battle Creek are being removed or provided with fish passage which 

will provide nearly 20 miles of additional stream access to salmon and steelhead upstream from 

Coleman NFH. 

Coleman NFH is equipped with a permanent barrier weir on Battle Creek which allows the 

hatchery to trap all upstream migrating adults and control upstream passage. The long-term goal is 

to restore a naturally spawning population upstream from the hatchery and develop a genetically 

integrated broodstock with a minimum of 2,000 natural-origin spawners in the upper watershed 

and 800 spawners in the hatchery each year.56 As the number of natural-origin adults trapped at 

Coleman NFH increases over time, the number of hatchery-origin fish released upstream to spawn 

naturally will be reduced until no hatchery-origin fish are released. 

The restoration program began in 1995, when hatchery-origin fish were first passed upstream. 

During the 2002–03 return year, more than 500 natural-origin adults were trapped at Coleman 

NFH, of which approximately 40 were retained for broodstock and 487 were passed upstream to 

spawn naturally. In addition, nearly 800 hatchery-origin fish were passed upstream for 

supplementation spawning. 

The table below shows one proposed sliding scale for controlling the number of hatchery-origin 

(HOR) and natural-origin (NOR) fish passed upstream to spawn naturally, as a function of the 

total number of NOR fish trapped at Coleman NFH. 

56 The plan is to spawn 800 adults for the hatchery each year, but the number of eyed eggs for each full-sib family would be culled by 

approximately 50% for those families in which both parents were of hatchery-origin. This approach is designed to double the effective 

population size of the broodstock and equalize family size. Genetic integration is being initiated by spawning 760 HOR and 40 NOR adults. 

These numbers will eventually evolve to 720 HOR and 80 NOR adults with the goal that NOR adults will make a 20% genetic contribution to 

released progeny each year. 
Emerging Issues - Genetic Integration versus Segregation B-27 

_____________________________________________________________ 

Number of NORs Numbers of fish passed 

Trapped at Coleman NFH upstream in Battle Creek 

---------------------------------- --------------------------------------------------- 

 No. for % of 

Total hatchery total NORs HORs Total %HORs 

______________________________________________________________ 

200 40 20.0% 160 320 480 67% 

500 40 8.0% 460 920 1380 67% 

750 40 5.3% 710 1290 2000 65% 

1000 50 5.0% 950 1050 2000 52% 

1500 75 5.0% 1425 575 2000 29% 

1750 80 4.6% 1670 330 2000 17% 

2000 80 4.0% 1920 80 2000 4% 

2080 80 3.8% 2000 0 2000 0% 

>2080 80 <3.8% >2000 0 >2000 0% 

_________________________________________________________
B-28 Emerging Issues – Hatchery Salmon Carcasses for Nutrification 

USING HATCHERY SALMON CARCASSES FOR 

NUTRIFICATION OF FRESHWATER ECOSYSTEMS WHILE 

REDUCING ASSOCIATED FISH HEALTH RISKS.

Returning adult salmon are a unique vector for the delivery of marine nutrients into the freshwater 

ecosystem. The importance of these nutrients to consumers such as raccoons, bear, eagles and 

even man has been recognized for some time. Recent research also suggests that a significant 

portion of nitrogen in plants and animals in streams where adult salmon are abundant is derived 

from those returning adults (Mathison 1988, Kline et al. 1993). Marine-derived nutrients from 

returning adult salmon have been found to make a significant contribution to riparian vegetation 

and even old-growth forests (Reimchen 1994, Bilby et al.1996). In streams in interior British 

Columbia, Johnston et al. (1997) found that where salmon carcasses were abundant, up to 60% of 

the nitrogen in benthic insects was derived from the carcasses. They also found that juvenile 

salmon show higher growth rates in streams where adult salmon spawn than in streams without 

spawning adults. Use of hatchery salmon carcasses as a source of these marine-derived nutrients 

was found to increase the density of age 0+ coho and age 0+ and 1+ steelhead in small, 

southwestern Washington streams (Bilby et al. 1998). 

The deliberate distribution of hatchery salmon carcasses into watersheds for purposes of 

nutrification can have a positive ecological benefit to natural salmonid stocks. This practice may, 

however, also pose a fish health risk to these stocks if not properly managed. It is well recognized 

that disease organisms present in salmon carcasses can be transmitted to other salmonids 

following the release of these organisms into water or through their direct consumption. In order 

to reduce this risk, the HSRG recommends: 

• Certifying that adult broodstock is free of viral pathogens prior to planting. The adult 

sampling level should be a minimum of 60 fish for carcass plantings within the same 

watershed and 150 fish for plantings in different watersheds within the same fish health 

management zone. 

• Freezing carcasses prior to planting to reduce the infectious titers of pathogenic organisms 

in the salmon carcasses. This measure will decrease the risk of transmission of certain of 

these disease organisms (see, for example, Margolis 1977 for a metazoan parasite, and 

Evelyn 2001 for two important bacterial fish pathogens). 

• Planting carcasses only within the historic range of the species being used for nutrient 

enhancement. 

• Avoiding the planting of adults or juveniles that may have died of infectious disease. This 

would include pre-spawning adult mortalities and juvenile mortalities from hatchery 

ponds. 
Emerging Issues – Hatchery Salmon Carcasses for Nutrification B-29 

References

Bilby, R.E., B.R. Fransen, and P.A. Bisson. 1996. Incorporation of nitrogen and carbon from 

spawning coho salmon into the trophic system of small streams: evidence from stable 

isotopes. Can. J. Fish. Aquat. Sci. 53:164-173. 

Bilby, R.E., B.R. Fransen, P.A. Bisson, and J.K. Walter. 1998. Response of juvenile coho salmon 

(Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss) to the addition of salmon 

carcasses to two streams in southwestern Washington, U.S.A. Can. J. Fish Aquat. Sci. 

53:164-173. 

Evelyn, T.P.T. 2001. The effects of chilling, freezing and cold-smoking on the infectious titre of 

certain microbial fish pathogens that may occasionally be present in marketed salmon 

flesh. p. 225-229. In C.J. Rodgers, ed. Risk Analysis in Aquatic Animal Health. 

Proceedings of an International Conference, Paris, France, 8-10 February, 2000. 

Johnston, N.T., J.S. Macdonald, K.J. Hall, and P.J. Tschaplinski. 1997. A preliminary study of the 

role of sockeye salmon (Oncorhynchus nerka) carcasses as carbon and nitrogen sources 

for benthis insects and fishes in the ‘Early Stuart’ stock spawning streams, 1050 km from 

the ocean. Fisheries project report no. RD55, Fisheries Branch, Ministry of Environment, 

Lands, and Parks, British Columbia, Canada. 

Kline, T.C. Jr., J.J. Goering, O.A. Mathisen, P.H. Poe, P.L. Parker. 1990. Recycling of elements 

transported upstream by runs of Pacific salmon. 15N and 13C evidence in Sashin Creek, 

southeastern Alaska. Can. J. Fish. Aquat. Sci. 47: 136-144. 

Mathisen, O.A., P.L. Parker, J.J. Goering, T.C. Kline, P.H. Poe and R.S. Scalan. 1988. Recycling 

of marine elements transported into freshwater systems by anadromous salmon. Verh. 

Internat. Verein. Limnol. 23:2, 249-258. 

Margolis, L. 1977. Public health aspects of “codworm” infection: a review. J. Fish Res. Bd. Can. 

34:887-898. 

Reimchen, T.E. 1994. Further studies of predator and scavenger use of chum salmon in stream and 

estuarine habitats at Bag Harbour,Gwaii Haanas. Technical report prepared for Canadian 

Parks Service. Queen Charlotte City, British Columbia, Canada. 
B-30 Emerging Issues – Smolt Quality and the Wild Salmon Template 

HATCHERY SMOLT QUALITY AND ACHIEVING THE WILD 

SALMON TEMPLATE

Smoltification

Anadromous salmonids undertake a metamorphosis, the parr-smolt transformation, as they prepare 

for migration to the sea. Photoperiod-induced changes in physiology, body shape, and behavior 

transform the cryptic, bottom-oriented resident form, or parr, to the migratory, schooling form. 

This metamorphosis is termed smoltification and the resulting migrant is termed a smolt. The 

process of smoltification is a major life history event, with fundamental changes in body form and 

function likened to the metamorphosis of a frog to a prince (Grimm’s Fairy Tales). 

Timing and duration of the metamorphosis and downstream migration to the sea is determined by 

a species-specific, genetically-determined life history pattern and environmental events governing 

growth rate and size. For example, chum and pink salmon smoltify almost immediately upon 

absorption of their yolk sacs and swim up in the late winter or early spring. Chinook, coho, 

sockeye, and steelhead normally smolt as yearlings or two year-olds during the period of 

increasing day length in late spring. Depending on life history type (stream or ocean form), or the 

size attained in their first year of life, some Chinook may smoltify as yearlings or sub-yearlings. In 

some instances, Chinook salmon may exhibit smolt-like characteristics during declining 

photoperiod in the fall of the year, and migrate seaward to the estuary. 

Smolted salmonids exhibit rapid downstream migration, increased hypo-osmoregulatory capability 

(enhanced seawater tolerance), sustained growth in the ocean and high survival to adulthood. The 

linkage between smoltification, growth rate, and seawater tolerance and migration rate has been 

reported frequently in the literature (Wagner et al. 1969; Varnavsky et al. 1992). These processes 

are under hormonal control and mediated primarily by photoperiod. The same hormones 

controlling growth rate (growth hormone, insulin-like growth factor-I) also stimulate the 

development of seawater tolerance in salmonids (Sakamoto and Hirano 1993). It is also 

recognized that survival is not the only valuable quality measure of released hatchery fish, 

especially in integrated conservation programs,57 where fish are released to intermingle with their 

wild counterparts. 

Defining Quality Hatchery Smolts

During the course of its regional reviews of hatchery programs, the HSRG has noted that the 

quality of hatchery-origin fish was almost always described in terms of size, numbers, or condition 

index of fish produced, and whether they meet a pre-determined time window for release. Fish size 

at release almost invariably seems to be used as a surrogate for fish quality. In some cases, the 

health of released fish is discussed as a measure of quality at the time of release from the hatchery, 

 

57 See Emerging Issues paper on Integrated vs. Segregated programs. 
Emerging Issues – Smolt Quality and the Wild Salmon Template B-31 

but rarely is fish quality adequately described, or monitored, prior to or following release. Most 

hatchery personnel have difficulty defining smolt or fingerling quality beyond obvious behavioral 

and silver coloration changes, yet the scientific literature is rich in descriptions of physiological, 

morphological, and behavioral definitions of a quality smolt. This deficiency may stem from past 

hatchery practices and the focus and direction of past research. 

It is interesting to note that following the advent of the coded wire tag, most hatchery 

improvement studies were aimed at manipulating the size and time of release of smolts to 

maximize survival. Additionally, some researchers concentrated on the role of nutrition 

(proximate composition, constituent quality, etc.) in optimizing adult survival. But in most cases, 

optimization has meant manipulating fish size and timing of release. In contrast to the 1970s and 

1980s, the hatchery operator now has many additional tools with which to measure and manipulate 

the quality of smolts during the culture phase. 

The quality of a smolt is embodied in the rate and completeness of the parr-smolt transformation. 

In the hatchery, the timing, magnitude, and duration of the metamorphosis are a surrogate for 

smolt quality and can be quantified using physiological, morphological, and behavioral measures. 

Therefore, it is strongly recommended that the definition of smolt quality be expanded to include 

additional physiological, morphological, and behavioral measurements taken throughout the 

culture cycle. Examples include some specific physiological measures of smoltification status 

linked to improved survival such as gill Na-K ATPase enzyme activity, blood concentrations of 

thyroid hormones, growth hormone, insulin, insulin-like growth factor, and body lipid levels, 

among others. A simple measure of physiological smolt development easily measured at the 

hatchery is the rate of change in growth rate, immediately preceding and during the parr-smolt 

transformation (Beckman et al., 1996). The definition of a quality hatchery smolt is therefore 

equal to the definition of a quality natural smolt. Smolt quality is defined as a metamorphosed, 

anadromous salmonid that exhibits rapid downstream migration, increased hypo-osmoregulatory 

capability (enhanced seawater tolerance), sustained growth in the ocean, and high survival to 

adulthood. Smolt quality is measured along a continuum of physiological, morphological, and 

behavioral changes that occur during the metamorphosis from fingerling to migrant. 

Wild Salmon Template

In the years following ESA listings, researchers and managers have recognized the need to 

conserve and recover depleted natural stocks and have used hatcheries as one potential tool. 

Research emphasis is now concentrated on the physiological, morphological and behavioral traits 

of hatchery fish that may impart benefits when released. In these programs, the wild fish may 

provide the best template for duplicating a quality hatchery smolt. For example, mimicking the 

growth pattern, size, and out-migration timing of natural fish has been shown to produce higher 

quality hatchery smolts with greater smolt-to-adult survival. An added advantage would be an 

equivalent hatchery contribution to adult harvest with fewer smolts released. Producing, high 

quality smolts that migrate downstream rapidly reduces opportunity for hatchery-wild fish 

interactions and minimizes negative ecological impacts of hatchery fish on wild fish. Rapidly 

migrating smolts will be less likely to residualize and imprint on inappropriate stream sites, and 

therefore be less likely to stray during their homing migration. 
B-32 Emerging Issues – Smolt Quality and the Wild Salmon Template 

If one were to use wild salmon as a template, for juvenile hatchery fish, what morphological, 

behavioral, physiological, and genetic fitness traits would characterize locally adapted stocks? The 

following dialogue gives examples of physiological, morphological and behavioral templates 

characteristic of wild fish: 

Physiology 

Conditions in the hatchery environment affect physiological fitness. Water quality affects the 

duration and rate of smolt development and other physiological processes in the hatchery 

environment. Primary amongst these are temperature and photoperiod. Physical and chemical 

characteristics such as suspended solids; dissolved gases, pH, and mineral content may also 

control physiological processes such as fish health (immune resistance) and osmoregulation. 

Energy reserves and growth rate affect physiological fitness. Growth, survival and the 

physiological processes of smoltification and maturation in salmonids are controlled in part by the 

availability and quality of forage organisms. During periods of declining day length, circulating 

levels of the metabolic hormones IGF-1 and growth hormone are low and protein synthesis rates 

in the body are reduced. Fish convert both dietary protein and lipid into stored body fat during 

these periods. In contrast, when day lengths increase, as during the period of spring smolting, body 

metabolism patterns change, with increases in protein synthesis rates and lypolysis, resulting in 

lower percentage whole body fat levels. In late autumn and early winter wild fish reduce growth 

rate, feeding activity, and metabolism and lose substantial amounts of body fat over the winter 

(Beckman et al. 1998). In late winter and early spring, wild yearlings dramatically increase 

feeding, accumulate body fat, resume growth and exhibit a dynamic pattern of physiological 

development (Dickhoff et al. 1997). In contrast, hatchery salmonids are fed diets high in lipids at 

feeding levels that encourage sustained rapid growth, even during cold winter periods when 

growth of natural fish is zero. In natural salmonids there is a positive relation between growth rate 

during the two months immediately proceeding out migration and survival to adulthood (Dickhoff 

et al. 1995). Furthermore, increased spring growth of spring Chinook salmon improves their 

downstream movement. 

In general, wild smolts differ from hatchery smolts in four ways; wild fish are generally smaller 

than hatchery fish; show more rapid growth rate during the smolting period; have less body fat 

than hatchery smolts; and show a more dynamic change in physiological and metabolic status 

from over-wintering to the spring smolting period. 

Morphology 

Conditions in the hatchery environment should promote morphological fitness by emulating 

natural fish body size, body shape, and coloration. For example, body size affects foraging 

effectiveness, vulnerability to predators, fecundity and reproductive success. 

The size of a juvenile salmonid affects its ability to compete with its peers, escape predators, adapt 

to seawater, migrate rapidly, mature early, and most importantly, survive and recruit into the 

fishery or spawning population (Bilton et al. 1982, Martin and Wertheimer 1989). Natural 
Emerging Issues – Smolt Quality and the Wild Salmon Template B-33 

populations generally contain fish within a size range governed by hatch time, available food 

resources, and environmental conditions. 

Releasing young, high-quality smolts within a size range similar to the natural population from 

which they are derived, as opposed to releasing larger smolts, will reduce competition with wild 

smolts and minimize selection pressures that occur when there is clear disparity in size. 

Cryptic coloration. In nature, salmonid eggs incubate, and alevins develop, in the darkened, 

matrix-rich environment of the gravel substrate of the redd. Following hatch, juveniles rear in a 

complex lighted environment of shade, sunlight filtering through riparian vegetation, and lightabsorbing dark gravel substrate. This environment produces cryptic coloration and body 

camouflage patterns most likely to reduce vulnerability to predators. At smoltification, guanine is 

deposited in the epidermal tissues, and the fish becomes silvery in appearance as it undertakes its 

downstream migration. Hatcheries can simulate these conditions through the use of enriched 

environments. 

The body shape of a wild salmonid changes with the season of the year and the availability of 

nutritional resources. During winter, a period of low feed availability or even starvation, body 

weight and condition (relationship between body length and weight) drops, resulting in a slimmer 

fish with lower body fat. In spring, prior to smoltification, resident non-migratory juveniles feed 

heavily and regain body fat and condition. During the parr-to-smolt transformation, and as the 

period of downstream migration nears, the condition index changes again and a slimmer, more 

streamlined, silvery smolt is produced. 

Overall, fecundity is generally lower in hatchery fish, owing to juvenile rearing protocols and 

smaller age at maturity. In some species, the release of large hatchery fish results in a larger 

percentage of precocious males in the population, early return of females to the hatchery, and 

smaller age and lowered fecundity at return. 

Behavior 

Conditions at the hatchery should promote the competency of juvenile fish to migrate, establish 

territory, and displace other individuals, prey and forage. 

Social behavior Juvenile salmonids have been shown to reduce their territory size as fish density 

increases. Territory size may limit the maximum density of juvenile salmonids in streams 

(McNicol and Noakes 1984). Density is an important factor in adult survival, with high-density 

culture causing a breakdown in social hierarchies in cultured salmonids. 

Migration/homing/straying Before out-migration, juvenile salmon learn odors associated with 

their natal streams, which guide their homing migrations as adults. Imprinting in salmon may 

occur at multiple life history stages. To maximize imprinting opportunity, juvenile salmon must 

experience the odors of their natal system at various times and physiological states when the odors 

can be learned. It is well-known that olfactory imprinting occurs during sensitive periods 

associated with surges in plasma thyroxin levels during parr-smolt transformation (Dittman et al 

1995). This may indicate the occurrence of multiple pre-smolt imprinting periods. 
B-34 Emerging Issues – Smolt Quality and the Wild Salmon Template 

Predation avoidance behavior Natural salmon juveniles experience and observe predation of their 

cohorts by birds, fish and a variety of mammals. Observed predation, or attempted predation on 

themselves and other salmonids, results in expression of an innate predator-avoidance response 

that protects natural salmon juveniles. Because they are protected in the hatchery environment, 

hatchery salmon are lacking this naturally learned predator-avoidance response. 

Foraging ability From the time of first feeding to returning as adults, natural salmon learn to feed 

on a variety of swimming, moving, prey organisms. The recognition of a specific type of prey 

movement is probably recognizable to naturally rearing salmon juveniles. By comparison, 

hatchery salmon are fed a regimen of prepared feeds that are generally uniform in size, color and 

movement. Hatchery fish have been shown to be less successful in stalking and capturing natural 

prey organisms. 

Genetics 

Genetic changes from artificial propagation can affect both the productivity and viability of wild 

populations (Reisenbichler and Rubin 1999). To produce a quality smolt for use in conservation 

and recovery of wild populations, hatchery practices should minimize both random and directional 

selective changes that contribute to domestication and loss of local adaptation. Domestication is 

the process of a population changing over time in response to an artificial or human-controlled 

environment and is manifested in directly-measurable genetic characteristics (e.g. allele 

frequencies) as well as in physiological, morphological, and behavioral traits discussed above. 

Principal factors that lead to domestication include relaxation of natural selection that would 

naturally occur in the wild, natural selection to the hatchery environment, and direct humancontrolled selective breeding. 

Maintenance and Selection of Broodstock

The goal of developing a wild-template smolt is to minimize the changes that contribute to 

domestication. The level of domestication selection is affected by both hatchery practices and the 

amount of exchange between hatchery and wild populations. Hatchery practices that minimize 

changes in physiological, morphological and behavioral traits, as well as such traits as time, age 

and size of return will decrease the risk of domestication, as many of these traits have inheritable 

components. 

Broodstocks should be selected from locally-adapted populations. Introduction of spawners from 

exogenous populations should be avoided, to minimize risks of outbreeding depression. The 

periodic infusion of adults of natural-origin spawners retards the rate and level of domestication, 

but may not completely eliminate its effects (Ford, in press). 

Effective population size 

Hatchery practices should be designed to maximize effective population size to maintain genetic 

diversity and reduce potential detrimental effects of inbreeding. Small effective population sizes 

can increase the likelihood of deleterious effects by random drift, even in the absence of an altered 

selective environment. Effective population size is defined in terms of numbers of reproducing 

adults (breeders) per year and the generation time of the population. Techniques that ensure every 
Emerging Issues – Smolt Quality and the Wild Salmon Template B-35 

adult has an equal probability of producing progeny maximize effective population size. These 

techniques include equal sex ratio, equal family size, and mating protocols that equalize 

contributions among individuals. 

The effective population size of the hatchery program can also directly affect the health and 

viability of the wild population. A reduction in diversity and in the effective size of the wild 

population can result from “genetic swamping,” where a large number of hatchery fish from 

relatively few parents interbreed with wild fish. This is particularly likely if the effective 

population size of the hatchery population is substantially less than that of the wild population, 

(Ryman and Laikre 1991). 

Achieving the Wild Fish Template in the Hatchery

How would a hatchery manager rear fish to approximate the wild fish template? The following 

section describes hatchery methods that can be employed to mimic the wild fish template in 

hatchery fish: 

Physiology 

Swimming efficiency (stamina, stride efficiency) 

Solution: exercise, growth modulation. 

Smolt development (silvering-guanine deposition, hormonal and enzyme cycles, hypoosmoregulatory ability)

Solution: growth modulation, dietary salt, photoperiod control, rearing density. 

Energy stores (whole body proximates, liver glycogen, hepatosomatic index)

Solution: feed amount, growth modulation. Simulate proximate composition by 

controlling diet composition. 

Morphology 

Growth pattern (seasonal change in length, weight, and condition factor).

Solution: growth modulation. Simulate growth rate and body size by controlling water 

temperature and feeding rates. Slow growth during winter followed by rapid growth 

during spring ensures better quality smolts. 

Length frequency distribution (mean length/weight, variance, skewness)
B-36 Emerging Issues – Smolt Quality and the Wild Salmon Template 

Solution: feed amounts and frequency of feeding, staggered egg take, thermal control of 

incubation, rearing density, feed schedule. Fish are grown using methods of feed ration 

and/or water temperature manipulations to match growth cycles of hatchery fish to growth 

patterns of wild fish. Growth of hatchery fish will be reduced in the winter and accelerated 

in the spring. 

Smolt development (condition factor, coloration, body shape, fin quality, dentition, cloacal folds)

Solution: dietary salt, growth modulation, rearing density, environmental enrichment. 

Out-migration timing 

Solution: volitional, forced, staggered release. 

Behavior 

Competition for feed. 

Solution: environmental enrichment, forage training on live foods, rearing density. 

Competition for space (territoriality) 

Solution: environmental enrichment, reduced rearing density. 

Migratory behavior (schooling, downstream orientation, restlessness, migration)

Solution: growth modulation, exercise? 

Predator avoidance 

Solution: exercise, predator conditioning, avoid human feeder imprinting. 

Genetics 

Minimize Domestication Selection (selection in the hatchery environment)

Solution: select locally adapted broodstock, periodically infuse wild spawners. 

Run timing 

Solution: monitor run timing, adjust egg take to emulate wild timing, modulate 

developmental rates to emulate wild timing, cull as needed. 

Age at maturity (age structure, precocity)
Emerging Issues – Smolt Quality and the Wild Salmon Template B-37 

Solution: utilize cohorts in proportion to wild run. 

Size at maturity (average size at age)

Solution: monitor size at age changes within hatchery relative to wild populations; 

minimize directional changes in hatchery by equalizing contributions of individuals 

irrespective of size within age cohort within the bounds of the wild template. 

Maximize effective population size (inbreeding and variance effective population size)

Solution: equalize sex ratio, follow fertilization protocols that equalize contributions 

among individuals (e.g. factorial matings, pairwise matings), equalize family size, cull as 

needed. 

References

Beckman, BR, DA Larsen, B. Lee-Pawlak, and WW Dickhoff. 1996. Physiological assessment 

and behavior interaction of wild and hatchery juvenile salmonids: The relationship of fish 

size and growth to smoltification in spring Chinook salmon. BPA Report, October 1996. 

Beckman, B.R., W.W. Dickhoff, W.S. Zaugg, C. Sharpe, S. Hirtzel, R. Schrock, D.A. Larsen, 

R.D. Ewing, A. Palmisano, C.B. Schreck, and C.V.W. Mahnken. 1998 Growth, 

smoltification, and smolt-to-adult return of spring Chinook salmon (Oncorhynchus 

tshawytscha) from hatcheries on the Deschutes River, Oregon. Trans. Am. Fish. Soc. 

Bilton, H.T., D.F. Alderdice, and J.T. Schnute. 1982. Influence of time and size at release of 

juvenile coho salmon (Oncorhynchus kisutch) on returns at maturity. Can. J. Fish. Aquat. 

Sci. 39:426-447. 

Dickhoff, W.W., B.R. Beckman, D.A. Larsen, C.V.W. Mahnken, C.B. Schreck, C. Sharpe, and 

W.S. Zaugg. 1995. Quality assessment of hatchery-reared spring Chinook salmon smolts 

in the Columbia River Basin. Symposium of the American Fisheries Society 15:292-302. 

Dittman, A.H., T.P. Quinn, and G.A. Nevitt. 1995. Timing of imprinting to natural and artificial 

odors by coho salmon (Oncorhynchus kisutch). Can. J. Fish. Aquat. Sci. 53:434-442. 

Dickhoff, WW, BR Beckman, DA Larsen, B Lee-Pawlak. 1997. Physiology of migration in 

salmonids. Mem. Fac. Fish. Hokkaido Univ. 44:14-16. 

Ford, M. In Press. Selection in captivity during supportive breeding may reduce fitness in the wild. 

Conservation Biology. 

Martin, R.M. and A. Wertheimer. 1989. Adult production of Chinook salmon reared at different 

densities and released as two smolt sizes. Prog. Fish-Cult. 51: 194-200. 
B-38 Emerging Issues – Smolt Quality and the Wild Salmon Template 

McNicol, R. E. and D. L. G. Noakes. 1984. Environmental influences on territoriality of juvenile 

brook char, Salvelinus fontinalis, in a stream environment. Environmental Biology of 

Fishes 10: 29-42 

Reisenbichler, R. R. and S. P. Rubin. 1999. Genetic changes from artificial propagation of Pacific 

salmon affect the productivity and viability of supplemented populations. ICES Journal of 

Marine Science 56: 459-466. 

Ryman, N. and L. Laikre. 1991. Effects of supportive breeding on the genetically effective 

population size. Conservation Biology 5: 325-3329. 

Sakamoto, T. and T. Hirano: 1993. Expression of insulin-like growth factor I gene in 

osmoregulatory organs during seawater adaptation of the salmonid fish: Possible mode of 

osmoregulatory action of growth hormone. Pro. Natl. Acad. Sci. USA, 90, 1912-1916. 

Wagner, H.H., F.P. Conte, and J.L. Fessler. 1969. Development of osmotic and ionic regulation in 

two races of Chinook salmon Oncorhynchus tshawytscha. Comparative Biochemistry and 

Physiology 29: 325-341. 

Varnavskiy, V.S., N.V. Varnavskay, S.V. S. Kalinin, and N.M. Kinas. 1992. RNA/DNA index as 

an indicator of growth rate of coho salmon (Oncorhynchus kisutch) during early marine 

life. J. Ichthyol. 32:10-19. 
Emerging Issues – Benefits of Hatchery Fish as a Source of Food B-39 

BENEFITS OF HATCHERY FISH AS A SOURCE OF FOOD

In the development of its Scientific Framework for the Artificial Propagation of Salmon and 

Steelhead, the Hatchery Scientific Review Group recognized that hatcheries will likely experience 

more frequent large surpluses of returning adults because of increased protection of co-mingled 

natural stocks. Because of this, it is important for the hatchery operators and fishery managers to 

devise creative solutions for providing harvest opportunities, and to use surplus returns in ways 

that provide additional benefits from the hatchery programs. 

One creative use of hatchery surplus fish is as a source of food. Historically, a small portion of 

fish returning to state hatcheries has been used as food for state institutions or distributed to tribes 

for subsistence purposes. The majority has been sold to buyers who use the carcasses primarily for 

products such as fish meal for pet food. Tribal hatcheries have generally been the exception to this 

rule. Most tribal hatcheries have considered distribution of salmon to tribal members as the 

preferred use of this resource. Some, like the Nisqually and Skokomish tribes, have expanded their 

distribution system to include charitable organizations, food banks and even members of the 

general public that visit the hatchery on spawning days specifically to pick up fish to be used for 

food. In the last ten years, the Nisqually Tribe alone has distributed an average of 70,000 pounds 

of hatchery returns annually for use as food (Bill St. Jean, Nisqually Indian Tribe and Dave 

Herrera, Skokomish Indian Tribe, personal communications). 

In the past few years, the State of Washington has also recognized the value of fish returning to 

hatcheries as a food source. Under state law, the Washington State Department of Fish and 

Wildlife (WDFW) has the authority to donate hatchery returns, as excess state property, to needy 

citizens of the state. Current recipients of hatchery fish include 40 different organizations ranging 

from small groups such as senior centers, Salvation Army branches, churches and gleaning 

organizations that receive from 10–200 fish per visit, to a large, statewide distribution network 

that has an outlet in every county of the state. 

The small organizations arrange to pick up hatchery adults from a specific hatchery in their area 

and handle the processing and distribution to their organization themselves. In the case of the 

statewide network, a contracted processor picks up the hatchery adults, processes and freezes them 

as skinless fillets, and distributes them statewide through Seattle First Harvest. In order to defray 

his cost, the processor keeps the by-products: skeletal remains, skin, and eggs (which are used for 

fish meal), bait eggs and caviar. 

In the first year of operation (2000), this program took 30,000 pounds of hatchery adults and 

distributed them as food. In 2001, 450,000 pounds of fish were used to produce fillets. Projections 

for 2002 were for 1.5–2.0 million pounds of fish to be used to produce 500,000–700,000 pounds 

of frozen skinless fillets; the equivalent of 2.0–2.8 million servings of protein. Because of the 

success of this program, providing hatchery fish to feed needy residents is now a high priority for 

good quality fish, second only to meeting the needs of the hatchery program and providing fish for 

natural spawning areas (Andy Appleby, Washington Department of Fish and Wildlife, personal 

communication). 
B-40 Emerging Issues – Benefits of Hatchery Fish as a Source of Food 

In 2002, the State of Oregon placed a higher priority on using surplus hatchery adults as a food 

source. The Oregon Department of Fish and Wildlife has made arrangements with the same 

processor used by WDFW. In exchange for the right to process and sell the by-products, fish are 

processed into skinless fillets and distributed frozen by the Oregon Food Bank. Projections for the 

2002 contribution from Oregon hatcheries were similar to Washington’s—approximately 140,000 

fish to be processed into 500,000 pounds of food (Bill Otto, Oregon Department of Fish and 

Wildlife, personal communication). 
Emerging Issues – Marine Carrying Capacity B-41 

MARINE CARRYING CAPACITY

The present hatchery system for Pacific salmon was developed to produce increasingly higher 

numbers of fish in a constant oceanic ecosystem, believed to be near limitless in its capacity to 

accommodate hatchery salmon. Until recently, these oceanic systems were believed to be stable, 

internally regulated, and to behave in a deterministic manner. The more current view is of an open 

system in near constant flux - a system without long-term stability, and one that is often under the 

influence of stochastic factors, many originating outside the ecosystem itself. The modern view of 

the ecosystem is one characterized by ecological uncertainty (Mahnken et al. 1998). 

Based on the assumption that ocean carrying capacity was unlimited, or had not yet been reached, 

the goal of increasing the size of a fishery was simply achieved by building more hatcheries and 

releasing more fish. As a result, for more than 20 years there has been massive growth in salmon 

hatchery releases in the Pacific Northwest (Mahnken et al. 1998), with more smolts entering the 

ocean from the Pacific Northwest hatchery system than at any time in the past. An example of this 

general increases in hatchery output is the Columbia River Basin. The Northwest Power Planning 

Council (NWPPC 1986) estimated that annual natural abundance before 1850 was 264 million 

smolts. Since the late 1980s, public hatcheries in the Columbia River Basin have reared between 

200 - 300 million juveniles annually for release (Chapman 1986, Schiewe et al. 1989). In 1992, for 

example, based on releases of nearly 203 million hatchery fish and an estimated 145 million wild 

fish, almost 350 million smolts were in the Basin that year, or 32 % above the historic high of 

1850. Such vast numbers of out-migrants clearly place a heavy demand on the food production 

capabilities of any ecosystem, whether in the natal streams and rivers, the coastal estuaries, or in 

the ocean itself. Furthermore, in the intense competition for food, which must occur, the dramatic 

increases in numbers of hatchery fish have obviously affected the chances for survival of the 

smaller numbers of native stocks. 

Studies on abundance of stocks in widely separate geographic areas over time have indicated 

oceanic conditions are primarily responsible for changes in annual returns of adult salmon (Cooper 

and Johnson 1992, Beamish and Bouillon 1993, Lichatowich 1993, Olsen and Richards 1994). 

The way in which these physical, chemical, and biological processes conditions can impact fish 

populations and production trends are reasonably well known. 

Based on analysis of climatic trends and the productivity of salmon fisheries in the North Pacific, 

Beamish and Bouillon (1993) noted that the strategy of releasing large numbers of artificially 

reared smolts during a period of decreasing marine survival was not appropriate. Concerns over 

the limits of ocean carrying capacity, and other factors, are conspiring to force a re evaluation of 

industrial hatchery production of North Pacific salmonids (Mahnken et al. 1998). Concerns 

include (i) high harvest rates of wild fish in fisheries targeted on the more abundant hatchery 

stocks, (ii) over-production of hatchery chum salmon in Japan, and both pink and chum salmon in 

Alaska, (iii) declining fish size, and (iv) altered return timing and age at maturity, and (v) widely 

varying ocean survivals. Concern for declining size and increasing age at maturity observed in 

North Pacific stocks of five salmon species suggests that large-scale hatchery production may be 

resulting in density-dependent growth reduction (Kaeriyama and Urawa 1992, Rogers and 

Ruggerone 1993, Bigler and Helle 1994). 
B-42 Emerging Issues – Marine Carrying Capacity 

Although ocean harvest rates are generally scaled back when the abundance or productivity of 

wild stocks is low and regime shifts become evident, hatchery production is not. Rather, the 

tendency in the 1970-90 period has been to increase hatchery production in the Pacific Northwest 

as ocean productivity decreased (Mahnken et al, 1998). Given that the carrying capacity of the 

ocean has a primary impact on salmon returns, it is eminently sensible that hatchery releases 

should be reduced during periods of poor ocean survival to protect wild fish. Scientific ignorance 

of oceanic regime shifts, and their impact on the variability of fish abundance and survival, has 

acted against wild fish populations through poorly informed or ill-considered hatchery production 

and harvest policies. 

Regime shifts, or major changes in ocean productivity, occur only infrequently but are becoming 

increasingly predictable. By interpreting physical, chemical, and biological signals of changing 

oceanic productivity, certain impacts can now be anticipated. Fishery managers now know they 

should decrease harvest rates during periods of lower productivity, that is, they should scale 

fisheries to the natural spatial and temporal patterns of abundance of wild fish populations. 

Likewise, hatchery production should be curtailed during periods of increased density dependant 

mortality to protect wild stocks and to reduce monetary waste. Modern hatcheries should program 

their production to accommodate the natural spatial and temporal patterns of abundance in wild 

fish populations. 

References

Beamish, R.J. and D. Bouillon. 1993. Pacific salmon production trends in relation to climate. Can. 

J. Fish. Aquat. Sci. 50:1002-1016. 

Bigler, B.S. and J.H. Helle. 1994. Decreasing size of North Pacific salmon (Oncorhynchus spp.): 

possible causes and consequences. Presented to the Annual Meeting of the North Pacific 

Anadromous Fisheries Commission, Vladivostok, Russia, October 1994. 

Chapman, D.W. 1986. Salmon and steelhead abundance in the Columbia River in the nineteenth 

century. Trans. Am. Fish. Soc. 115:622-670. 

Cooper, R. and T. Johnson. 1992. Trends in steelhead abundance in Washington and along the 

Pacific Coast of North America. Washington Department of Wildlife and Fisheries, 

Management Report 92-20. 

Kaeriyama, M. and S. Urawa. 1992. Future research by the Hokkaido Salmon Hatchery for the 

proper maintenance of Japanese salmon stocks. In Y. Ishida, K. Nagasawa, D. Welch, K. 

Meyers, and A. Shershnev (editors), Future salmon research in the North Pacific Ocean, 

Special Publication Nat. Res. Inst. Far Seas Fish. 20:57-62. 

Lichatowich, J.A. 1993. Ocean carrying capacity. Technical Report No. 6, Recovery issues for 

threatened and endangered Snake River salmon. Prepared for Bonneville Power 

Administration, Portland, OR. 
Emerging Issues – Marine Carrying Capacity B-43 

Mahnken, C.V.W., G.T. Ruggerone, F.W. Waknitz, and T. A. Flagg. 1998. A historical 

perspective on salmonid production from Pacific Rim hatcheries. N. Pac. Anadr. Fish. 

Comm. Bull. 1:38-53. 

NWPPC (Northwest Power Planning Council). 1986. Staff issue paper. Hydropower responsibility 

for salmon and steelhead losses in the Columbia River Basin, April, 1986 (S/III.A.2). 

Northwest Power Planning Council, Portland, OR. 

Olsen, D. and J. Richards. 1994. Inter-basin comparison study: Columbia River salmon production 

compared to other west coast production areas, Phase II analysis. Report to the Army 

Corps of Engineers, Portland, OR. 29 p. 

Rogers, D.E. and G.T Ruggerone. 1993. Factors affecting marine growth of Bristol Bay sockeye 

salmon. Fish. Res. 18:89-103. 

Schiewe, M.H., D. Miller, E. Lawley, R. Ledgerwood, and R. Emmett. 1989. Quality and behavior 

of juvenile salmonids in the Columbia River estuary and nearshore ocean. NMFS/NWFSC 

and Department of Oceanography, Oregon State University. 38 p. 
B-44 Emerging Issues – Outplanting and Net Pen Release of Hatchery Fish 

OUTPLANTING AND NET PEN RELEASE OF HATCHERYORIGIN FISH

A large system of fish hatcheries exists in the Pacific Northwest for propagating Pacific salmon 

and steelhead (Oncorhynchus spp). A significant proportion of those released fish support 

commercial, Tribal, and recreational fisheries to specifically mitigate for fish and habitat losses 

associated with land- and water-use development. For example, approximately 85% of all 

returning adult salmon and steelhead in the Columbia River are of hatchery origin. 

The vast majority of salmon hatcheries in the Pacific Northwest operate largely as adult spawning 

and juvenile rearing facilities through the smolt stage of development. Upstream-migrating adults 

are trapped and/or are diverted into adult holding ponds and then spawned when they reach sexual 

maturity. The fertilized eggs are incubated and hatched, and the resulting progeny are reared to the 

smolt stage prior to release into a freshwater stream. Age at release varies considerably among the 

various species of Pacific salmon (including steelhead), ranging from a few days or weeks after 

yolk absorption for pink and chum salmon (O. gorbuscha and O. keta, respectively) to 

approximately 15–20 months post-fertilization for steelhead, coho salmon (O. kisutch), and spring 

Chinook salmon (O. tshawytscha). 

The standard method of propagation is to release juveniles into the stream areas where returning 

adults can be recaptured for broodstock. The homing and recapture of returning adults may be 

further maximized if smolt releases and adult trapping occur “on-station” at the hatchery. Fish 

returning elsewhere where they cannot be trapped are known as “strays”. The recapture and 

removal of unharvested, hatchery-origin adults reduces potential genetic and ecological risks to 

naturally spawning populations when the purpose of those hatchery-origin fish is strictly harvest. 

On the other hand, smolts are often released from a site where adult collection facilities do not 

exist. In many situations, smolts are transported by hatchery truck—oftentimes into other 

watersheds and sometimes over relatively large distances (e.g. >100 km)—and then released. In 

general, salmon and steelhead return as adults to the areas where they are released, not where they 

are reared (reviewed by Quinn 1993). 

Releasing smolts into streams geographically removed from a hatchery or adult collection facility 

is commonly called “outplanting.” Steelhead programs in Washington state, for example, have 

often used outplanting to support recreational fisheries in a large number of small streams where 

no hatchery or adult collection facilities exist. More recently, saltwater net pens have been used 

increasingly to acclimate and release salmon smolts in marine areas where a targeted marine 

fishery on returning adults is desired. In these latter net pen releases, juvenile salmon are 

transferred to brackish or salt water (i.e., at a nearshore, estuarine location) at the early stages of 

smoltification and then fed in the net pens for one to three months prior to release. Significant 

harvests on returning adults can then occur in the near shore marine areas in the general vicinities 

of the net pens. 
Emerging Issues – Outplanting and Net Pen Release of Hatchery Fish B-45 

A common feature of outplanting and net pen programs is the release of smolts where no facilities 

exist to trap returning adults that escape target fisheries. In these latter situations, non-harvested 

adults may spawn unintentionally in streams far-removed from the source hatchery or geographic 

location where their parents were trapped for broodstock. Outplanting juvenile and/or adult 

salmonids also occurs in restoration and recovery programs where natural spawning by hatcheryorigin adults is explicitly desired; however, these latter programs are not the subject of the 

discussion here. 

Homing to natal streams is an important biological characteristic of salmonid fishes, allowing 

evolution of local adaptations in life history and other fitness traits (Quinn 1993; Altukhov and 

Salmenkova 1994; Quinn et al. 2001). Stock-specific, genetically-based adaptations include size 

and age at sexual maturity, adult return and spawn timing, pre-hatch developmental rate, length of 

freshwater residence prior to outmigration, and marine migration patterns (e.g., Smoker et al. 

1998). Despite the biological importance of homing, natural straying also plays an important role 

related to colonization of new habitats and maintaining connectivity between geographically 

adjacent populations (Shapovolov and Taft 1954; Milner 1997; Quinn 1997). 

Many studies have shown that salmon and steelhead seek alternative spawning habitats if no 

appropriate habitat is immediately available (Pascual and Quinn 1994). Such behavior is most 

apparent when natal streams are blocked by catastrophic, environmental events. For example, 

siltation resulting from the 1980 eruption of Mount St. Helens resulted in significant numbers of 

Chinook salmon and steelhead straying from the Cowlitz River to the Kalama and Lewis rivers 

(Leider 1989; Quinn et al. 1991). 

Tagging and genetic studies have shown that outplanting and net pen programs promote stray rates 

that far exceed natural levels (Candy and Beacham 2000; Mackey et al. 2001). The absence of 

freshwater imprinting by fish released from saltwater net pens can lead to unpredictable straying 

by large numbers of unharvested adults to streams where natural spawning is not desired. 

Similarly, significant numbers of adults returning to outplanted streams typically escape targeted 

fisheries and potentially spawn with natural-origin fish. Consequently, outplanting and net pen 

releases can pose significant genetic risks to natural populations by promoting high stray rates to 

freshwater areas where interbreeding with naturally spawning populations is not desired. 

Outplanted smolts may also outmigrate from freshwater at a much slower rate compared to smolts 

resulting from on-station releases (Hawkins and Tipping 1999; Pearsons and Fritts 1999). Such 

delayed outmigraton rates may result in increased predation on, and competition with, wild fish. 

Although side-by-side comparisons have not been done, outmigration rates of outplanted steelhead 

smolts have been documented at 2.9 km/day (Tipping and Byrne 1996) and 1.6 km/day (Tipping 

et al.1995), whereas on-station releases have documented 33 km/day (Dawley et al.1977; Harza 

1998). This travel time difference could substantially increase smolt predation opportunities on 

wild salmonid fry. Also, the desired benefit of changing adult distributions within a river for 

supporting fisheries may be minimally affected by outplanting smolts in rivers downstream of a 

hatchery. Tipping and Hillson (2002) found that on the Lewis River—where steelhead smolts 

were reared near the upstream anadromous terminus—adult returns of winter steelhead were only 

slightly changed by downstream smolt release location, and summer steelhead were unaffected. 
B-46 Emerging Issues – Outplanting and Net Pen Release of Hatchery Fish 

 

Outplanting and net pen releases from segregated hatchery programs58 are especially problematic 

because of the potentially high level of genetic divergence between the hatchery stock and natural 

populations where straying and natural spawning may occur. Although the natural spawning 

success of hatchery-origin fish may be less than that of natural-origin fish when they occur in the 

same stream, those same data indicate that significant numbers of hatchery-origin fish from nonnative or long-standing “domesticated” populations do indeed spawn successfully and can 

contribute significant numbers of progeny to naturally spawning populations (Chilcote et al. 1986; 

Campton et al. 1991; Mackey et al. 2001; Kostow et al. 2003; McLean et al. 2003). Kostow et al. 

(2003) presented data supporting a conclusion that hatchery summer steelhead adults and their 

offspring may have contributed to wild winter steelhead population declines through competition 

for spawning and rearing habitats. 

Many studies have further indicated a genetic component to homing such that non-native fish, or 

their hybrid progeny, stray at higher rates than identically-reared native fish (Bams 1976; McIsaac 

and Quinn 1988; Pascual et al. 1995; Candy and Beacham 2000). This latter characteristic further 

confounds the genetic risks associated with straying of returning, outplanted fish by potentially 

increasing stray rates among natural-origin fish representing the progeny of hatchery-origin adults 

that reproduced successfully in nature. Consequently, based on the available scientific and fishery 

research data, both published and unpublished, the HSRG concludes that outplanting and net pen 

releases of hatchery-origin smolts pose significant, and potentially unacceptable, genetic risks to 

naturally spawning populations. 

The HSRG has concluded that the simplest way to reduce risks associated with outplanting and net 

pen releases is to reduce the number and/or size of existing programs. However, the HSRG also 

recognizes that many of these programs support important tribal, commercial and/or recreational 

fisheries. As a result, significant trade-offs may exist between the fishery benefits of such 

programs and the risks they pose to naturally spawning populations. Consequently, the HSRG 

recommends that the biological risks of outplanting and saltwater net pen programs also be 

reduced by implementing the following actions: 

• Mark all net pen released and outplanted fish each year, and tag a significant proportion of 

released fish with coded-wire tags, to assess the direct contribution of those fish to 

targeted fisheries and to assess stray rates and biological risks to natural populations. 

Systematically tagging a portion of the released fish each year, coupled with marking all 

outplanted and net pen released fish, will allow the co-managers to assess the degree to 

which these programs meet harvest goals while posing risks to natural populations. 

• Conduct intensive harvest of hatchery-origin fish and/or use adult traps to reduce potential 

natural spawning of unharvested, hatchery-origin fish. 

• Restrict releases of hatchery-origin fish to areas where adult collection facilities exist or 

can be easily developed. In some cases, adult traps can be added to existing smolt release 

ponds. In other cases, release sites can be restricted to streams with existing adult 

58

 See Emerging Issues section on Integrated versus Segregated hatchery programs. 
Emerging Issues – Outplanting and Net Pen Release of Hatchery Fish B-47 

 

collection facilities. The wild steelhead management zones recommendations for steelhead 

would also help meet this recommendation (see below). 

• Use locally-adapted and genetically integrated59 hatchery stocks for net pen releases and 

outplanting wherever possible. That is, minimize—or eliminate—the use of “out-ofregion” stocks and fish from genetically segregated hatchery stocks for these high-risk 

programs. Fish outplanted or net-pen reared for harvest-driven programs should be 

obtained from genetically integrated hatchery stocks and/or stocks native to the region or 

watershed where the net pen or outplanting programs occur. One possible exception to this 

latter recommendation would be hatchery populations that have been selectively bred, or 

otherwise manipulated genetically or phenotypically, for reproductive traits (e.g. spawn 

timing) that result in low probabilities of successful natural reproduction in the specific 

streams or geographic area where smolts are released. For example, hatchery-propagated 

populations of steelhead have often been selectively bred for early run and spawn timing, 

and these fish may have low reproductive success in watersheds driven hydrodynamically 

by snow-melt. However, these latter assumptions must be carefully tested and evaluated 

for such actions to be considered scientifically defensible. 

• Implement the HSRG’s recommendation for wild steelhead management zones to 

substantially reduce outplanting and thereby reduce risks to naturally spawning 

populations.60 Similar region-wide guidelines and changes are needed to reduce biological 

risks of net pen releases and other outplanting programs, especially where no adult 

collection facilities are present for trapping non-harvested adults. 

• Evaluate the benefits and risks of each program every two to three years. Programs 

imposing significant risks relative to benefits should be reduced or terminated. 

• Monitor and evaluate high-risk programs annually to ensure that adverse effects to wild 

populations are minimal, that straying risks are appropriately managed, and that offstation releases are appropriately located such that non-harvested, hatchery-origin adults 

do not spawn in undesirable locations. 

• Develop system-wide risk management guidelines and protocols for outplanting and net 

pen programs. 

The HSRG believes these recommendations should be implemented as soon as possible as a first 

step alternative to terminating outplanting and saltwater net pen programs that are conferring 

significant fishery benefits. Many of the HSRG’s specific recommendations within each region 

reflect the more generalized recommendations presented above. 

59

 See Emerging Issues section on integrated versus segregated hatchery programs. 

60 See HSRG Hatchery Reform Recommendations, February 2003, System-wide Recommendations. 
B-48 Emerging Issues – Outplanting and Net Pen Release of Hatchery Fish 

References 

Altukhov, Y.P. and Salmenkova, E.A. 1994. Straying intensity and genetic differentiation in 

salmon populations. Aquaculture and Fisheries Management 25: 99-120. 

Bams, R.A. 1976. Survival and propensity for homing as affected by presence or absence of 

locally adapted paternal genes in two transplanted populations of pink salmon 

(Oncorhynchus gorbuscha). Journal of the Fisheries Research Board of Canada 33: 2716-

2725. 

Campton, D.E., Allendorf, F.W., Behnke, R.J., Utter, F.M., Chilcote, M.W., Leider, S.A., and 

Loch, J.J. 1991. Reproductive success of hatchery and wild steelhead. Transactions of the 

American Fisheries Society 120: 816-827. 

Candy, J. R., and T. D. Beacham. 2000. Patterns of homing and straying in southern British 

Columbia coded-wire tagged Chinook salmon populations. Fisheries Research 47:41-56. 

Chilcote, M.W., Leider, S.A., and Loch, J.J. 1986. Differential reproductive success of hatchery 

and wild summer-run steelhead under natural conditions. Transactions of the American 

Fisheries Society 115: 726-735. 

Hasler, A.D. and Scholz, A.T. 1983. Olfactory imprinting and homing. Springer-Verlag, Berlin. 

134 p. 

Hawkins, R. S., and J. M.. Tipping. 1999. Predation by juvenile hatchery salmonids on wild fall 

Chinook salmon fry in the Lewis River, Washington. California Fish and Game 

85(3):124-129. 

Kostow, K. E., A. R. Marshall, and S. R. Phelps. 2003. Naturally spawning hatchery steelhead 

contribute to smolt production but experience low reproductive success. Transactions of 

the American Society 132:780-790. 

Leider, S.A. 1989. Increased straying by adult steelhead trout, Salmo gairdneri, following the 1980 

eruption of Mt. St. Helens. Environ. Biol. Fishes 24: 219-229. 

Mackey, G., McLean, J.E., and Quinn, T.P. 2001. Comparisons of run timing, spatial distribution, 

and length of wild and newly established hatchery populations of steelhead in Forks 

Creek, Washington. North Am. J. Fisheries Management 21: 717-724. 

McIsaac, D.O. and Quinn, T.P. 1988. Evidence for a hereditary component in homing behavior of 

Chinook salmon (Oncorhynchus tshawytscha). Can. J. Fish. Aquat. Sci. 45: 2201-2205. 

McLean, J. E., P. Bentzen, and T. P. Quinn. 2003. Differential reproductive success of sympatric, 

naturally spawning hatchery and wild steelhead trout through the adult stage. Canadian 

Journal of Aquatic Sciences 60:433-440. 
Emerging Issues – Outplanting and Net Pen Release of Hatchery Fish B-49 

Milner, A. M. 1997. Glacial recession and freshwater ecosystems in coastal Alaska, pages 303-

330. In Milner, A.M. and Oswood, M.W. (editors), Freshwaters of Alaska. Ecological 

Studies : Analysis and Synthesis. 97. Springer-Verlag, Berlin. 

Pasqual, M.A. and Quinn, T.P. 1994. Geographical patterns of straying of fall Chinook salmon, 

Oncorhynchus tshawytscha (Walbaum), from Columbia River (USA) hatcheries. 

Aquaculture and Fisheries Management 25: 17-30. 

Pasqual, M.A., Quinn, T.P., and Fuss, H. 1995. Factors affecting the homing of fall Chinook 

salmon from Columbia River hatcheries. Trans. Am. Fish. Soc. 124: 308-320. 

Pearsons, T. N., and A. L. Fritts. 1999. Maximum size of Chinook salmon consumed by juvenile 

coho salmon . North American Journal of Fisheries Management 19:165-170. 

Quinn, T.P. 1997. Homing, straying, and colonization, pages 73-85. In W.S. Grant (editor), 

Genetic effects of straying on non-native hatchery fish into natural populations. 

Proceedings of the Workshop, June 1-2, 1995, Seattle, Washington. NOAA Technical 

Memorandum NMFS-NWFSC-30. U.S. Dept. of Commerce, National Marine Fisheries 

Service, Seattle, Washington. 

Quinn, T.P. 1993. A Review of Homing and Straying of Wild and Hatchery-Produced Salmon. 

Fisheries Research 18: 29-44. 

Quinn, T.P., Kinison, M.T., and Unwin, M.J. 2001. Evolution of Chinook salmon (Oncorhynchus 

tshawytscha) populations in New Zealand: pattern, rate, and process. Genetica 112: 493-

513. 

Quinn, T.P., Nemeth, R.S., and McIsaac, D.O. 1991. Homing and straying patterns of fall Chinook 

salmon in the lower Columbia River. Transactions of the American Fisheries Society 120: 

150-156. 

Shapovalov, L. and Taft, A.C. 1954. The life histories of the steelhead rainbow trout (Salmo 

gairdneri gairdneri) and silver salmon (Oncorhynchus kisutch) with special reference to 

Waddell Creek, California, and recommendations regarding their management. Calif. 

Dept. Fish Game Fish. Bull. 98: 1-375. 

Smoker, W.W., Gharrett, A.J., and Stekoll, M.S. 1998. Genetic variation of return date in a 

population of pink salmon: a consequence of fluctuating environment and dispersive 

selection? Alaska Fishery Research Bulletin 5: 46-54. 

Tipping, J. M., R. V. Cooper, J. B. Byrne, and T. H. Johnson. 1995. Length and condition factor of 

migrating and nonmigrating hatchery-reared winter steelhead smolts. Progressive FishCulturist 57:120-123. 
B-50 Emerging Issues – Outplanting and Net Pen Release of Hatchery Fish 

Tipping, J. M., and J. B. Byrne. 1996. Reducing feed levels during the last month of rearing 

enhances emigration rates of hatchery-reared steelhead smolts. Progressive Fish-Culturist 

58:128-130. 

Tipping, J. M., and T. D. Hillson. 2002. Adult recoveries of winter and summer steelhead by 

release location on the Lewis River, Washington. California Fish and Game 88(2):49-56. 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-51 

ASSESSING THE POTENTIAL FOR PREDATION ON WILD 

SALMONID FRY BY HATCHERY-REARED SALMONIDS IN 

WASHINGTON61

Juvenile salmonids are subject to predation by a variety of avian, mammalian, and piscine 

predators, and predation has been implicated as an important source of mortality in a number of 

salmon populations (Fresh 1997; Mather 1998). Recently, concern has been expressed about the 

potential for hatchery-reared salmon and steelhead to prey on wild juvenile Pacific salmonids 

(Oncorhynchus spp.) and the impact that this predation may have on threatened or endangered 

salmonid populations (Lichatowich 1999; Levin et al. 2001). 

The potential for predation of wild salmonids by hatchery-reared smolts will depend on the sizes, 

numbers, and spatial distribution of predators and prey, the functional and numerical responses of 

the predators, and the amount of time that predators and prey are in proximity. Here we review the 

evidence for predation on wild salmonids by hatchery-reared fish and propose a strategy to 

estimate risks to wild salmonid populations from predation by hatchery-reared salmonids. 

Evidence for Intrageneric Predation by Oncorhynchus 

Spp. 

Freshwater 

Predation on wild salmonid fry by salmonids is probably most likely in the freshwater 

environment, where potential salmonid predators are concentrated and exposed to large numbers 

of prey in a relatively small area. There is abundant evidence that salmonid smolts may prey on 

wild Pacific salmon fry in streams. Ricker (1941) reported that coho salmon were an important 

predator of sockeye fry in Cultus Lake, British Columbia (BC). Hunter (1959) reported that coho 

salmon smolts preyed on chum and pink salmon fry in Hooknose Creek, BC, and used his and 

other data from BC to estimate that each coho smolt might have consumed 1.5–2.0 fry per day. 

McCart (1967) reported that coho salmon smolts, rainbow trout, and cutthroat trout were 

important predators of sockeye salmon fry in the Babine River, BC, with coho smolts consuming 

an estimated mean of 3.7 sockeye per fish. Parker (1971) suggested that the primary source of 

mortality of chum and pink salmon fry was predation by coho salmon, but presented no data to 

support this. Fresh and Schroder (1987) reported that coho salmon consumed a large number of 

chum salmon fry in Big Beef Creek, Washington (WA), as did resident rainbow and cutthroat 

trout. Hargreaves and LeBrasseur (1986) found that coho salmon smolts selectively preyed on 48–

50 mm chum salmon fry. Ruggerone and Rogers (1992) estimated that 59% of the sockeye fry 

population in the Chignik Lakes, Alaska (AK), was consumed by juvenile coho. Seiler et al. 

 

61 This paper was drafted for the HSRG by Stephen C. Riley, Julie A. Scheurer, and Conrad V. W. Mahnken, NOAA Fisheries, Northwest 

Fisheries Science Center, Manchester Research Station, PO Box 130, Manchester, WA 98353; and H. Lee Blankenship, Northwest Marine 

Technology, 955 Malin Lane SW, Suite B, Tumwater, WA 98501; March 2003. 
B-52 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

(2002) found salmonid prey in the stomachs of juvenile steelhead, coho, Chinook and cutthroat 

trout that were captured in a screw trap on the Green River, WA. 

There are several studies that have reported predation by hatchery salmonids on wild salmonid fry. 

Sholes and Hallock (1979) estimated that millions of wild Chinook were consumed by hatcheryreared Chinook and steelhead in the Feather River, California (CA), and Cannamela (1993) 

estimated that hatchery-reared steelhead smolts consumed up to 24,000 wild Chinook fry in the 

Salmon River, Idaho (ID), over the course of 50 days; these estimates were based on extrapolation 

from small sample sizes. Menchen (1981) found that steelhead smolts released into Battle Creek, 

CA, were significant predators on naturally-produced Chinook fry. Beauchamp (1995) reported 

that wild steelhead smolts were the primary predator of sockeye salmon fry in the Cedar River, 

although hatchery-reared steelhead smolts, which were released during the latter half of the 

sockeye migration, did not appear to prey on sockeye fry. Hawkins and Tipping (1999) observed a 

small proportion of hatchery reared coho, steelhead, and cutthroat smolts preying on wild Chinook 

smolts. Beauchamp (1990) found that rainbow trout stocked into Lake Washington did not 

become primarily piscivorous until they reached approximately 250 mm, and did not consume 

many salmonids at any size, although sockeye salmon fry were available in the lake. 

Because hatchery-reared salmonids may not feed as well as wild conspecifics (Sosiak et al. 1979; 

Bachman 1984; Olla et al. 1998), one might expect that they would be less efficient as predators, 

although wild and hatchery-reared brown trout in a Norwegian reservoir were observed to have 

similar rates of piscivory (L’Abée-Lund et al. 2002). Moreover, any reduced feeding might be 

offset by the generally larger size of hatchery-reared smolts. Although there is evidence that 

predation of salmonid fry by migrating smolts may be common in streams, the estimation of risk 

to wild salmonid fry from predation by hatchery-reared smolts in WA streams is hindered by a 

lack of published data on the comparative feeding habits of hatchery and wild smolts. Recent 

sampling by the Washington Department of Fish and Wildlife (WDFW) indicates that migrating 

smolts of hatchery and wild coho and steelhead may prey on chum salmon fry in Washington 

rivers (H. J. Fuss, WDFW, Olympia, personal communication). 

The high potential for encounters between hatchery-reared predators and wild salmonid prey in 

freshwater environments may be tempered by the fact that hatchery-reared smolts generally spend 

very little time in rivers before migrating to sea. Although we are unaware of any published data 

on residence times of hatchery-reared smolts in freshwater, it is widely believed that the majority 

of these fish migrate out of rivers very quickly. Recent work in Willapa Bay tributaries suggests 

that over 95% of steelhead, coho and Chinook smolts leave the immediate area of release within 

several hours (Riley et al. 2001; 2002). 

Although most hatchery-reared smolts may migrate out of rivers relatively quickly, some 

steelhead smolts released from hatcheries have been observed to remain in rivers for months or 

years after release; these fish are known as ‘residual’ steelhead. Recent snorkeling in WA coastal 

streams has reported counts of residual steelhead between 1.25–37.7 fish per km several months 

after release, and stomach sampling on one stream revealed that five of 44 (11%) residual 

steelhead sampled contained salmonid remains, and a further 11% contained unidentifiable fish 

remains (Riley et al. 2001). McMichael and Pearsons (2001) found that residual hatchery-reared 

steelhead migrated up to 12.8 km upstream of their release point and outnumbered wild salmonid 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-53 

yearlings in several stream reaches. Martin et al. (1993) reported that residual hatchery-reared 

steelhead preyed on wild Chinook fry in the Tucannon River. Predation by residual steelhead on 

wild salmonids may represent an important impact on wild salmon populations and deserves 

further study. 

Estuarine and Nearshore Marine Environments 

Juvenile salmon and steelhead may spend considerable time in estuaries and nearshore 

environments before moving into offshore marine habitats (Healey 1980; Simenstad et al. 1982; 

McCabe et al. 1986; Pearcy 1992). The amount of time spent in estuaries by different salmonid 

species varies from several days to several months among estuaries and among years, and is 

probably related to environmental conditions (e.g., temperature, prey availability, stream flow) 

and the physical characteristics of individual estuaries (Simenstad et al. 1982). There is evidence 

that all five species of Pacific salmon may co-occur in habitats within the Campbell River estuary, 

BC (Korman et al. 1997), indicating that the potential for intrageneric predation exists in these 

habitats, although Macdonald et al. (1987) found that larger fish tended to occupy deeper water in 

these habitats. 

Compared to freshwater studies, there is little evidence that wild salmonids are preyed on by other 

salmonids in estuarine or nearshore environments. Diets of juvenile Pacific salmon in the 

nearshore marine environment are often dominated by invertebrates (Manzer 1969; Feller and 

Kaczynski 1973; Craddock et al. 1976; Kjelson et al. 1982; Shreffler et al. 1992; Simenstad et al. 

1992; Perry et al. 1996; Miller and Simenstad 1997; Moulton 1997; Gray et al. 2002), but may 

contain fish after the fish grow larger and move offshore (Healey 1991b; Tadokoro et al. 1996; 

Landingham et al. 1998), although salmonids have rarely been identified as prey. Emmett (1997) 

and Simenstad et al. (1992) suggested that the primary fish predators of juvenile salmon in 

estuaries were cutthroat trout and steelhead smolts, but did not cite any data to support this, and 

McCabe et al. (1983) suggest that intrageneric predation on salmonids was rare in the Columbia 

River estuary. Durkin (1982) reported that the diet of coho salmon smolts (128–138 mm) in the 

Columbia River estuary was composed almost entirely of invertebrates, and found no evidence 

that salmonids were utilized as prey. Murphy et al. (1988) found no evidence that coho salmon 

smolts preyed on chum or pink fry in a southeast AK estuary. Macdonald et al. (1987) did not 

report any salmonids in the diets of coho or Chinook smolts in the Campbell River estuary. 

Similarly, no salmonids were identified in the stomachs of juvenile Chinook salmon captured in 

nearshore habitats in Puget Sound (Miller et al. 1977; Fresh and Schroder 1984; Buckley 1999). 

Recent sampling in Puget Sound, however, has revealed that cutthroat trout may be significant 

predators of wild salmonid fry in nearshore areas (D. Beauchamp, UW, personal communication). 

The results of numerous investigations suggest that intrageneric predation of wild juvenile 

salmonids is not common in estuarine or nearshore marine environments, but this may reflect 

difficulties in sampling and the relative paucity of work that has been conducted in these 

environments compared to freshwater. Because predation of juvenile salmonids by marine fishes 

may be significant in these environments (e.g., Beamish et al. 1992), the relative risk of predation 

by hatchery-reared salmonids may be low. However, we are not aware of any studies that have 

been specifically designed to look for predation by hatchery-reared salmonids in estuarine or 
B-54 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

nearshore habitats. Hatchery-reared Chinook salmon smolts may spend less time (Levings et al. 

1986) and use different habitats (Levings et al. 1986; Macdonald et al. 1987) in the Campbell 

River estuary than wild smolts, which may affect their predation potential compared to wild fish. 

More research on the feeding habits of hatchery-reared salmonids in nearshore and estuarine 

environments is necessary if predation risk to wild salmonids is to be estimated. 

Offshore Marine Environment 

There is little evidence of intrageneric predation among salmonid species in the offshore marine 

environment. Although fish may make up a significant component of the diets of juvenile Chinook 

and coho in offshore marine environments, salmonid remains have rarely been identified as prey 

(Manzer 1969; Peterson et al. 1982; Brodeur 1989; Brodeur and Pearcy 1990; Pearcy et al. 1990; 

Brodeur et al. 1992; Landingham et al. 1998; Buckley 1999; Hunt et al.1999). In a sample of 

stomach contents collected between 1996 and 2002 from 86,266 ocean age-0 salmon (12,005 of 

which were hatchery-origin) from Puget Sound and the waters off Vancouver Island, only one fish 

was observed to have salmonid remains in its stomach (Ruston Sweeting, Canadian Department of 

Fisheries and Oceans, Pacific Biological Station, Nanaimo, BC, unpublished data). Although 

many of these studies used small sample sizes and were not designed to look for evidence of 

intrageneric predation, the fact that virtually all of the data collected indicate that salmonids do not 

feed on other salmonids offshore indicates that offshore predation by salmonids is probably not an 

important source of mortality to Washington salmon and steelhead stocks. 

Offshore predation on wild salmonids by hatchery-reared smolts may be rare because encounter 

rates between the two may be low. Larger fish may move offshore earlier than smaller fish (Pearcy 

1992), and the two may not co-occur in the marine environment when wild fry are small enough to 

be preyed upon by hatchery smolts. Future studies of salmonid diets in the offshore environment 

should estimate the density of potential predators and prey to evaluate how likely they are to 

encounter each other. 

Relative Size of Predators and Prey

There is evidence that salmonids are capable of preying on fish that are up to approximately 50% 

of their body length, but the majority of prey is probably much smaller. Keeley and Grant (2001) 

provide linear regression relationships for salmonid body size and prey size based on a variety of 

salmonid diet studies. Their results for salmonids feeding on fish in streams suggest that the mean 

prey size for 100–200 mm salmonids is between 13–15% of predator body size. There was very 

little variability among salmonid species in these predator/prey size relationships. Damsgard 

(1995) developed a maximum prey size relationship for salmonids (based on mouth size) which 

suggests that salmonids are physically capable of consuming prey that are 49–51% of their body 

length. 

In a laboratory experiment, Pearsons and Fritts (1999) found that hatchery-reared coho salmon 

consumed Chinook salmon that were up to 46% of their body length. Several other studies suggest 

that small juvenile salmonids will prey on fish up to about 40–45% of their body length (Martin et 

al. 1993; McConnaughey 1998), although Hargreaves and LeBrasseur (1986) found that yearling 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-55 

coho salmon very occasionally preyed on juvenile chum that were up to 75% of their body length. 

A recent study of Arctic char feeding on conspecifics suggests that the maximum relative prey size 

was approximately 47% of predator length (Finstad et al. 2001). It is therefore reasonable to 

assume that salmonid predators are capable of consuming prey up to approximately 50% of their 

body length. 

The relative sizes of downstream-migrating smolts or fry of different species of salmonids in 

Washington suggest that several possible predator/prey combinations are likely to occur. Virtually 

all Oncorhynchus species could be potential prey for larger salmonids in freshwater when they are 

small, but those that migrate to sea at a small size are probably most vulnerable because they 

become concentrated in the downstream reaches of rivers. The relative vulnerability of wild 

juvenile salmonids to predation in freshwater depends on the release location of hatchery fish; if 

fish are released near the mouth of the river, then migrating fry are probably most vulnerable to 

predation. Hatchery fish that are released further upstream may encounter concentrations of all 

species of salmonid fry that occur in a given river. 

Pink and chum salmon typically migrate at the smallest size of all species of Pacific salmonids 

(Heard 1991; Salo 1991; Hard et al. 1996; Johnson et al. 1997), often less than 50 mm in length. 

Ocean-type Chinook migrate as fry or smolts at sizes ranging from 30–100 mm (Myers et al. 

1998, Healey 1991a). Smolts from WA sockeye salmon populations usually migrate to sea as 90–

150 mm yearlings, but fry may be vulnerable to predation during earlier migrations to lake habitat 

and within lakes (Gustafson et al. 1997). These species are probably most likely to be preyed upon 

by hatchery-reared salmonids in WA. 

Hatchery-reared chum, pink, sockeye, and ocean-type (underyearling) Chinook are unlikely to 

prey on wild salmonids due to their relatively small size at release and their non-piscivorous 

feeding habits. Yearling coho, Chinook, and steelhead smolts are typically released from WA 

hatcheries at sizes ranging from 115–140, 150–180, and 180–240 mm, respectively (H. Fuss, 

WDFW, personal communication); these species have the greatest likelihood of preying on wild 

salmonid fry due to their large size. Although some hatchery-reared smolts, particularly steelhead, 

are large enough to feed on wild yearling salmonids, it is less likely that they would do so because 

yearlings would be far less abundant than fry. Hatchery-reared steelhead might be expected to 

prey on the largest size-range of prey due to their larger size; at 50% of body size, coho, Chinook 

and steelhead smolts could consume prey up to 70, 90 and 120 mm in length, respectively (Figure 

1). Hatchery-reared coho, however, are probably the most likely species to have significant effects 

on wild salmonid populations in WA due to the large numbers released: WDFW released 

approximately 32.7 million coho in 2000, compared with 10 million steelhead and 3.5 million 

yearling Chinook (H. Fuss, WDFW, personal communication). 
B-56 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

Figure 1. Relative sizes of hatchery-reared salmonid predators (at release) and their potential

migratory salmonid prey in Washington, assuming that predators may consume fish up to 50% of 

their body size. 

Spatial and Temporal Overlap of Potential Predators 

and Prey

Predators and prey must show significant overlap in time and space in order for predation to have 

an impact on prey populations. Estimation of the risk to wild salmonid populations in WA from

hatchery-reared salmonid predation is complicated because both predators and prey may be 

migratory and the spatial and temporal overlap between predators and potential prey may vary

among locations and years. The likelihood that hatchery-released juvenile salmonids will prey on 

wild salmonids will depend on, among other factors, the spatial and temporal distribution of wild 

salmonids relative to hatchery-reared predators. 

Spatial Overlap 

Hatchery-reared yearling coho, Chinook and steelhead are released from a number of hatcheries 

throughout WA. For example, yearling Chinook are released from hatcheries on 15 rivers in 

coastal (Sol Duc, Dungeness), Puget Sound (Skagit, Nooksack, Skykomish, Green, Deschutes), 

and Columbia River (Cowlitz, Kalama, Lewis, Klickitat, Tucannon, Yakima, Wenatchee, 

Methow) regions (H. Fuss, WDFW, personal communication). The distribution of potential wild 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-57 

salmonid prey within WA varies widely by species. For example, sockeye salmon populations 

occur in only six drainages in WA (Gustafson et al. 1997), pink salmon occur in eleven (Hard et 

al. 1996), while coho occur in most drainages capable of supporting salmon. An initial step that 

should be taken, as we suggest below, is to tabulate the distribution of hatchery-reared yearling 

salmonid smolts and their potential salmonid prey to identify basins where predation by hatcheryreared fish might be expected to be most important. 

The previous section suggests that predation on wild salmonid fry by hatchery-reared salmon and 

steelhead is most likely to occur in freshwater, although the potential for predation in estuarine 

and nearshore environments deserves more study. Relatively little is known about the distribution 

and habitat use of wild and hatchery-reared salmonids in estuarine and nearshore environments, 

which makes it difficult to determine the potential for spatial overlap of hatchery predators and 

wild prey. For example, the likelihood that hatchery-reared salmonids might migrate within the 

nearshore environment (e.g., among estuaries) is unknown. Further research on salmonid use of 

nearshore and estuarine environments is necessary to determine the potential for predation of wild 

salmonids by hatchery-reared fish. 

Temporal Overlap 

Chum salmon fry emerge from the gravel between late-January and June and usually begin 

migrating downstream immediately after emergence (Johnson et al. 1997), although some reside 

in freshwater for up to one month before migrating (Simenstad et al. 1982). Peak chum migrations 

usually occur between March and April in WA streams (Healey 1982). In WA, juvenile 

migrations are usually short, ranging from just a few hours to a few days, because chum salmon 

generally spawn in the lower reaches of rivers. Simenstad et al. (1982) found that the average 

residence time per estuary was ten weeks and 24.5 days for individuals. Chum salmon juveniles 

spend more time rearing in estuaries than most other anadromous salmonid species. 

Pink salmon have the shortest freshwater residence phase of all Oncorhynchus species. Most adult 

returns occur in odd years in WA (except for an even-year run in the Snohomish River), so 

juveniles are primarily present in freshwater in even years (Hard et al. 1996). Juvenile pink salmon 

begin migrating immediately upon emerging from the gravel (Simenstad et al. 1992). Emergence 

and migration typically occur between March and April in WA, but may extend into May. The 

duration of residence in the estuary ranges from a few days to three months, but is generally short 

(Healey 1982). Later emerging fry tend to move directly into salt water without pausing long in 

the estuary (Hurley and Woodall 1968). 

During the period of emergence and migration to the nursery lake, sockeye fry are highly 

vulnerable to predation by other fish and birds (Gustafson et al. 1997). Fry emerge in the Cedar 

River, WA between January and early June, with peak emergence from early-March through midMay (Stober and Hämäläinen 1979, 1980; Seiler and Kishimoto 1996). Most sockeye in WA 

smolt and migrate seaward after one year of lake residence (Gustafson et al. 1997). 

Ocean-type Chinook salmon migrate seaward as subyearlings during one of three distinct phases, 

here referred to as immediate, fry, and fingerling migrants. The immediate phase fish migrate soon 

after yolk resorption (Lister et al. 1971, Healey 1991a). Most Chinook salmon migrate as fry 
B-58 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

between March and June after rearing for 60-150 days in freshwater. Fingerling migrants stay in 

the river until late summer of their first year (Myers et al. 1998). Juvenile fall Chinook salmon are 

therefore likely to be present in freshwater anytime between emergence in late-January or 

February through September. Ocean-type Chinook juveniles make greater use of estuaries for 

rearing than their spring-type counterparts, and earlier migrating smolts spend proportionately 

more time rearing in the estuary environment. Levings et al. (1986) reported that individual wild 

Chinook fry resided in the Campbell River, BC estuary for 40 to 60 days. Estuary residence times 

in southern BC (e.g. Campbell River estuary) may be shorter than elsewhere due to the abundant 

sheltered coastal habitat available in that region. Simenstad et al. (1992) found individuals residing 

in large WA estuaries for up to 189 days. McCabe et al. (1986) reported subyearling Chinook 

present in the Columbia River estuary year-round, but most numerous from May through 

September. Fall Chinook are present in the estuary environment throughout the spring, summer 

and fall (Healey 1982). 

In summary, chum and Chinook salmon have the longest estuary residencies whereas pink and 

sockeye typically spend less time rearing in this environment (Healey 1982; Simenstad et al. 

1992). Pink and chum salmon typically migrate to the estuary soon after emergence, whereas 

Chinook and sockeye spend a few months to a year rearing in freshwater before migration. The 

active rather than passive migration, nocturnal movement, and schooling behaviors of pink, 

sockeye and to a lesser extent chum salmon are behavioral adaptations to reduce predation risk 

during migration (Burgner 1991). 

We have identified hatchery-reared yearling coho, fall and spring Chinook, and steelhead smolts 

as potential predators of wild salmonid fry, and a comparison of their release dates with the stream 

and estuary residencies of wild fry may identify periods when intrageneric predation could occur. 

In Puget Sound, hatchery-reared yearling coho smolts are released from late-April through June 

(Fuss and Ashbrook 1995). Yearling fall Chinook are released between March and May; yearling 

spring Chinook are released in April and May. Yearling summer Chinook smolts are released from 

late-March through early-April. Hatchery steelhead generally smolt after one year and are released 

from April through June. As we suggest below, determining the potential temporal overlap 

between hatchery-reared smolts and their potential prey in rivers where hatchery smolts are 

released is an important first step in determining the likelihood of predation by hatchery-reared 

smolts. 

Predator Functional and Numerical Responses

The functional response of a predator is the relationship between the consumption rate of a 

predator and the abundance of prey. For example, predator consumption may be limited unless 

sufficient numbers of prey are available, and predators may be ‘swamped’ at high prey densities. 

There is relatively little information on the functional response of salmonid predators to 

congeneric prey, although Fresh and Schroder (1987) found that consumption of chum fry by fish 

predators (primarily rainbow trout and coho) leveled off at higher densities of prey, suggesting 

that relative predator consumption was limited at higher prey densities. Peterman and Gatto 

(1996), however, suggested that predators on salmonid fry were not likely to be swamped by all 

but the largest prey populations. 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-59 

The functional response of hatchery-reared salmonids may depend on a number of factors, 

including prey behavior (e.g., schooling, sheltering), habitat use of predators and prey, 

physiological condition of predators (e.g., smolt status), habitat availability, temperature, 

discharge, and turbidity. For example, chum salmon do not form tight schools and typically 

migrate at night (Mason 1974; Salo 1991), while pink salmon fry migrate in tight schools near the 

water surface. This may mean that chum fry may be more widely dispersed than pinks, which may 

make them less vulnerable to predation by larger fishes. 

The numerical response describes how predators respond in terms of numbers to prey abundance. 

For example, some predators have been shown to aggregate in areas where salmonid prey are 

abundant (Larsson 1985; Beamish et al. 1992). We are aware of no published studies that describe 

the migratory behavior of hatchery-reared salmonids with respect to the abundance of potential 

prey. For example, if hatchery-reared smolts delay migration in order to feed on wild fry in 

freshwater or estuarine environments, the impact of predation on wild salmon populations might 

be greater. 

A Strategy to Estimate Risks to Wild Salmon and 

Steelhead Populations from Hatchery-Reared Salmonid 

Predation 

1. Describe Spatial and Temporal Overlap of Predators and Prey 

Based on WDFW and other agency stocking programs, the spatial distribution, migration timing, 

and size of yearling hatchery-reared salmonids should be tabulated for freshwater, estuarine, and 

offshore habitat. The spatial distribution, migration timing and size of potential prey in basins 

where hatchery predators are present should similarly be tabulated. This information will allow the 

identification of areas where predation on wild fry by hatchery-reared fish is likely to be 

important. 

2. Conduct Research to Estimate Predation Rates on Wild 

Salmonids 

Within areas identified in step 1, field research should be conducted to determine the importance 

of predation by hatchery-reared salmonids on wild salmonid fry in freshwater and estuarine 

environments. The data collected should include, but not be limited to, predation rates by hatchery 

fish, density and habitat use of hatchery and wild fish, residence time of wild and hatchery-reared 

fish in freshwater and estuarine environments, the proportion of wild fry consumed by predators, 

and the relative importance of predation by hatchery fish versus other predators. 

Laboratory research could be combined with field work to examine questions about how predator 

and prey behavior and habitat use may affect predation rates, how environmental factors 

(temperature, flow, turbidity) may affect predation, and the functional response of predators to 

multiple prey types. The ultimate goal of this research would be to obtain estimates of predation 
B-60 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

rates of hatchery-reared fish on wild salmonid fry and to determine how these are likely to vary in 

order to develop models to estimate risk to wild salmonid populations from predation by hatchery 

fish. 

3. Develop Models to Estimate the Risk of Predation by 

Hatchery-Reared Smolts. 

The risk to wild salmon and steelhead populations associated with predation by hatchery-reared 

fish should be estimated by developing models based on data collected from specific locations 

where predation is determined to be likely. These models could then be applied to other areas to 

determine the likelihood that predation by hatchery-reared smolts effects wild salmonid 

populations throughout the state. 

Models have previously been developed to estimate the impacts of predators on migrating 

salmonids (e.g., Petersen and DeAngelis 1992). Recent research indicates that the scale at which 

modeling is conducted may have significant effects on results, and that modeling should be 

undertaken at the smallest temporal and spatial scales that are relevant (Petersen and DeAngelis 

2000; DeAngelis and Petersen 2001). The type of models that are to be developed should be 

determined before data collection begins in order to ensure that data are collected at the 

appropriate scale to provide relevant results. 

References

Bachman, R. A. 1984. Foraging behavior of free-ranging wild and hatchery brown trout in a 

stream. Trans. Am. Fish. Soc. 113:1-32. 

Beamish, J.R., B.L. Thomson, and G.A. McFarlane. 1992. Spiny dogfish predation on Chinook 

and coho salmon and the potential effects on hatchery-produced salmon. Trans. Am. Fish. 

Soc. 121:444-455. 

Beauchamp, D. A. 1990. Seasonal and diel food habitats of rainbow trout stocked as juveniles in 

Lake Washington. Trans. Am. Fish. Soc. 119:475-482. 

Beauchamp, D. A. 1995. Riverine predation on sockeye salmon fry migrating to Lake 

Washington. N. Am. J. Fish. Manage. 15:358–365. 

Brodeur, R. D. 1989. Neustonic feeding by juvenile salmonids in coastal waters of the Northeast 

Pacific. Can. J. Zool. 67:1995-2007. 

Brodeur, R. D., and W. G. Pearcy. 1990. Trophic relations of juvenile Pacific salmon off the 

Oregon and Washington coast. Fish. Bull 88:617-636. 

Brodeur, R. D., R. C. Francis, and W. G. Pearcy. 1992. Food consumption of juvenile coho 

(Oncorhynchus kisutch) and Chinook salmon (O. tshawytscha) on the continental shelf off 

Washington and Oregon. Can. J. Fish. Aquat. Sci. 49: 1670-1685. 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-61 

Buckley, R. M. 1999. Incidence of cannibalism and intra-generic predation by Chinook salmon 

(Oncorhynchus tshawytscha) in Puget Sound, Washington. Washington Department of 

Fish and Wildlife, Resource Assessment Division, Olympia, WA. 22 p. 

Burgner, R. L. 1991. Life history of the sockeye salmon (Oncorhynchus nerka). In: C. Groot and 

L Margolis (editors), Pacific salmon life histories, p. 3-117. Univ. British Columbia Press, 

Vancouver. 

Cannamela, D. A. 1993. Hatchery steelhead smolt predation of wild and natural juvenile Chinook 

salmon fry in the upper Salmon River, Idaho. Idaho Department of Fish and Game 

unpublished report, Boise, ID. 

Craddock, D.R., T.H. Blahm, and W.D. Parente. 1976. Occurrence and utilization of zooplankton 

by juvenile Chinook salmon in the lower Columbia River. Trans. Am. Fish. Soc. 105:72-

76. 

Damsgard, B. 1995. Arctic charr, Salvelinus alpinus (L.), as prey for piscivorous fish – a model to 

predict prey vulnerabilities and prey size refuges. Nordic J. Freshw. Res. 71: 190-196. 

DeAngelis, D. L., and J. H. Petersen. 2001. Importance of the predator’s ecological neighborhood 

in modeling predation on migrating prey. Oikos 94:315-325. 

Durkin, J. T. 1982. Migration characteristics of coho salmon (Oncorhynchus kisutch) smolts in the 

Columbia River and its estuary. In: V. S. Kennedy (editor), Estuarine comparisons, p. 

343-364. Academic Press, New York. 

Emmett, R.L. 1997. Estuarine survival of salmonids: the importance of interspecific and 

intraspecific predation and competition. In: Emmett, R.L., and M.H. Schiewe (editors). 

Estuarine and ocean survival of Northeastern Pacific salmon: Proceedings of the 

workshop. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSC-29, 313 p. 

Feller, R. J., and V. W. Kaczynski. 1973. Size selective predation by juvenile chum salmon 

(Oncorhynchus keta) on epibenthic prey in Puget Sound. J. Fish. Res. Bd. Can. 32: 1419-

1429. 

Finstad, A.G., P. A. Jansen, and A. Langeland. 2001. Production and predation rates in a 

cannibalistic Arctic char (Salvelinus alpinus L.) population. Ecol. Freshw. Fish 10: 220-

226. 

Fresh, K. L. 1997. The role of competition and predation in the decline of Pacific salmon and 

steelhead. In D. J. Stouder, P. A. Bisson, and R. J Naiman (editors) Pacific salmon and 

their ecosystems: status and future options. Chapman and Hall, New York. 

Fresh, K. L. and S. L. Schroder. 1984. Salmon-herring predator/competitor interactions project – 

Phase 111. Washington Department of Fish and Wildlife unpublished report, Olympia, 

WA. 
B-62 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

Fresh, K.L, and S.L. Schroder. 1987. Influence of abundance, size, and yolk reserves of juvenile 

chum salmon (Oncorhynchus keta) on predation by freshwater fishes in a small coastal 

stream. Can. J. Fish. Aquat. Sci. 44: 236-243. 

Fuss, H. J., and C. Ashbrook. 1995. Hatchery operation plans and performance summaries. Vol. 1, 

No. 2-Puget Sound, Washington Department of Fish and Wildlife unpublished report, 

WDFW, Olympia, WA. 

Gray, A., C. A. Simenstad, D. L. Bottom, and T. J. Cornell. 2002. Contrasting functional 

performance of juvenile salmon habitat in recovering wetlands of the Salmon River, 

Oregon, USA. Restor. Ecol. 10:514-526. 

Gustafson, R. G., T. C. Wainwright, G. A. Winans, F. W. Waknitz, L. T. Parker, and R. S. 

Waples. 1997. Status review of sockeye salmon from Washington and Oregon. U. S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-33, 282 p. 

Hard, J. J., R. G. Kope, W. S. Grant, F. W. Waknitz, L. T. Parker, and R. S. Waples. 1996. Status 

review of pink salmon from Washington, Oregon, and California. U.S. Dep. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-25, 131 p. 

Hargreaves, N. B., and R.J. LeBrasseur. 1986. Size selectivity of coho (Oncorhynchus kisutch) 

preying on juvenile chum salmon (O. keta). Can. J. Fish. Aquat. Sci. 43: 581-586. 

Hawkins, S.W., and J.M. Tipping. 1999. Predation by juvenile hatchery salmonids on wild fall 

Chinook salmon fry in the Lewis River, Washington. Cal. Fish and Game 85: 124-129. 

Healey, M. C. 1980. Utilization of the Nanaimo River estuary by juvenile Chinook salmon, 

Oncorhynchus tshawytscha. Fish. Bull. 77:653-668. 

Healey, M. C. 1982. Juvenile Pacific salmon in estuaries: the life support system. In: V. S. 

Kennedy (editor), Estuarine Comparisons, p. 315-341. Academic Press, New York. 

Healey, M. C. 1991a. Life history of Chinook salmon (Oncorhynchus tshawytscha). In: C. Groot 

and L Margolis (editors), Pacific salmon life histories, p. 311-393. Univ. British Columbia 

Press, Vancouver. 

Healey, M. C. 1991b. Diets and feeding rates of juvenile pink, chum, and sockeye salmon in 

Hecate Straight, British Columbia. Trans. Am. Fish. Soc. 120:303-318. 

Heard, W. R. 1991. Life history of pink salmon (Oncorhynchus gorbuscha). In: C. Groot and L 

Margolis (editors), Pacific salmon life histories, p. 121-230. Univ. British Columbia Press, 

Vancouver. 

Hunt, S. L., T. J. Mulligan, and K. Komori. 1999. Oceanic feeding habits of Chinook salmon, 

Oncorhynchus tshawytscha, off northern California. Fish. Bull. 97:717-721. 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-63 

Hunter, J. G. 1959. Survival and production of pink and chum salmon in a coastal stream. J. Fish. 

Res. Bd. Can. 16:835-886. 

Hurley, D. A., and W. L. Woodall. 1968. Responses of young pink salmon to vertical temperature 

and salinity gradients. Int. Pac. Salmon Fish. Comm. Prog. Rep. 19:80 p. 

Johnson, O. W., W. S. Grant, R. G. Kope, K. Neely, F. W. Waknitz, and R. S. Waples. 1997. 

Status review of chum salmon from Washington, Oregon, and California. U. S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-32, 280 p. 

Keeley, E.R, and J.W.A. Grant. 2001. Prey size of salmonids fishes in streams, lakes, and oceans. 

Can. J. Fish. Aquat. Sci. 58: 1122-1132. 

Kjelson, M.A., P.F. Raquel, and F.W. Fisher. 1982. Life history of fall-run juvenile Chinook 

salmon, Oncorhynchus tshawytscha, in the Sacramento-San Joaquin estuary, California. In 

V. S. Kennedy, editor. Estuarine Comparisons, p. 393-411. Academic Press, New York, 

New York. 

Korman, J., B. Bravender, and C. D. Levings. 1997. Utilization of the Campbell River estuary by 

juvenile Chinook salmon (Oncorhynchus tshawytscha) in 1994. Can. Tech. Rep. Fish. 

Aquat. Sci. 2169. 

L’Abée-Lund, J. H., P. Aass, and H. Sægrov. 2002. Long-term variation in piscivory in a brown 

trout population: effect of changes in available prey organisms. Ecol. Freshw. Fish 

11:260-269. 

Landingham, J. H, M. V. Sturdevant, and R. D. Brodeur. 1998. Feeding habits of juvenile Pacific 

salmon in marine waters of southeastern Alaska and northern British Columbia. Fish. 

Bull. 96:285-302. 

Larsson, P. O. 1985. Predation on migrating smolt as a regulating factor in Baltic salmon, Salmo 

salar, populations. J. Fish. Biol. 26:391-397. 

Levin, P. S., R. W. Zabel, and J. G. Williams. 2001. The road to extinction is paved with good 

intentions: negative associations of fish hatcheries with threatened salmon. Proc. Royal 

Soc. London B, Series B 268:1-6. 

Levings, C. D., C. D. McAllister, and B. D. Chang. 1986. Differential use of the Campbell River 

estuary by wild and hatchery-reared juvenile Chinook salmon (Oncorhynchus 

tshawytscha). Can. J. Fish. Aquat. Sci. 43: 1386-1397. 

Lichatowich, J. 1999. Salmon without rivers. Island Press, Washington, D.C. 

Lister, D. B., C. E. Walker, and M. A. Giles. 1971. Cowichan River Chinook salmon escapements 

and juvenile production 1965-1967. Can. Fish. Serv. 1971-3, 8 p. 
B-64 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

Macdonald, J. S., I. K Birtwell, and G. M. Kruzynski. 1987. Food and habitat utilization by 

juvenile salmonids in the Campbell River estuary. Can J. Fish. Aquat. Sci. 44:1233-1246. 

Manzer, J. I. 1969. Stomach contents of juvenile Pacific salmon in Chatham Sound and adjacent 

waters. J. Fish. Res. Bd. Can. 26: 2219-2223. 

Martin, S.W., A.E. Viola, and M.L. Schuck. 1993. Investigations of the interactions among 

hatchery reared summer steelhead, rainbow trout, and wild spring Chinook salmon in 

southeast Washington. WDFW, Report 93-4, Olympia. 

Mason, J. C. 1974. Behavioral ecology of chum salmon fry (Oncorhynchus keta) in a small 

estuary. J. Fish. Res. Bd. Can. 31:83-92. 

Mather, M. E. 1998. The role of context-specific predation in understanding patterns exhibited by 

anadromous salmon. Can. J. Fish. Aquat. Sci. 55(Suppl. 1):232-246. 

McCabe, G. T., W. D. Muir, R. L. Emmett, and J. T. Durkin. 1983. Interrelationships between 

juvenile salmonids and nonsalmonid fish in the Columbia River estuary. Fish. Bull. 

81:815-826. 

McCabe, G. T., R. L. Emmett, W. D. Muir, and T. H. Blahm. 1986. Utilization of the Columbia 

River estuary by subyearling Chinook salmon. Northwest Science 60:113-124. 

McCart, P. 1967. Behaviour and ecology of sockeye salmon fry in the Babine River. J. Fish. Res. 

Bd. Can. 24:375-428. 

McConnaughey, J. 1998. Predation by coho salmon smolts (Oncorhynchus kistuch) in the Yakima 

and Klickitat Rivers. Yakama Indian Nation report, Toppenish, WA. 

McMichael, G. A., and T. N. Pearsons. 2001. Upstream movement of residual hatchery steelhead 

into areas containing bull trout and cutthroat trout. N. Am. J. Fish. Manage. 21: 943-946. 

Menchen, R. S. 1981. Predation by yearling steelhead Salmo gairdneri released from Coleman 

National Fish Hatchery on naturally produced Chinook salmon Oncorhynchus 

tshawytscha fry and eggs in Battle Creek, 1975. California Department of Fish and Game 

unpublished report. 

Miller, B. S., C. A. Simenstad, L L. Moulton, K. L. Fresh, F. C. Funk, W. A. Carp, and S. F. 

Borton. 1977. Puget Sound baseline program nearshore fish survey. Fish Res. Inst. Univ. 

Wash. FRI-UW-7710. 

Miller, J.A., and C.A. Simenstad. 1997. A comparative assessment of a natural and created 

estuarine slough as rearing habitat for juvenile Chinook and coho salmon. Estuaries 

20:792-806. 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-65 

Moulton, L. L. 1997. Early marine residence, growth, and feeding by juvenile salmon in northern 

Cook Inlet, Alaska. Alask. Fish. Res. Bull. 4:154-177. 

Murphy, M. L., J. F. Thedinga, and K. V. Koski. 1988. Size and diet of juvenile Pacific salmon 

during seaward migration through a small estuary in southeastern Alaska. Fish. Bull. 

86:213-222. 

Myers, J. M., R. G. Kope, G. J. Bryant, D. Teel, L. J. Lierheimer, T. C. Wainwright, W. S. Grant, 

F. W. Waknitz, K. Neely, S. T. Lindley, and R. S. Waples. 1998. Status review of 

Chinook salmon from Washington, Idaho, Oregon, and California. U. S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-35, 443 p. 

Olla, B. L., M. W. Davis, and C. H. Ryer. 1998. Understanding how the hatchery environment 

represses or promotes the development of behavioral survival skills. Bull. Mar. Sci. 

62:531-550. 

Parker, R. R. 1971. Size selective predation among juvenile salmonid fishes in a British Columbia 

inlet. J. Fish. Res. Bd. Can. 28: 1503-1510. 

Pearcy, W. G., R. D. Brodeur, and J. P. Fisher. 1990. Distribution and biology of juvenile 

cutthroat trout Oncorhynchus clarki clarki and steelhead O. mykiss in coastal waters off 

Oregon and Washington. Fish. Bull. 88:697-711. 

Pearcy, W. G. 1992. Ocean ecology of north Pacific salmonids. University of Washington Press, 

Seattle. 

Pearsons, T.N., and A.L. Fritts. 1999. Maximum size of Chinook salmon consumed by juvenile 

coho salmon. N. Am. J. Fish. Manage. 19: 165-170. 

Perry, R. I., N. B. Hargreaves, B. J. Waddell, and D. L Mackas. 1996. Spatial variation in feeding 

and condition of juvenile pink and chum salmon off Vancouver Island, British Columbia. 

Fish. Oceanogr. 5: 73-88. 

Peterman, R. M., and M. Gatto. 1976. Estimation of functional responses of predators on juvenile 

salmon. J. Fish. Res. Bd. Can. 35:797-808. 

Petersen, J. H., and D. L. DeAngelis. 1992. Functional response and capture timing in an 

individual-based model: predation by northern squawfish (Ptychocheilus oregonensis) on 

juveniles salmonids in the Columbia River. Can J. Fish. Aquat. Sci. 49:2551-2565. 

Petersen, J. H., and D. L. DeAngelis. 2000. Dynamics of prey moving through a predator field: a 

model of migrating juvenile salmon. Mathematical Biosciences 165:97-114. 

Peterson, W. T., R. D. Brodeur, and W. G. Pearcy. 1982. Food habits of juvenile salmon in the 

Oregon coastal zone, June 1979. Fish. Bull. 80:841-851. 
B-66 Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids 

Ricker, W. E. 1941. The consumption of young sockeye salmon by predacious fish. J. Fish. Res. 

Bd. Can. 5: 293-313. 

Riley, S. C., H. J. Fuss, and L. L. LeClair. 2001. Development of field methods to determine the 

effects of hatchery releases on wild juvenile salmonids. Report to the Hatchery Scientific 

Review Group of the Interagency Committee for Outdoor Recreation, Olympia, WA. 

Riley, S. C., H. J. Fuss, and L. L. LeClair. 2002. Development of field methods to determine the 

effects of hatchery releases on wild juvenile salmonids. Report to the Hatchery Scientific 

Review Group of the Interagency Committee for Outdoor Recreation, Olympia, WA. 

Ruggerone, G.T., and D.E. Rogers. 1992. Predation on sockeye salmon fry by juvenile coho 

salmon in the Chignik lakes, Alaska: implications for salmon management. N. Am. J. 

Fish. Manage. 12: 87-102. 

Salo, E.O. 1991. Life history of chum salmon, Oncorhynchus keta. In: C. Groot and L Margolis 

(editors), Pacific salmon life histories, p. 231-309. Univ. British Columbia Press, 

Vancouver. 

Seiler, D., and L. E. Kishimoto. 1996. Annual report 1995 Cedar River sockeye salmon fry 

production evaluation program. WDFW report. 9 p., Olympia, WA. 

Seiler, D., G. Volkhardt, L. Kishimoto, and P. Topping. 2002. 2000 Green River juvenile 

salmonid production evaluation. Washington Department of Fish and Wildlife Report 

#FPT 02-03. 

Sholes, W. H., and R. J. Hallock. 1979. An evaluation of rearing fall-run Chinook salmon, 

Oncorhyncus tshawytscha, to yearlings at Feather River Hatchery with a comparison of 

returns from hatchery and downstream releases. Cal. Fish Game 65:239-255. 

Shreffler, D.K., C.A. Simenstad, and R.M. Thom. 1992. Temporary residence by juvenile salmon 

in a restored estuarine wetland. Can. J. Fish. Aquat. Sci. 47:2079-2084. 

Simenstad, C. A., K. L. Fresh, and E. O. Salo. 1982. The role of Puget Sound and Washington 

coastal estuaries in the life history of Pacific salmon: an unappreciated function. In: V. S. 

Kennedy (editor), Estuarine comparisons, p. 343-364. Academic Press, New York. 

Sosiak, A. J., R. G. Randall, and J. A. McKenzie. 1979. Feeding by hatchery-reared and wild 

Atlantic salmon (Salmo salar) parr in a stream. J. Fish. Res. Bd. Can. 36:1408-1412. 

Stober, Q. J., and A. H. Hämäläinen. 1979. Cedar River sockeye salmon production. Univ. Wash. 

Fish. Res. Inst. FRI-UW-7917. 52 p., Seattle, WA. 

Stober, Q. J., and A. H. Hämäläinen. 1980. Cedar River sockeye salmon production. Univ. Wash. 

Fish. Res. Inst. FRI-UW-8016. 59 p., Seattle, WA. 
Emerging Issues – Potential for Predation on Wild Salmonids by Hatchery Salmonids B-67 

Tadokoro, K., Y. Ishida, N. Davis, S. Ueyangagi, and T. Sugimoto. 1996. Change in chum salmon 

(Oncorhynchus keta) stomach contents associated with fluctuation of pink salmon (O. 

gorbuscha) abundance in the central sub arctic Pacific and Bering Sea. Fish. Oceanogr. 

5:89-99. 
B-68 Emerging Issues – Using Acclimation Ponds in the Rearing of Salmon 

USING ACCLIMATION PONDS IN THE REARING OF 

SALMON62

Introduction

Acclimation ponds are frequently used in Pacific Northwest anadromous salmonid hatchery 

programs to redistribute adult salmon and steelhead returns. A literature review indicates that coho 

salmon, spring Chinook salmon and steelhead home to acclimation locations, but not fall Chinook 

salmon released as sub-yearlings (Slatick et al 1988; Vander Haegen and Doty 1995; Castle et al. 

2002). Because returning adult fish often spawn near acclimation ponds, some conservation 

programs use acclimation ponds to increase spawning in under seeded areas. In harvest programs, 

homing to acclimation ponds can help managers by allowing returning adult fish to be removed 

before the fish spawn, important in the genetic management of wild fish. 

Many acclimation ponds provide a more natural rearing environment, including aquatic 

macrophytes and dirt bottoms, and produce fish with increased post-release survivals (Tipping 

1998; Tipping 2001). Acclimation ponds also allow smolt release directly at the site, which may 

decrease smolt travel times compared to trucked releases (Dawley et al.1977; Harza 1998; Tipping 

et al.1995; Tipping and Byrne 1996), and reduce the time that hatchery smolts prey on or compete 

with wild fish. 

Homing to Acclimation Ponds

The homing ability of salmon and steelhead to natal areas has long been recognized. This ability 

has been shown to be heavily influenced by olfactory responses to chemical characteristics of 

natal waters (Brannon et al. 1984) and may also be genetically influenced (McIsaac and Quinn 

1988). Imprinting appears to occur when fish undergo smoltification and emigration (Dittman et 

al. 1996). 

The practice of outplanting smolts from hatcheries is being increasingly scrutinized due to the 

potential genetic damage to wild fish caused by straying of returning hatchery adults. Homing to 

acclimation ponds provides managers with the opportunity to remove adult hatchery fish before 

they spawn naturally. 

Coho 

Slatick et al. (1988) reported that most Columbia River coho salmon imprinted for 48 hours 

demonstrated a positive homing response to their point of release, be it a hatchery or upper or 

lower river release site. Vander Haegen and Doty (1995) analyzed the homing of coho salmon 

from Washington state hatcheries and found that similar rates of straying were observed for 

 

62 This paper was drafted for the HSRG by Jack Tipping, Washington Department of Fish and Wildlife, July 2003. 
Emerging Issues – Using Acclimation Ponds in the Rearing of Salmon B-69 

hatchery coho released on-station and wild coho. However, the stray rate increased for coho 

transported and released in-basin. 

Fall Chinook 

Slatick et al. (1988) found that fish released from Columbia River hatcheries generally homed 

back to those hatcheries. However, homing of adults to a mid-river site where juveniles had been 

imprinted for 9–44 days was considered poor. The majority of these fish strayed to the hatchery of 

origin and elsewhere. Quinn et al. (1991) reported that straying of fall Chinook in the lower 

Columbia River ranged from 8–19.3%. Vander Haegen and Doty (1995) reported that in-basin and 

out-of-basin releases resulted in more adult strays than on-station releases. 

Spring Chinook 

Castle et al. (2002) found that subyearling spring Chinook homed to the North Fork Nooksack 

River at a slightly higher rate than transported fish when acclimated to a pond on a North Fork 

tributary (Deadhorse Creek) (Table 1). 

Table 1.Adult return distribution of spring Chinook salmon on the Nooksack River with and 

without use of an acclimation pond on a tributary of the North Fork Nooksack Rive (note that the 

hatchery is located relatively low on the North Fork). 

______________________________________________________________________________ 

Recovery Location 

Year Release strategy North Fork Middle Fork Hatchery South Fork

1996 Acclimated 61.1% 1.0% 36.3% 1.5% 

 Unacclimated 54.4% 2.0% 41.1% 2.5% 

1997 Acclimated 80.2% 0.0% 12.5% 7.3% 

 Unacclimated 68.7% 12.1% 16.6% 2.6% 

Mean Acclimated 70.7% 0.5% 24.4% 4.4% 

 Unacclimated 61.6% 7.1% 28.9% 2.6% 

______________________________________________________________________________ 
B-70 Emerging Issues – Using Acclimation Ponds in the Rearing of Salmon 

Steelhead 

Kenaston et al. (2001) found no difference in homing rates between steelhead that were acclimated 

for 30 days in portable raceways and those trucked from a hatchery and directly released. They 

concluded that acclimation of juvenile steelhead is not necessary to achieve a high rate of homing 

to a release site. Slatick et al. (1988) reported that for the Columbia River, indigenous stocks of 

adult steelhead showed a high fidelity of return rates to the release site, but non-indigenous stocks 

did not. On rivers with an upstream hatchery, adult return distribution may be minimally affected 

by downstream smolt releases. Slaney et al. (1993) found small but significant release-site fidelity 

differences, but also observed substantial dispersal of lower-river-released fish to the upper river 

near the rearing hatchery. Tipping and Hillson (2002) found that adult return distributions from 

downstream smolt releases were only slightly changed for winter steelhead, while summer 

steelhead were unaffected. 

Survival

The act of acclimating salmonids does not appear to enhance fish survival. Survival enhancements 

from acclimation ponds are probably due to the more natural rearing environment and/or trucking 

stress mollification. Kenaston et al. (2001) acclimated steelhead in portable raceways, similar to 

hatchery concrete raceways, and found no post-release survival enhancement over fish that were 

directly released into the same waters. Further, Kenaston et al. (2001) mentioned an ongoing 

evaluation of acclimated steelhead groups that showed no clear survival advantage. Using similar 

rearing raceways for acclimated and non-acclimated spring Chinook yearlings, Appleby et al. 

(2002) reported similar post-release survival for both groups. Acclimated subyearling spring 

Chinook in an asphalt bottom pond had lower survival than unacclimated fish on the Nooksack 

River (Castle et al. 2002). 

Acclimation ponds with a more natural rearing environment have been shown to improve postrelease survival of fish. Adult survival of hatchery sea-run cutthroat trout was doubled for fish 

reared in an acclimation-type semi-natural rearing pond versus a concrete raceway (Tipping 1998; 

Tipping 2001). The improved survivals may be associated with reduced rearing densities (Banks 

1994; Ewing and Ewing 1995); possible cryptic coloration differences for pond-reared fish that 

helps them avoid predation (Donnelly and Whoriskey 1991; Maynard et al. 1996); increased 

exposure to natural feed that may help in post-release foraging ability (Savino et al. 1993; 

Maynard et al. 1996); and the acclimation process allowing trucking stress to be mollified prior to 

release (Specker and Schreck 1980; Schreck et al. 1989). Trucking stress was shown to reduce 

post-release survival in coho salmon by 20% (Johnson et al. 1990). However, for steelhead, no 

survival enhancement was observed for trucked smolts that were allowed to rest before release, 

suggesting that an acclimation pond for stress mollification would not benefit survival (Tipping 

1998). In addition, steelhead and sea-run cutthroat reared in acclimation ponds have lower 

condition factors (measure of plumpness) than fish from raceways. This lower condition factor has 

been associated with improved survivals (Ewing et al. 1984; Tipping et al. 1995). 

Duration of exposure to natural-type acclimation ponds appears to influence post-release 

survivals. Survival of sea-run cutthroat increased an average of 31% for fish placed in an 
Emerging Issues – Using Acclimation Ponds in the Rearing of Salmon B-71 

acclimation pond for four to seven months prior to release, compared to fish exposed for one 

month prior to release (Tipping 2001). Importantly, fish exposed for even one month prior to 

release had 2.0 times better survival than fish reared in raceways; fish reared for four to seven 

months in acclimation ponds had 2.6 times better survival than fish reared in raceways. 

Due to the large size and surface water source of many acclimation ponds, water temperatures 

within may fluctuate. Wagner (1974) found that hatchery steelhead smolts exposed to a variable 

temperature cycle emigrated in larger numbers than did those under constant temperature. Bjorn 

and Ringe (1984) reported that steelhead transferred to a pond with cold water (four to ten degrees 

centigrade) for two to three months prior to release had higher survivals than fish held in 15°C 

water until release. Wedemeyer (1982) showed that gill ATPase activity in coho salmon and 

steelhead could be markedly increased with a sudden temperature change. Temperature 

fluctuations were used to accelerate smolt development and downstream movement in yearling 

Chinook salmon (Muir et al. 1994). However, yearling spring Chinook that were acclimatized in 

the same rearing vessels from 10°C well water to four to ten degree centigrade surface water for 

three or six weeks prior to release had no survival enhancement (Appleby et al. 2002). 

Smolt Travel Times

Although side-by-side comparison data are lacking, there is some evidence that outplanted smolts 

may have longer travel times compared to smolts from on-station releases. Mean travel time for 

ten groups of trucked steelhead smolts in one study was 2.9 km/day (Tipping and Byrne 1996), 1.6 

km/day in another study (Tipping et al.1995) and 7.1 km/day in another instance (Pat Hulett, 

WDFW, personal communication). Meanwhile, travel times of steelhead released directly from a 

hatchery was 33 km/day in two studies (Dawley et al.1977; Harza 1998). Smolt emigration time is 

important because faster emigration reduces the time that hatchery smolts can compete and prey 

(Hawkins and Tipping 1999) on wild fish. 

References

Appleby, A. A., J. M. Tipping, and G. E. Vander Haegen. 2002. Effects of surface water 

acclimatization on post-release survival of yearling spring Chinook salmon. North 

American Journal of Aquaculture 64:301-304. 

Banks, J. L. 1994. Raceway density and water flow as factors affecting spring Chinook salmon 

during rearing and after release. Aquaculture 119:201-217. 

Bjornn, T. C. and R. R. Ringe. 1984. Evaluation of conditioning steelhead trout in cold water after 

rearing at 15 C. Idaho cooperative fishery research unit. University of Idaho, Moscow. 

Brannon, E. L., R. P. Whitman and T. P.Quinn. 1984. Responses of returning adult coho salmon to 

home water and population-specific odors. Transactions of the American Fisheries Society 

113:374-377. 
B-72 Emerging Issues – Using Acclimation Ponds in the Rearing of Salmon 

Castle, P., N. Currence, A. Chapman, D. Huddle, and D. Griggs. 2002. Potential modifications to 

the Kendall Hatchery Chinook program. Unpublished manuscript. 

Dawley, E., C. W. Sims, R. D. Ledgerwood. 1978. A study to define the migrational 

characteristics of Chinook and coho salmon and steelhead trout in the Columbia River 

estuary. Coastal Zone and Estuarine Studies Annual Report. 

Dittman, A. H., T. P. Quinn, and G. A. Nevitt. 1996. Timing of imprinting to natural and artificial 

odors by coho salmon. Canadian Journal of Fisheries and Aquatic Sciences 53:434-442. 

Donnelly, W. A. and F. G. Whoriskey, Jr. 1991. Background-color acclimation of brook trout for 

crypsis reduces risk of predation by hooded mergansers. North American Journal of 

Fisheries Management 11:206-211. 

Ewing, R. D., M. D. Evenson, and E. K. Birks, and A. R. Hemmingsen. 1984. Indices of parrsmolt transformation in juvenile steelhead trout undergoing volitional release at Cole 

Rivers Hatchery, Oregon. Aquaculture 40:209-221. 

Ewing, R. D., and S. K. Ewing. 1995. Review of the effects of rearing density on survival to 

adulthood for Pacific salmon. Progressive Fish-Culturist 57:1-25. 

Harza. 1999. The 1997 and 1998 Technical Study reports, Cowlitz River Hydroelectric Project 

Volume 2. Tacoma Power, Tacoma. 

Hawkins, R. S., and J. M.. Tipping. Predation by juvenile hatchery salmonids on wild fall Chinook 

salmon fry in the Lewis River, Washington. California Fish and Game 85(3):124-129. 

Johnson, S. L., M. F. Solazzi, and T. E. Nickelson. 1990. Effects on survival and homing of 

trucking yearling coho salmon to release sites. North American Journal of Fisheries 

Management 10:427-433. 

Kenaston, K.R., R.B. Lindsay, and R.K. Schroeder. 2001. Effect of acclimation on the homing and 

survival of hatchery winter steelhead. North American Journal of Fisheries Management 

21:765-773. 

Maynard, D. J., T. A. Flagg, and C.V. Manhken. 1995. A review of semi-natural culture strategies 

for enhancing the post release survival of anadromous salmonids. Pages 307-314 in H.L. 

Schramm, Jr. and R. G. Piper, editors. Uses and effects of cultured fishes in aquatic 

ecosystems. American Fisheries Society, Symposium 15, Bethesda, Maryland. 

Maynard, D. J., G. C. McDowell, E. P. Tezak, and T. A. Flagg. 1996. Effect of diets supplemented 

with live food on the foraging behavior of cultured fall Chinook salmon. Progressive FishCulturist 58:187-191. 

McIsaac, D. O., and T. P. Quinn. 1988. Evidence for a hereditary component in homing behavior 

of Chinook salmon. Canadian Journal of Fisheries and Aquatic Sciences 45:2201-205. 
Emerging Issues – Using Acclimation Ponds in the Rearing of Salmon B-73 

Muir, W. D., W. S. Zaugg, A.E. Giorgi, and S. McCutcheon. 1994. Accelerating smolt 

development and downstream movement in yearling Chinook salmon with advanced 

photoperiod and increased temperature. Aquaculture 123: 387-399. 

Piper, R. G. and five coauthors. 1982. Fish hatchery management. U. S. Fish and Wildlife Service, 

Washington, D. C. 

Quinn, T. P., R. S. Nemeth and D. O. McIsaac. 1991. Homing and straying patterns of fall 

Chinook salmon in the lower Columbia River. Transactions of the American Fisheries 

Society 120:150-156. 

Savino, J. F., M.. G. Henry, and H. L. Kincaid. 1993. Factors affecting feeding behavior and 

survival of juvenile lake trout in the Great Lakes. Transactions of the American Fisheries 

Society 122:366-377. 

Schreck, C. B., M. F. Solazzi, S. L. Johnson, and T. E. Nickelson. 1989. Transportation stress 

affects performance of coho salmon. Aquaculture 82:15-20. 

Schroeder, R. K., R. B. Lindsay, and K. R. Kenaston. 2001. Origin and straying of hatchery winter 

steelhead in Oregon coastal rivers. Transactions of the American Fisheries Society 

130:431-441. 

Slaney, P.A., L. Berg and A.F. Tautz. 1993. Returns of hatchery steelhead relative to site of 

release below an upper-river hatchery. North American Journal of Fisheries Management 

13:558-566. 

Slatick, E., and 7 co-authors. 1988. Imprinting hatchery reared salmon and steelhead trout for 

homing, 1978-1983. Bonneville Power Administration, Portland. 

Specker, J. L., and C. B. Schreck. 1980. Stress responses to transportation and fitness for marine 

survival in coho salmon smolts. Canadian Journal of Fisheries and Aquatic Sciences 

37:765-769. 

Tipping, J. M., R. V. Cooper, J. B. Byrne and T. H. Johnson. 1995. Length and condition factor of 

migrating and nonmigrating hatchery-reared winter steelhead smolts. Progressive FishCulturist 57:120-123. 

Tipping, J. M., and J. B. Byrne. 1996. Reducing feed levels during the last month of rearing 

enhances emigration rates of hatchery-reared steelhead smolts. Progressive Fish-Culturist 

58:128-130. 

Tipping, J. M. 1998. Return rates of hatchery-produced sea-run cutthroat trout reared in a pond 

versus a standard or baffled raceway. Progressive Fish-Culturist 60:109-113. 

Tipping, J. M. 1998. Return rates of transported steelhead smolts with and without a rest period 

before release. Progressive Fish-Culturist 60:284-287. 
B-74 Emerging Issues – Using Acclimation Ponds in the Rearing of Salmon 

Tipping, J. M. 2001. Adult returns of hatchery sea-run cutthroat trout reared in a semi natural pond 

for differing periods prior to release. North American Journal of Aquaculture 63:131-133. 

Tipping, J. M., and T. D. Hillson. 2002. Adult recoveries of winter and summer steelhead by 

release location on the Lewis River, Washington. California Fish and Game 88(2):49-56. 

Vander Haegen, G., and D. Doty. 1995. Homing of coho and fall Chinook salmon in Washington. 

Washington Department of Fish and Wildlife #H95-08. Olympia. 

Wagner, H. H. 1969. Effect of stocking location of juvenile steelhead trout on adult catch. 

Transactions of the American Fisheries Society 98:27-34. 

Wagner, H. H. 1974. Photoperiod and temperature regulation of smolting in steelhead trout. 

Canadian Journal of Zoology 52:219-234. 

Wedemeyer, G. A. 1982. Effects of environmental stressors in aquacultural systems on quality, 

smoltification and early marine survival of anadromous fish. Proceedings of the North 

Pacific Aquaculture Symposium. Alaska Sea Grant Report 82-2. University of Alaska, 

Anchorage. 
Operational Guidelines C-1 

C. Operational Guidelines 

OVERVIEW

The Hatchery Scientific Review Group’s Operational Guidelines are intended to describe 

operational practices that are most likely to meet conditions for success, as defined in the 

Scientific Framework for the Artificial Propagation of Salmon and Steelhead. They were 

developed primarily for use by the Hatchery Scientific Review Group (HSRG) in its regional 

hatchery reviews, but can also be useful in future reviews of these and other programs. The 

guidelines were then turned into a series of questions for each operational phase that can be asked 

about every hatchery program. A positive response to a question implies consistency with the 

conditions for success from the scientific framework. A negative response to a question identifies 

a potential risk to meeting the conditions for success. 

Since objectives, as well as habitat and stock status, vary among hatchery programs, conditions for 

success may also vary among programs. No program is expected to meet all guidelines described 

in his document. Hatcheries are by their very nature a compromise, where risks must be balanced 

against benefits. For example, to meet survival objectives, some genetic or ecological risks may be 

acceptable. To meet objectives for proper ecological function, certain risks to fish health goals 

may be acceptable. The purpose of these guidelines is to assure that potential risks and benefits are 

clearly identified and managed. 
C-2 Operational Guidelines 

BROODSTOCK CHOICE

QUESTIONS GUIDELINES

3.1, 4.2, 5.1

Does the broodstock chosen represent

natural populations native or adapted to the

watersheds in which hatchery fish will be

released?

The broodstock chosen should represent the 

natural populations native or adapted to the 

watersheds in which hatchery fish will be

released.

B B - SH

3.1, 4.2, 5.1

Have eggs or adults been introduced from

outside the watershed since the inception of

the hatchery program?

Program should avoid the use of stocks

from outside the watershed. B B

5.2 Does the broodstock chosen minimize

negative ecological interactions?

A broodstock should be chosen that will

minimize negative ecological interactions. S H

4.2 Does the broodstock chosen have a history

of no pathogens?

The broodstock chosen should have a

history of no pathogens. S H

4.4.1

Does the broodstock chosen or developed 

have the desired life history traits to meet

harvest goals?

The broodstock chosen or developed should

have the desired life history traits to meet

harvest goals.

S H

Applicability

Operational Guidelines for Choice of Broodstock

Framework

Section

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
Operational Guidelines C-3

BROODSTOCK COLLECTION

QUESTIONS GUIDELINES

3.1, 4.1 Are adults randomly selected among all 

returning adults?

Broodstock should be selected at random

from all returning adults. B B

3.1, 4.1

Are representative samples of donor and 

hatchery populations collected with respect 

to size, age, sex ratio, run and spawn timing,

and other traits important to long-term

fitness?

Representative samples of donor and

hatchery populations should be collected

with respect to size, age, sex ratio, run and 

spawn timing, and other traits important to

long-term fitness.

B B - SH

4.1, 5.1

Were sufficient numbers of donors collected

from the natural stock to minimize founder

effects when the program was initiated?

When initiating a hatchery program,

sufficient numbers of donors should be 

collected from the natural stock to minimize

founder effects.

B B - SH

3.2, 4.1

Are sufficient broodstock collected to

maintain an effective population size of

1000 fish per generation?

Sufficient broodstock should be collected to 

maintain an effective population size of

1000 fish per generation.

B B

3.1, 4.1, 5.1 Is the composition of hatchery and wild fish 

in the broodstock known and controlled?

The composition of the broodstock should 

be monitored and controlled. I B

3.1, 4.1

 If goal is to minimize genetic divergence, is 

10 - 20% of the broodstock derived from

wild fish each year?

If goal is to minimize genetic divergence, 

10-20% of the broodstock should be derived 

from wild fish each year.

I B

3.2 Is the necessary security of the stocks 

maintained?

Necessary security of the stocks should be

maintained. B B

3.2

 If the wild population has 150 fish or more, 

is collection of wild broodstock limited to

30% of the population?

If the wild population has 150 fish or more, 

limit collection of wild broodstock to 30%

of the population. 

I C

3.2, 4.1 Does prespawning mortality exceed 10%? Prespawning mortality should not exceed 

10%. B B

3.1, 4.1, 4.2.4

 Does the program avoid stock transfers and 

subsequent releases of eggs or fish from

outside the watershed?

Program should avoid stock transfers and 

subsequent releases of eggs or fish from

outside the watershed.

B B

3.1, 4.1, 5.1

Do you have guidelines for acceptable

contribution of hatchery origin fish to

natural spawning?

Hatchery programs should adopt explicit

guidelines for acceptable contribution of 

hatchery fish to all potentially affected

natural spawning populations.

B B

3.1, 4.1, 5.1 Is the proportion of naturally spawning fish 

that are of hatchery origin known?

The annual contribution of hatchery fish to

natural spawing should be directly or

indirectly estimated.

3.1, 4.1, 5.1

Are guidelines for hatchery contribution to

to natural spawning met for all affected

naturally spawning populations?

Guidelines for hatchery contribution to to 

natural spawning should be met.

B B

Framework

Section

Operational Guidelines for Collection of Broodstock

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
C-4 Operational Guidelines 

QUESTIONS GUIDELINES

3.1, 4.1 Is the duration of the program clearly

defined?

The duration of the program should be 

clearly defined. I C

4.2

Is the broodstock maintained on natural 

water temperature profiles to provide 

optimum maturation and gamete

development?

The broodstock should be maintained on

natural water temperature profiles to

provide optimum maturation and gamete

development.

B B - SH

2.1, 2.1, 5.2

Does the number of broodstock collected 

maintain program size within carrying 

capacity of the natural environment?

The number of broodstock collected should

maintain program size within carrying

capacity of the natural environment.

B B

2.3, 5.2 Are adult fish or carcasses provided for 

upstream planting?

Consideration should be given to provide 

adult fish or carcasses for upstream

planting.

B B

4.2.4

If broodstock choice is from another

drainage, are eggs preferentially

transferred? Are fish or eggs held in

quarantine as described in the Salmonid

Disease Control Policy of the Fisheries CoManagers of Washington State (disease 

control policy).

If broodstock choice is from another 

drainage, are eggs should be preferentially

transferred. Fish or eggs should be held in

quarantine as described in the Salmonid

Disease Control Policy of the Fisheries CoManagers of Washington State (disease 

control policy).

B B

4.2.4 Are broodstock maintained on pathogenfree and/or fish-free water supply?

Broodstock should be maintained on

pathogen-free and/or fish-free water supply. B B

4.2.4

Does attending fish pathologist monitor and

recommend treatments to maximize survival

as needed?

Attending fish pathologist should monitor

and recommend treatments to maximize

survival as needed.

B B

5.2

Are pre-spawning mortalities disposed of in

a manner that prevents pathogen

transmission to the receiving watershed?

Pre-spawning mortalities should be

disposed of in a manner that prevents

pathogen transmission to the receiving 

watershed.

B B

Framework

Section

Operational Guidelines for Collection of Broodstock (Cont'd.)

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
Operational Guidelines C-5

SPAWNING

QUESTIONS GUIDELINES

3.1, 4.1 Are males and females available for

spawning on a given day randomly mated?

Males and females available for spawning 

on a given day should be randomly mated. B B - SH

3.1, 3.2, 4.1

Do fish selected for broodstock have an

equal opportunity to make a genetic

contribution to the progeny gene pool?

Fish selected for broodstock should have an

equal opportunity to make a genetic

contribution to the progeny gene pool.

B B - SH

4.2.4

Is pathogen sampling at spawning sufficient

to provide quantitative and qualitative

information for needed pathogen control 

measures that may be necessary for resultant 

transfers or rearing of progeny?

Pathogen sampling at spawning sould be

sufficient to provide quantitative and 

qualitative information for needed pathogen

control measures that may be necessary for

resultant transfers or rearing of progeny.

B B

4.2.4

Are eggs water-hardened in iodophor

solution as described in the disease control

policy?

Eggs should be water-hardened in iodophor

solution as described in the disease control

policy.

B B

4.2.4

Are disinfection procedures implemented 

that prevent pathogen transmission between

stocks of fish on site?

 Disinfection procedures should be

implemented that prevent pathogen

transmission between stocks of fish on site.

B B

5.2 Is spawning waste collected and disinfected

prior to discharge to receiving water?

Spawning waste should be collected and

disinfected prior to discharge to receiving

water.

B B

5.2

Are carcasses disposed of in a manner that

prevents pathogen transmission to the 

receiving watershed?

Carcasses should be disposed of in a 

manner that prevents pathogen transmission

to the receiving watershed.

B B

Framework

Section

Operational Guidelines for Spawning

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
C-6 Operational Guidelines 

INCUBATION

QUESTIONS GUIDELINES

3.1, 3.2, 4.1

Are eggs incubated under conditions that

maximize the probability that all segments 

of the population contribute equally to the 

release population?

Eggs should be incubated under conditions 

that maximize the probability that all 

segments of the population contribute

equally to the release population.

I B

3.1, 3.2, 4.1

Are eggs incubated under environmental 

conditions that tend to maximize survival of

all segments of the population? (e.g. control

temperature of incubation water to

synchronize ponding of fry)

Eggs should be incubated under 

environmental conditions that tend to

maximize survival of all segments of the

population. (e.g. control temperature of

incubation water to synchronize ponding of

fry)

I B

3.1, 3.2, 4.1, 4.2

Are eggs incubated under environmental 

conditions that tend to maximize individual 

fitness of fry? (e.g. allow volitional ponding 

of fry, incubate under environmental 

conditions that simulate the natural rearing 

environment)

Eggs should be incubated under 

environmental conditions that tend to

maximize individual fitness of fry. (e.g. 

allow volitional ponding of fry, incubate

under environmental conditions that

simulate the natural rearing environment)

B B

3.1, 3.2, 4.1 Does incubation take place in home stream

water?

Incubation should be take place in home

stream water. I C

3.2, 4.1 Are full sib families incubated separately? For integrated programs, full sib families 

should be incubated separately. I C

4.2, 5.2

Does the program use water sources that 

result in hatching/emergence timing similar

to that of the naturally produced 

population?

Program should use water sources that

result in hatching/emergence timing similar

to that of the naturally produced population.

I B

2.1, 2.2, 5.2

Does the number of eggs incubated maintain

program size within the carrying capacity of

the natural environment?

The number of eggs incubated should

maintain program size within the carrying

capacity of the natural environment.

B B

4.2.4 Does incubation occur on pathogen-free 

and/or fish-free water supply?

Incubation should occur on pathogen-free 

and/or fish-free water supply. B B

4.2.4

Are species-specific incubation 

recommendations followed for water

quality, flows, temperature, substrate, and 

density parameters to prevent syndromes 

such as “gas bubble disease”, “cold water 

disease”, “blue sac”, etc.)?

Species-specific incubation

recommendations should be followed for

water quality, flows, temperature, substrate,

and density parameters to prevent 

syndromes such as “gas bubble disease”, 

“cold water disease”, “blue sac”, etc.).

B B

Framework

Section

Operational Guidelines for Incubation

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation, 

H = Harvest, B = 

Both)
Operational Guidelines C-7

QUESTIONS GUIDELINES

4.2.4 Are incubating eggs treated when 

recommended by attending fish pathologist?

Incubating eggs should be treated when

recommended by attending fish pathologist.

B B

4.2.4

Following eye-up stage, are eggs 

inventoried, and dead or undeveloped eggs 

removed and disinfected, as described in the 

disease control policy?

Following eye-up stage, eggs should be 

inventoried, and dead or undeveloped eggs

removed and disinfected, as described in the 

disease control policy.

B B

4.2.4

 Are disinfection procedures implemented 

that prevent pathogen transmission between

stocks of fish on site?

Disinfection procedures should be 

implemented that prevent pathogen

transmission between stocks of fish on site.

B B

4.2.4

Are eggs monitored when needed to

determine fertilization efficiency and

embryonic development?

Eggs should be monitored when needed to

determine fertilization efficiency and 

embryonic development.

B B

4.2.4

Are fry removed from incubation units when

80-90% of observed fry have yolk-sac 

material that is 80-90% utilized and 

contained within body cavity (“button-up”)

Fry should be removed from incubation

units when 80-90% of observed fry have

yolk-sac material that is 80-90% utilized

and contained within body cavity (“buttonup”).

B H

4.2.4

Are appropriate water temperature profiles

maintained to provide optimum embryo

development?

Appropriate water temperature profiles

should be maintained to provide optimum

embryo development.

B B

4.2.4

Are incubator loading and densities 

maintained at levels that ensure optimum

survival of eggs and fry?

Incubator loading and densities should be

maintained at levels that ensure optimum

survival of eggs and fry.

B B

4.2, 4.2.4

Is substrate used to promote suitable fry

distribution, optimum size, and appropriate 

emergence timing?

Substrate should be used to promote 

suitable fry distribution, optimum size, and

appropriate emergence timing.

B B

5.2

Are eggs (dead or culled) discarded in a 

manner that prevents pathogen transmission

to the receiving watershed?

Eggs (dead or culled) should be discarded 

in a manner that prevents pathogen 

transmission to the receiving watershed.

B B

Framework

Section

Operational Guidelines for Incubation (Cont'd.)

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
C-8 Operational Guidelines 

REARING

QUESTIONS GUIDELINES

3.1, 3.2, 4.1

Are fish reared under conditions that

maximize the probability that all segments 

of the population contribute equally to the 

release population?

Fish should be reared under conditions that

maximize the probability that all segments

of the population contribute equally to the 

release population.

I B

3.1, 3.2, 4.1

Are all fish reared under environmental 

conditions that tend to maximize survival of

all segments of the population?

All fish should be reared under 

environmental conditions that tend to

maximize survival of all segments of the

population.

B B - SH

3.1, 4.1

Are families within spawning groups mixed

randomly at ponding so that unintentional

rearing differences affect families equally?

Families within spawning groups should be

mixed randomly at ponding so that

unintentional rearing differences affect

families equally.

I B

3.1, 3.2, 4.1 Are excess juveniles culled randomly when

necessary?

Excess juveniles should be culled randomly

when necessary. B B - SH

3.1, 3.2, 4.1

Are fish reared in multiple facilities or with 

redundant systems to reduce the risk of

catastrophic loss?

Fish should be reared in multiple facilities 

or with redundant systems to reduce the risk

of catastrophic loss.

B C

3.1, 4.1 Are fish reared for the shortest period 

possible?

Fish should be reared for the shortest period

possible. I C

3.1, 3.2, 4.1

For captive broodstocks, are fish maintained 

on natural photoperiod to ensure normal 

maturation and water temperatures below

120

C to minimize disease?

For captive broodstocks, fish should be 

maintained on natural photoperiod to ensure

normal maturation and water temperatures

below 120C to minimize disease.

S C

3.1, 3.2, 4.1

For captive broodstocks, are diets and 

growth regimes selected that produce

potent, fertile gametes and reduce excessive

early maturation of fish?

For captive broodstocks, diets and growth

regimes should be selected that produce 

potent, fertile gametes and reduce excessive 

early maturation of fish.

S C

3.2, 4.1 Are families reared individually to maintain

pedigrees?

Families should be reared individually to

maintain pedigrees. B C

3.2, 4.1 If required, are larger families culled to

minimize family size variation?

If required, larger families should be culled

to minimize family size variation. I B

2.3, 3.1, 4.1,

5.1, 5.2

Are fish reared under conditions that

maximize homing fidelity?

Fish should be reared under conditions that

maximize homing fidelity. B B - SC

4.2, 5.2 Does the program use a diet and growth

regime that mimics natural growth patterns?

Program should use a diet and growth

regime that mimics natural growth patterns. B B - SH

Framework

Section

Operational Guidelines for Rearing

Applicability

Program Type

(S = Segregated, I =

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
Operational Guidelines C-9

QUESTIONS GUIDELINES

4.2, 5.2

Are natural rearing conditions simulated for 

rearing density, temperature, photoperiod,

hydraulic characteristics, feeding 

conditions, and predator avoidance training?

Natural rearing conditions should be

simulated for rearing density, temperature,

photoperiod, hydraulic characteristics,

feeding conditions, and predator avoidance

training.

I B

4.2, 5.2

Are the fish produced qualitatively similar

to natural fish in size, morphology, 

behavior, growth rate, physiological status, 

health, and other attributes?

Fish produced should be qualitatively

similar to natural fish in size, morphology, 

behavior, growth rate, physiological status,

health, and other attributes.

I B

2.1, 2.2, 5.2

Does the number of fish reared maintain 

program size within carrying capacity of the 

natural environment?

The number of fish reared should maintain

program size within carrying capacity of the

natural environment.

B B

2.4 Are adequate flows maintained in the bypass reach?

Adequate flows should be maintained in the 

by-pass reach. B B

2.4

Has a riparian management plan been 

implemented that incorporates vegetation

management, herbicide and pesticide use,

and surface water management provisions?

A riparian management plan been should be

implemented that incorporates vegetation 

management, herbicide and pesticide use,

and surface water management provisions.

B B

2.3, 2.4

Does the facility operate within the

limitations established in National Pollution 

Discharge Elimination System permit?

The facility should operate within the 

limitations established in National Pollution 

Discharge Elimination System permit.

B B

2.4 Has an on or off-site habitat mitigation plan

been implemented?

An on or off-site habitat mitigation plan

should be implemented. B B

4.2.4 Does rearing occur on pathogen-free and/or 

fish free water supply?

Rearing should occur on pathogen-free 

and/or fish free water supply. B B

4.2.4

Are fish health examinations performed at a 

minimum of once per month and more 

frequently when required?

Fish health examinations should be

performed at a minimum of once per month

and more frequently when required.

B B

4.2.4

Whenever possible, are vaccines used to

minimize the use of antimicrobial

compounds?

Whenever possible, vaccines should be used 

to minimize the use of antimicrobial

compounds.

B B

4.2.4

Are fish treated with appropriate chemicals

or drugs as recommended by fish

pathologist?

Fish should be treated with appropriate 

chemicals or drugs as recommended by fish

pathologist.

B B

4.2.4

Are disinfection procedures implemented 

that prevent pathogen transmission between

stocks of fish on site?

Disinfection procedures should be 

implemented that prevent pathogen

transmission between stocks of fish on site.

B B

Framework

Section

Operational Guidelines for Rearing (Cont'd.)

Applicability

Program Type

(S = Segregated, I =

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
C-10 Operational Guidelines 

QUESTIONS GUIDELINES

4.2.4

Are predators excluded from ponds to

prevent the spread of pathogens between

containers?

Predators should be excluded from ponds to

prevent the spread of pathogens between

containers.

S B

4.2.4

In the event of an epizootic, are: Treatment 

recommendations of attending pathologist

followed? Are affected containers isolated?

Is effluent sanitized if possible?

In the event of an epizootic: Treatment 

recommendations of attending pathologist 

should be followed. Affected containers 

should be isolated? Effluent should be 

sanitized if possible.

B B

2.4, 4.2.4

Are settleable solids, unused feed and feces 

periodically removed to ensure proper 

cleanliness of rearing container?

Settleable solids, unused feed and feces 

should be periodically removed to ensure 

proper cleanliness of rearing container.

B B

4.2

Does the operator follow proper feeding

rates, conduct periodic feed quality analysis, 

and store feed under proper conditions to 

prevent nutritional disorders?

The operator should follow proper feeding

rates, conduct periodic feed quality analysis,

and store feed under proper conditions to

prevent nutritional disorders.

B B

4.2

Are appropriate physical and chemical

characteristics of water inflow and effluent 

(suspended solids, temperature, dissolved 

gases, pH, mineral content, and potential

toxic metals) maintained to promote growth 

and survival?

Appropriate physical and chemical

characteristics of water inflow and effluent 

(suspended solids, temperature, dissolved 

gases, pH, mineral content, and potential

toxic metals) should be maintained to

promote growth and survival.

B B

4.2

Are accurate fish inventory data maintained

(e.g. Hat-Pro) with a minimum of handling 

stress?

Accurate fish inventory data should be 

maintained (e.g. Hat-Pro) with a minimum

of handling stress.

B B

4.2

 Are appropriate flow and density indexes 

maintained for the species and life stage 

being reared?

Appropriate flow and density indexes

should be maintained for the species and life

stage being reared.

B B

4.2

Is the correct amount and type of food 

provided to achieve the desired growth rate, 

body composition, and condition factors for 

the species and life stage being reared?

The correct amount and type of food should

be provided to achieve the desired growth 

rate, body composition, and condition

factors for the species and life stage being 

reared.

B B

4.2.5, 5.2

Are mortalities removed daily and disposed 

of in a manner that prevents pathogen

transmission to the receiving watershed?

Mortalities should be removed daily and 

disposed of in a manner that prevents

pathogen transmission to the receiving 

watershed.

B B

4.4.1

Are facility and species-specific

recommendations for water quality,

temperature, loading, and density followed

to maximize recruitment to fisheries?

Facility and species-specific 

recommendations for water quality, 

temperature, loading, and density should be

followed to maximize recruitment to

fisheries.

S H

Framework

Section

Operational Guidelines for Rearing (Cont'd.)

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
Operational Guidelines C-11

RELEASE AND ADULT MIGRATION

QUESTIONS GUIDELINES

2.3, 3.1, 4.1,

5.1, 5.2

Are fish released at life stages and locations

that maximize homing fidelity?

Fish should be released at life stages and 

locations that maximize homing fidelity. B B - SC

3.1, 4.1, 5.1

Are marking/tagging techniques used to

distinguish among segments of the hatchery

population and between the hatchery and

natural populations?

Marking/tagging techniques should be used

to distinguish among segments of the

hatchery population and between the

hatchery and natural populations.

B B

4.1, 5.1 Are fish identified with nonlethal detectable

identification marks or tags?

Fish should be identified with nonlethal

detectable identification marks or tags. I C

2.3, 3.1, 4.1,

5.1, 5.2

Is the straying of hatchery fish into the wild 

controlled?

Straying of hatchery fish into the wild 

should be controlled. B H

2.3, 3.1, 5.1, 5.2 Is the attraction of hatchery fish maximized 

and that of wild fish minimized?

The attraction of hatchery fish should be

maximized and that of wild fish minimized. S H

3.2, 5.3 Are hatchery fish identified so the status of 

the natural population is not masked?

Hatchery fish should be identified so the

status of the natural population is not

masked.

B B - SC

4.2, 5.2

Are fish released within the size range of

naturally produced fish from which the 

hatchery population is derived?

Fish should be released within the size

range of naturally produced fish from which 

the hatchery population is derived.

I B

3.1, 4.1, 4.2, 5.2 Are volitional releases during natural outmigration timing practiced?

Volitional releases during natural outmigration timing should be practiced. I B

4.2, 5.2

Are fish released at sizes and life history

stages similar to those of natural fish of the 

same species?

Fish should be released at sizes and life

history stages similar to those of natural fish

of the same species.

I B

2.3, 5.2

Are fish released in areas or at life history

stages where they are unlikely to encounter

or prey upon natural fish of the same or

other species?

Fish should be released in areas or at life

history stages where they are unlikely to 

encounter or prey upon natural fish of the

same or other species.

B B - SC

2.3, 5.2

Are fish released in a manner so they are

unlikely to encounter or prey upon natural 

fish of the same or other species?

Fish should be released in a manner so they

are unlikely to encounter or prey upon

natural fish of the same or other species.

B B - SC

2.1, 2.2, 2.3, 5.2

Are fish released in numbers that do not

exceed the carrying capacity for the natural

population?

Fish should be released in numbers that do

not exceed the carrying capacity for the

natural population.

B B - SC

Framework

Section

Operational Guidelines for Release and Adult Migration

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
C-12 Operational Guidelines 

QUESTIONS GUIDELINES

2.3, 5.2 Are fish released in stream reaches within 

the historic range of that species?

Fish should be released in stream reaches 

within the historic range of that species. B B - SC

3.1, 4.2, 5.2 Are fish released in a manner that simulates 

natural migratory patterns?

Fish should be released in a manner that

simulates natural migratory patterns. B B - SC

2.3, 3.1, 4.1,

5.1, 5.2

Are fish released in areas with adequate

imprinting to the facility or desired stream

reach?

Fish should be released in areas with

adequate imprinting to the facility or desired

stream reach.

B B - SC

2.3, 5.2

Are fish released at locations where they are 

unlikely to encounter natural fish that are

negatively affected by hatchery fish?

Fish should be released at locations where

they are unlikely to encounter natural fish

that are negatively affected by hatchery fish

B B - SC

2.1, 5.2 Are fish released into properly functioning 

freshwater, estuarine and marine habitat?

Fish should be released into properly

functioning freshwater, estuarine and marine 

habitat.

B B - SC

2.4

Does the hatchery operate to allow all

migrating species of all ages to pass through 

hatchery related structures to maximize use 

of natural habitat?

The hatchery should operate to allow all 

migrating species of all ages to pass through 

hatchery related structures to maximize use 

of natural habitat.

B B - SC

2.4 Are adults distributed upstream of hatchery

to meet habitat capacity?

Adults should be distributed upstream of

hatchery to meet habitat capacity. I B

2.4

Is unimpeded passage provided for wild fish

through hatchery structures and by-pass 

reaches?

Unimpeded passage should be provided for

wild fish through hatchery structures and bypass reaches.B B - SC

4.2.4

Are all fish examined for presence of

“reportable pathogens” as defined in the 

disease control policy at the assumed

pathogen prevalence Level (APPL) of 5%

no less than 3 weeks prior to release?

All fish should be examined for presence of

“reportable pathogens” as defined in the 

disease control policy at the assumed

pathogen prevalence Level (APPL) of 5% 

no less than 3 weeks prior to release.

B B - SC

4.2.4

Are attending fish pathologist

recommendations followed for treatments 

prior to release?

Attending fish pathologist recommendations 

should be followed for treatments prior to

release.

B B - SC

4.2.4 Are fish released in same drainage as

rearing facility?

Fish should be released in same drainage as

rearing facility. B B - SC

Framework

Section

Operational Guidelines for Release and Adult Migration (Cont'd.)

Applicability

Program Type

(S = Segregated, I =

Integrated, B = 

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
Operational Guidelines C-13

QUESTIONS GUIDELINES

4.2.4

Are transfers out of drainage inspected as

above and accompanied by appropriate 

notifications to responsible/regulatory

parties as described in the disease control 

policy?

Transfers out of drainage should be

inspected as above and accompanied by

appropriate notifications to

responsible/regulatory parties as described

in the disease control policy.

B B

2.1, 3.1, 4.1

Are fish released at times of the year and 

sizes to allow adoption of multiple life 

history strategies?

Fish should be released at times of the year

and sizes to allow adoption of multiple life

history strategies.

B B - SC

4.4.1

Are fish released at a time, size, location, 

and in a manner that maximizes recruitment 

to fisheries?

Fish should be released at a time, size, 

location, and in a manner that maximizes 

recruitment to fisheries.

S H

Framework

Section

Operational Guidelines for Release and Adult Migration (Cont'd.)

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
C-14 Operational Guidelines 

ACCOUNTABILITY

QUESTIONS GUIDELINES

6.1

Are all hatchery personnel aware of the 

goals for the hatchery with respect to 

conservation, harvest and other purposes?

All hatchery personnel should be aware of

the goals for the hatchery with respect to

conservation, harvest and other purposes

B B

6.1

Are expenditures tracked to assure that

funds are expended as intended for the 

hatchery program?

Expenditures should be tracked to assure 

that funds are expended as intended for the

hatchery program.

B B

6.1

Are KEY staff aware of the funding 

available for carrying out the various

activities in the production cycle so that it

can be done the most cost effective manner?

Key staff should be aware of the funding

available for carrying out the various

activities in the production cycle so that it

can be done the most cost effective manner.

B B

6.1

Is all new relevant information from

research or other sources made available to

hatchery staff and others and used for

attaining goals?

All new relevant information from research

or other sources should be made available to

hatchery staff and others and used for 

attaining goals.

B B

6.1

Is the most recent information obtained

from monitoring and evaluation programs

for the production cycle, including 

performance indicators and progress toward

goals, taken into consideration when

determining whether hatchery operations

should be changed or not?

The most recent information obtained from

monitoring and evaluation programs for the 

production cycle, including performance

indicators and progress toward goals, should

be taken into consideration when

determining whether hatchery operations 

should be changed or not.

B B

6.1

Is there a management program in place that

assures that information pertaining to items 

1-4 is available on a “real-time” basis and

that changes warranted by that information

are implemented?

There should be a management program in

place that assures that information

pertaining to items 1-4 is available on a 

“real-time” basis and that changes 

warranted by that information are

implemented.

B B

6.1

Are standards specified for in-culture and

post release performance of hatchery fish

and their offspring?

Standards should be specified for in-culture 

and post release performance of hatchery

fish and their offspring.

B B

6.1

Are there state or federal laws that constrain

the program by specifying objectives, such

as numbers and size of smolt produced? 

State or federal laws that constrain the 

program by specifying objectives, such as

numbers and size of smolt produced, should

be reviewed and conflicts reported. 

B B

Framework

Section

Operational Guidelines for Accountability

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
Operational Guidelines C-15

EDUCATION

QUESTIONS GUIDELINES

1.13 Is the hatchery facility open to the public

during hours of operation?

The hatchery facility should be open to the

public during hours of operation. B B

1.13 Are the hatchery operations visible to

facility visitors?

Hatchery operations should be visible to

facility visitors.

B B

1.13

Are hatchery operations (egg take,

incubation, rearing) demonstrated to the 

public?

Hatchery operations (egg take, incubation,

rearing) should be demonstrated to the

public.

B B

1.13

Does the facility have a fish ladder and/or

adult holding facilities that are open to the 

public?

If the facility has a fish ladder and/or adult 

holding facilities they should be are open to

the public.

B B

1.13

Does the hatchery have signage describing 

the facility, fish production goals, ties to

management goals, ecosystem function?

The hatchery should have signage

describing the facility, fish production

goals, ties to management goals, ecosystem

function.

B B

1.13 Is there a visible link to riparian zone such

as viewing boardwalk or bridge?

There should be a visible link to riparian

zone such as viewing boardwalk or bridge.

B B

1.13 Is the facility used by other fish and wildlife

programs?

When beneficial, the facility should be used 

by other fish and wildlife programs. B B

1.13 Does the hatchery schedule tours for 

groups?

The hatchery should schedule tours for

groups.

B B

1.13 Does the program provide opportunities for 

student interns?

The program should provide opportunities 

for student interns. B B

1.13 Does the program provide opportunities for 

citizen volunteer involvement?

The program should provide opportunities 

for citizen volunteer involvement.

B B

1.13 Does the agency maintain a web page

describing the hatchery program?

The agency should maintain a web page

describing the hatchery program. B B

1.13 Is a pamphlet or brochure describing agency

or hatchery programs available?

A pamphlet or brochure describing agency

or hatchery programs should be available. B B

Framework

Section

Operational Guidelines for Education

Applicability

Program Type

(S = Segregated, I =

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
C-16 Operational Guidelines 

QUESTIONS GUIDELINES

1.13 Are eggs or fish provided to volunteer

groups?

Are eggs or fish provided to volunteer

groups? B B

1.13 Are eggs or fish provided to educational 

groups i.e. “Salmon in the Classroom”?

Are eggs or fish provided to educational

groups i.e. “Salmon in the Classroom”? B H

1.13

Is hatchery staff involved in 

community/volunteer meetings or outreach 

programs?

Hatchery staff should be involved in

community/volunteer meetings or outreach

programs.

B B

1.13 Does hatchery staff regularly give classroom

presentations?

Does hatchery staff regularly give classroom

presentations? B B

1.13 Does hatchery staff participate in formal

professional presentations/seminars?

Hatchery staff should participate in formal

professional presentations/seminars. B B

1.13 Is the facility used or does staff participate

in agency research projects?

Where appropriate and benficial, the facility

should be used and staff should participate 

in agency research projects.

B B

1.13

Is the facility used or does staff participate

in university or other cooperative research 

projects?

Is the facility used or does staff participate

in university or other cooperative research

projects?

B B

1.13

Are data and information pertaining to the

program accessible to interested 

researchers?

Data and information pertaining to the

program should be accessible to interested

researchers.

B B

Framework

Section

Operational Guidelines for Education (Cont'd.)

Applicability

Program Type

(S = Segregated, I = 

Integrated, B =

Both)

Program

Purpose

(C = Conservation,

H = Harvest, B = 

Both)
Monitoring & Evaluation Criteria D-1 

D. Monitoring and Evaluation Criteria 

INTRODUCTION

Accountability and adaptive management are two of the cornerstones of hatchery reform. They require 

collecting and using information that tell us (1) if hatchery programs are successfully contributing to 

resource goals and (2) if they are not how they should change. A conceptual outline of a monitoring 

and evaluation strategy to achieve accountability and support adaptive management is contained in 

Chapter 6 of the Scientific Framework (Appendix A). The purpose of this Appendix is to show how a 

monitoring plan can be developed that generates the information needed to assess the performance of a 

hatchery program relative to its goals. The co-managers and the HSRG are currently engaged in an 

effort to develop a comprehensive, operational monitoring and evaluation plan, therefore this 

Appendix should be viewed as a preliminary report on a work in progress. 

This appendix first identifies and describes the conditions for success based on the concepts in the 

Scientific Framework. A set of evaluation questions, derived from the operational guidelines 

(Appendix C), are then identified that relate hatchery operations to the conditions for success. The 

monitoring criteria that follow identify the data that must be collected to answer the evaluation 

questions. The answers to the evaluation questions tell us to what extent a hatchery program is 

meeting specific conditions for success. In other words, the conditions for success represent the 

scientific rationale for the program: if the program is conducted consistent with the specified 

guidelines it will be successful (i.e. contribute to resource goals as intended), when guidelines are not 

met, resource goals may be at risk. 

SUMMARY OF CONDITIONS FOR SUCCESS

The following conditions for success are derived from the concepts decribed in the Scientific 

Framework. 

a) Genetic Conditions

The productivity of a hatchery population is determined jointly by the environment and by genetic 

conditions in both the hatchery population and any naturally spawning populations connected to it. 

Genetic conditions affect not only productivity; they also determine adaptability to environmental 

change, and include genetic composition, genetic diversity, and genetic population structure. 
D-2 Monitoring & Evaluation Criteria 

b) Biological Conditions

The survival and reproductive success of juvenile hatchery fish depends upon their physiological, 

morphological, behavioral, and health characteristics at the time of their release. The success is 

also shaped by their genetic makeup and the environmental conditions they are exposed to in the 

hatchery. One template for achieving healthy/viable hatchery populations is the biological 

characteristics of local, wild fish populations. Therefore, in order to achieve productivity similar to 

wild fish, the hatchery environment should produce fish that reflect the natural life history patterns 

of locally adapted stocks in: physiology, morphology, and behavior. 

c) Fish Health

Fish health, in the fish hatchery context, is a term used when considering the well-being of fish 

populations in hatcheries. The term does not indicate whether the fish are diseased or free of 

disease, be it of infectious or non-infectious cause. Health of the fish is important to the 

productivity and success of the hatchery for a number of reasons. First, losses experienced during 

rearing of healthy fish are usually much less than those for diseased fish. Second, the cost of trying 

to correct disease problems in hatcheries can be considerable. Third, rearing healthy fish obviates 

the need for using anti-microbial compounds. Some of these (e.g., formalin), may be harmful to 

hatchery personnel if not used strictly according to directions. Others (e.g., antibiotics) can result 

in the selection/production of antibiotic-resistant fish pathogens (Dixon 1994) and enhance levels 

of the resistant forms present in the environment (Herwig et al. 1997). Finally, healthy fish are 

more likely to survive following release from the hatchery than are sick fish. 

d) Hatchery and Receiving Environment

The health and viability of hatchery populations are affected by the environment in which the fish 

are reared and are dependent upon the culture techniques these fish experience. Each hatchery has 

a unique combination of water sources, rearing facilities, and release parameters. The viability of 

hatchery populations is also affected by the receiving habitat or environment into which fish are 

released. Providing proper hatchery and environmental conditions optimizes potential fish 

production. 

e) Hatchery Structures

The physical structures of hatcheries are located in riparian areas. Some hatchery structures have 

severe adverse effects on wild fish populations by creating obstacles to migration, changes in 

instream flows, and loss of water quality. Hatchery structures may affect wild fish and the 

environment in various ways: downstream fish passage (i.e., water intake screens), upstream fish 

passage, volitional entry into hatchery, water discharge quality, riparian alterations, and human 

harassment. 
Monitoring & Evaluation Criteria D-3 

f) Ecological Effects

After their release, hatchery fish become components of the ecosystem, affecting it in various 

ways. While many of these effects are difficult to predict, it is important to evaluate some of these 

consequences and consider them in the course of planning and evaluating hatchery programs. 

Released hatchery salmonids can interact with their wild cohorts to reduce survival, growth, 

migration, and reproduction. Ecological interactions caused by the release of hatchery-reared 

juveniles include: predation, competition, disease transmission, and ecological function. 

g) Genetic Interactions

Hatchery populations directly affect the genetic composition of natural populations through gene 

flow, the transfer of genes from hatchery populations into naturally spawning populations. Gene 

flow is influenced by the straying or stocking rate of hatchery populations into natural populations, 

as well as by the reproductive success of the hatchery fish. The effects of this gene flow are 

unpredictable and depend on the genetic composition of the hatchery population. Factors affecting 

genetic interactions include: change of diversity among populations, change of diversity within 

populations, decrease in fitness of a population, and changes in abundance. Hatchery releases may 

also have positive demographic effects on natural populations. 

h) Contribution to Conservation

Conservation hatcheries can play a vital part in the recovery of threatened and endangered species 

by maintaining their genetic diversity and natural behavior, and by reducing the short-term risk of 

extinction. Under proper conditions, conservation hatcheries can maintain severely depleted 

natural stocks in captive culture in gene banks to avoid extinction. Hatcheries have the capability 

to maintain large breeding populations of wild stocks to minimize the risk of demographic loss 

from unpredictable environmental events. Hatcheries, when operating in the conservation mode, 

can supplement under-recruited wild populations that are below their natural carrying capacity. 

Finally, in cases where wild stocks have been extirpated, conservation hatcheries have the 

capability to introduce and maintain naturally spawning stocks until they are self-sustaining. The 

conservation hatchery concept implies that following the recovery of target populations and 

receiving habitat, these programs will be terminated. In order to be effective, conservation 

hatchery programs must be integrated with habitat and harvest management programs that provide 

for rebuilding of self-sustaining, naturally spawning populations. 

i) Contribution to Harvest

The range of harvest issues and integration of harvest with artificial production are very complex. 

They are best addressed under comprehensive management plans developed by the fisheries comanagers. This section of the framework is meant to identify the general harvest conditions 

necessary for hatcheries to be successful, rather than to prescribe specific harvest management 

policies or solutions, which while important, is beyond the scope of the HSRG’s assignment. One 
D-4 Monitoring & Evaluation Criteria 

of the principal goals for hatcheries is to provide for sustainable harvest in subsistence, 

recreational, ceremonial, and commercial fisheries. In order to meet this goal, harvest methods and 

policies, as well as the repositioning of hatchery programs must be taken into consideration. 

Fisheries must have access to harvestable hatchery fish without significant adverse impacts to fish 

stocks of concern. Harvest access implies that hatcheries and harvest operations must be 

coordinated. They must also provide for: opportunity to meet harvest goals, protection of hatchery 

spawning requirements, and protection of co-mingled stocks of concern. 
Monitoring & Evaluation Criteria D-5 

EVALUATION QUESTIONS

Like the operational guidelines (Appendix C), the evaluation questions that follow are organized by 

operational phases of a hatchery program. The relative importance of the questions and monitoring 

criteria depends on the context (in terms of habitat and stock status), the goals (for conservation and 

harvest), and uncertainties associated with each program. Thus the order of the questions and the 

associated monitoring criteria do not reflect their priority order. 

BROODSTOCK CHOICE

a) Genetic Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the origin of the broodstock (SASI stock, GDU membership; include both major and 

minor sources)? 

• What is the stock-specific replacement rate (R/S)? 

• (Estimate recruitment in adult equivalents by brood year.) 

• Do the morphological, behavioral & physiological traits of the adults returning to the hatchery 

match those of the local stock? 

• What are the history of translocations to other facilities and the history of outplantings within 

and out of the watershed? 

• What is the genetic relationship of the extirpated stock to the donor stock? 

• Are the life history patterns of the extirpated stock similar to those of the donor stock? Are the 

freshwater and marine environments of the donor and receiving watersheds similar? 

Evaluation questions applicable to integrated programs and to both conservation and harvest

programs 

• Are allele frequencies being monitored for changes between broodstock and progenitor wild 

populations? 

• What are the morphological, behavioral & physiological traits of local stocks? 

c) Fish Health

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the disease history of the broodstock over the last decade? 

• What are the most serious pathogens in terms of pre-spawning mortality? 
D-6 Monitoring & Evaluation Criteria

e) Ecological Effects

Evaluation questions applicable to segregated programs and to harvest programs 

• Has the hatchery stock been isolated from the wild population through such purposeful 

mechanisms as run timing differences, or weirs, or is the hatchery stock of local origin?

i) Contribution to Harvest

Evaluation questions applicable to both integrated and segregated programs and to harvest

programs 

• What are the morphological, behavioral & physiological traits of local stocks? 

• Do the morphological, behavioral & physiological traits of the adults returning to the hatchery

match those of the local stock? 

• What desirable harvest traits does the broodstock possess (size at maturity, distribution in the 

marine environment, return time, percent jacks, etc.)?

Monitoring Criteria for Broodstock Choice by Species/Race/Stock: 

For all programs determine and/or record: 

1. Broodstock origin (GDU,ESU,SASSI) for introductions; provide rationale (similarity to

native stock) - annually

2. Composition (NOR vs. HOR) - annually 

3. Population characteristics (run timing, sex/age, fecundity, egg size, length) - annually

4. Tag recoveries in fisheries and escapement (to reconstruct recruitment and estimate 

productivity) - annually

5. Disease history for each broodstock - annually 

In addition for integrated programs determine and/or record: 

1. Population characteristics of natural spawners (as above plus morphology-body shape, 

coloration) - every generation 

2. Gene (allele) frequencies in hatchery and natural stocks - 3 BY/decade (1 BY/generation, 

each cohort every other generation) 
Monitoring & Evaluation Criteria D-7 

BROODSTOCK COLLECTION

a) Genetic Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What are the location, time, and method of broodstock capture? 

• What are the historical trends for size and age at maturity, and return and spawn timing, and 

other critical life history traits? 

• What are the morphological characteristics unique to the local and hatchery stocks (size and 

age at maturity, body form, secondary sexual characteristics, etc.)? 

• What is the hatchery entry date, over time for the population? 

• What is the number of NORs and HORs used for broodstock by sex by date? 

• What safeguards are employed to maintain the biosecurity of the broodstock(s)? 

• What are the history of translocations to other facilities and the history of outplantings within 

and out of the watershed? 

• What strategies are employed if the hatchery broodstock goal is not met? 

Evaluation questions applicable to integrated programs and to both conservation and harvest

programs 

• What is the number of NORs and HORs used for broodstock by sex by date? 

b) Biological Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Is there sufficient water of proper temperature to ensure good maturation and gamete 

development? 

• Are the flows sufficient to attract and separate adults into the hatchery? 

• Are there hatchery barriers to upstream passage or that would impede entry to hatchery? 

c) Fish Health

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the disease history of the broodstock over the last decade? 

• What are the most serious pathogens in terms of pre-spawning mortality? 

• How are the eggs of non-local species quarantined? 
D-8 Monitoring & Evaluation Criteria 

• How are pre-spawning mortalities collected and disposed of? 

• What is the cause of pre-spawning mortality? If infectious invoke pathogen treatment 

protocols. 

• How are pre-spawning mortalities collected and disposed of? 

• If maintained on-site, are the carcasses maintained under quarantine conditions? 

• Describe disinfection procedures for adult holding containers, equipment and personnel during 

and following spawning? 

d) Hatchery and Receiving Environment

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What are the adult holding densities? 

• What is the diurnal temperature cycle in the holding ponds? 

• What is the average pre-spawning mortality over the preceding decade? 

• How does the current year pre-spawning mortality compare? 

• How frequently are the spawners handled to determine ripeness? 

• Is the holding pond deep enough and flow adequate to minimize stress, and is human activity 

minimized? 

• Are night lights extinguished during adult holding? 

f) Ecological Effects

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Is sufficient escapement on natural/hatchery spawners allowed to maximize the natural 

productivity of the watershed? 

• Is the watershed deficient in nutrients? 

• Are hatchery carcasses sufficient to reach nutrient requirements of watershed? 

g) Genetic Interactions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What are the history of translocations to other facilities and the history of outplantings within 

and out of the watershed? 

Evaluation questions applicable to integrated programs and to conservation programs 

• What is the number of NORs and HORs used for broodstock by sex by date? 
Monitoring & Evaluation Criteria D-9

• What is the size of the naturally spawning population? 

• What is the composition of the natural spawning escapement in terms of NORs and HORs?

• What is the duration of the program? 

h) Contribution to Conservation

Evaluation questions applicable to both integrated and segregated programs and to conservation

programs 

• What is the relative probability of survival of the hatchery and wild components? 

Evaluation questions applicable to integrated programs and to both conservation and harvest

programs 

• What is the composition of the natural spawning escapement in terms of NORs and HORs?

Monitoring Criteria for Broodstock Collection by Species/Race/stock: 

For all programs determine and/or record: 

1. Number, composition (HOR, NOR), life stage (eggs, juveniles, or adults), and method of 

broodstock collection (Rationale for number and method of collection)- annually

2. Number of fish entering hatchery and number passed upstream of hatchery - weekly during 

run 

3. Disposition of all broodstock transferred out of hatchery - annually

4. Incidents of broodstock losses and their causes - each event 

5. Water temperature and flow in holding ponds - Daily 

6. Holding pond volume, temperature (daily), dissolved oxygen level (weekly) and flow 

(weekly) 

7. Natural spawners (HOR and NOR) in watershed - annually

8. Incidence and prevalence of pathogen in the broodstock - annually

9. Methods used to quarantine and/or disinfect ponds, equipment and personnel - annually

10. Type and duration of disease treatment of adults - annually

In addition for integrated programs determine and/or record: 

1. Indicators of biological significance and viability of natural population - annually

2. Quantity and quality of habitat (factors affecting whether to alter or terminate program) -

annually 

3. Water temperature in stream – continuously
D-10 Monitoring & Evaluation Criteria 

SPAWNING

a) Genetic Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What are the spawner selection protocols (e.g. random, size, ripeness, wild or hatchery 

origin)? 

• How are the gametes handled (pooling of milt and/or eggs? 

• What is the mating scheme (e.g. 1:1, factorial, multiple pooling)? 

Evaluation questions applicable to integrated programs and to both conservation and harvest

programs 

• Was a representative subsample of the population used for spawning? 

b) Biological Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What are the sex, age, and size composition of the spawning population? 

• What are the procedures for sexing and determining ripeness? 

• What is the age-specific fecundity of hatchery and wild fish (number eggs/female, distribution 

of fecundities, mean egg size, etc.)? 

• What is the relative reproductive success of hatchery-origin/wild-origin spawners? 

c) Fish Health

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What procedures are used for water hardening of eggs in iodophor solution (iodophor 

concentration, duration, etc.)? 

f) Ecological Effects

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Are adult fish or carcasses provided for upstream planting? 

• Are carcasses disposed of in a manner that prevents pathogen transmission to the receiving 

watershed? 

• Is spawning waste collected and disinfected prior to discharge to receiving water? 
Monitoring & Evaluation Criteria D-11

Monitoring Criteria for Spawning by Species/Race/Stock: 

For all programs determine and/or record: 

1. Number of NORs and HORs spawned by sex, fecundity, length, date and age - annually

2. Spawner selection protocol (e.g. random,,,) wrt size, run timing, HOR/NOR - annually

3. Number of NORs and HORs NOT spawned by sex, fecundity, length, date and age - annually

4. Mating scheme (e.g. 1:1, factorial, pooled gametes) - annually 

5. Number of carcasses distributed to watershed - annually

6. Method of carcass disposition - annually

7. Incidence and prevalence of pathogens - annually

8. Type and duration of disease treatment of eggs - annually

9. Disinfection methods for ponds, equipment and personnel - annually

In addition for captive brood programs determine and/or record: 

1. Genotype of selected mated pairs - annually

In addition for integrated programs determine and/or record: 

1. Genotype of selected mated pairs (where needed to separate stock components) - annually
D-12 Monitoring & Evaluation Criteria 

INCUBATION

a) Genetic Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• How are the gametes handled (pooling of milt and/or eggs? 

• What is the mating scheme (e.g. 1:1, factorial, multiple pooling)? 

• How are the gametes handled (pooling of milt and/or eggs? 

• What is the mating scheme (e.g. 1:1, factorial, multiple pooling)? 

• Evaluation questions applicable to integrated and to conservation programs 

• What is the incubation water source? (Essential IC, annually) 

Evaluation questions applicable to both integrated and segregated programs and to conservation

programs 

• How are families incubated? 

b) Biological Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• How does fertility, eyeing, hatch time, emergence timing and egg survival of hatchery fish 

compare to their naturally spawning counterparts? 

c) Fish Health

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the source of water in the incubation containers (well water, surface water, etc.)? 

• Are other salmonids of the same or other species present in the source water? 

• What diseases are indigenous to the source water? 

• What are the egg densities? 

• What is the diurnal temperature cycle in the incubators? 

d) Hatchery and Receiving Environment

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 
Monitoring & Evaluation Criteria D-13

• What is the percent egg mortality per day? 

• What are the cause(s) of egg losses (poor fertilization, disease, environmental, etc)? 

• What is the diurnal temperature cycle in the incubators? 

• What type of substrate used in incubators? 

f) Ecological Effects

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Will the juveniles resulting from the egg take equal or exceed the habitat carrying capacity

(quantity and quality of rearing habitat and accessibility)?

• What are the progeny to parent ratios of the hatchery and naturally spawning populations? 

• How are dead eggs collected and disposed of? 

• If maintained on-site, are the eggs sequestered under quarantine conditions? 

Monitoring Criteria for Incubation by Species/Race/Stock: 

For all programs determine and/or record: 

1. Incubation water source, flow, temperatures, and water quality by lots (to estimate 

developmental rates) - daily

2. Spawning dates, hatching dates, ponding dates by lots (to estimate developmental rates) - 

annually

3. Counts of fertilized eggs, eyed eggs, dead eggs, and ponded fry (to estimate survival by lots) - 

annually

4. Incubator type, substrate used, number of eggs per incubator - by lot 

5. Size of fry and % yolk absorption at ponding - by lot

6. Method of disposal of eggs - by lot 

7. Presence of pathogens in water - when water source changes 

8. Egg treatments (by event); disinfection procedures for incubating eggs, incubators, 

equipment, effluent water, and personnel - by lot 

In addition for integrated and conservation programs determine and/or record:

1. How families (or family groups) of eggs are incubated - annually

2. Hatching dates, developmental rates for natural population - annually
D-14 Monitoring & Evaluation Criteria 

REARING

a) Genetic Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What hatchery rearing protocols are used? 

• What is the mean size (length & weight) and length frequency distribution at release? 

• Are families reared individually? 

• What protocols are used to randomize distribution of family groups? 

• What culling procedures are used? 

Evaluation questions applicable to both integrated and segregated programs and to conservation

programs 

• What biosecurity procedures are used to minimize the risk of catastrophic loss during juvenile 

rearing? 

• Are families reared individually? 

• What protocols are used to randomize distribution of family groups? 

• Evaluation questions applicable to integrated programs and to conservation programs 

• What protocols are used to randomize distribution of family groups? 

• How long are fish reared in hatchery environment? 

b) Biological Conditions 

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Are growth patterns of hatchery fish similar to natural counterparts? 

• Does the rate of development compare favorably with natural fish in the receiving 

environment? 

Evaluation questions applicable to integrated programs and to both conservation and harvest 

programs 

• How does the hatchery water temperature cycle vary from ambient stream conditions? 

• Are the fish reared and incubated on ground water? 

• Are hatchery work/security lights used at night to extend the normal photoperiod? 

• What is the feeding regimen (times per day, amounts in %bow/day, etc.)? 
Monitoring & Evaluation Criteria D-15 

• Is environmental enrichment (cover, structure, substrate, etc.) employed and are the fish 

conditioned to avoid predators? 

c) Fish Health 

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the source of water in the rearing containers (well water, surface water, etc.)? 

• Are other salmonids of the same or other species present in the source water? 

• What diseases are indigenous to the source water? 

• Based on water flow, numbers and biomass of fish, what are the loading and densities? 

• What are the diurnal and seasonal temperature cycles in the raceways/ponds? 

• What is the date and developmental stage of fish at time at the time of vaccination? 

• What type, dosage and method of delivery of drugs and therapeutants used to treat diseases? 

d) Hatchery and Receiving Environment 

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Are settleable solids, unused feed and feces periodically removed to ensure proper cleanliness 

of rearing container? 

• Does the operator follow proper feeding rates, conduct periodic feed quality analysis, and 

store feed under proper conditions to prevent nutritional disorders? 

• Are appropriate physical and chemical characteristics of water inflow and effluent (suspended 

solids, temperature, dissolved gases, pH, mineral content, and potential toxic metals) 

maintained to promote growth and survival? 

• Are accurate fish inventory data maintained (e.g. Hat-Pro) with a minimum of handling stress? 

• Are appropriate flow and density indexes maintained for the species and life stage being 

reared? 

• Is the correct amount and type of food provided to achieve the desired growth rate, body 

composition, and condition factors for the species and life stage being reared? 

e) Hatchery Structures 

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the extent of the riparian zone in the immediate vicinity of the hatchery? 

• What is the quality of the riparian habitat impacted by hatchery structures? 
D-16 Monitoring & Evaluation Criteria 

• How much riparian habitat has been lost or impacted by hatchery structures and what actions 

have been taken to mitigate for this loss? 

• Is the hatchery in compliance with limitations established in National Pollution Discharge 

Elimination System permit for hatchery wastewater discharge? 

• Does the hatchery and effluent water meet water quality standards for normal growth & 

survival of the cultured species? 

• What are the objectives of the mitigation plan? 

• Is there a monitoring component to the mitigation plan? 

f) Ecological Effects 

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Will the resulting juveniles equal or exceed the habitat carrying capacity (quantity and quality 

of rearing habitat and accessibility)? 

• How are dead fish collected from the raceways/ponds and disposed of? 

• If maintained on-site, are the dead fish sequestered under quarantine conditions? 

g) Genetic Interactions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the source of rearing water? 

• What is the range in size and smoltification at release? 

• Is the rate of development just prior to release adequate to maximize homing fidelity? 

• Are acclimation ponds used? 

i) Contribution to Harvest

Evaluation questions applicable to both integrated and segregated programs and to harvest

programs 

• Are facility and species-specific recommendations for water quality, temperature, loading, and 

density followed to maximize recruitment to fisheries? 
Monitoring & Evaluation Cri tion Criteria D-17

Monitoring Criteria for Rearing by Species/Race/Stock: 

For all programs determine and/or record: s determine and/or record: 

1. Count of fish Count of fish at pondi at ponding or subsequent p subsequent pooling - by lot/fam ooling - by lot/family group at each event group at each event 

2. Culling num Culling numbers and ers and methods - each event ods - each event 

3. Water source Water sources, flows, volumes - a s, flows, volumes - as changes occur ges occur 

4. Temperatures, dissolved o eratures, dissolved oxygen levels - daily ygen levels - daily 

5. Pond types, substrate, structure, cover, pond ypes, substrate, structure, cover, pond cleaning frequenc cleaning frequency - as changes occur as changes occur 

6. Incidents of security Incidents of security or other kinds of failures affectin or other kinds of failures affecting rearing survival - by g rearing survival - by event 

7. Length and weight distribution (e.g. from random samples of 100 fish) - weekly/monthly

(varies by species and life stage) 

7. Length and weight distribution (e.g. from random samples of 100 fish) - weekly/monthly

(varies by species and life stage) 

8. Mortalities - Daily

9. Status of sm Status of smoltification (silvering, m oltification (silvering, migratory behavior) - weekly or) - weekly during sm during smoltification oltification 

10. Rearing Rearing methodology odology, including: densiti densities, durati es, duration, behavioral conditioning - behavioral conditioning - annuall annually by lot

11. Kinds and quantities of herbicides and pestic Kinds and quantities of herbicides and pesticides used ides used in riparian zone- each even in riparian zone- each event 

12. Kinds, quantities, and procedures of chemicals and drugs used for fish treatments and for 

disinfecting ponds, equipment and personnel - each event 

12. Kinds, quantities, and procedures of chemicals and drugs used for fish treatments and for 

disinfecting ponds, equipment and personnel - each event 

13. Water quality upstream and downstream: temperature, dissolved oxygen, pH, ammonia, 

nitrite, phosphorus, hardness, alkalinity, total suspended solids, settleable solids, and water 

flow through facility - as needed and consistent with NPDES 

13. Water quality upstream and downstream: temperature, dissolved oxygen, pH, ammonia, 

nitrite, phosphorus, hardness, alkalinity, total suspended solids, settleable solids, and water 

flow through facility - as needed and consistent with NPDES 

14. Feeding regi Feeding regimes: diet and ration, schedule (b mes: diet and ration, schedule (by lot), results of feed qualit esults of feed quality analyses - annually es - annually

15. Types and concentrations of contaminants in water source(s) (e.g. of dioxins, PCBs, dieldrin, 

mercury, cadmium, lead) - as needed 

15. Types and concentrations of contaminants in water source(s) (e.g. of dioxins, PCBs, dieldrin, 

mercury, cadmium, lead) - as needed 

16. Method of Method of disposal of culls and m sposal of culls and mortalities - by ies - by event for each lot for each lot 

17. Presence of Presence of microbial pathogens and microbial pathogens and parasites in water suppl ites in water supply - as changes occur changes occur 

18. Fish health exam Fish health examinations - m inations - monthly

19. Incidence of observed predation o Incidence of observed predation on hatchery fish - fish - by event 

In addition for In addition for captive brood captive brood programs, determine and record: d record: 

1. Length, weig Length, weight and m ht and maturity of in turity of individuals - annually als - annually 

2. Day length - daily

3. Spermatocrit, sperm tocrit, sperm motility, egg tility, egg quality, fecundit y, fecundity, egg size egg size 

4. Individual pedigrees 

In addition for integrated programs, determine and record: 

1. Length and weight distribution for naturally produced fish (e.g. from random samples of 100 

fish) - weekly/monthly (varies by species and life stage) 

1. Length and weight distribution for naturally produced fish (e.g. from random samples of 100 

fish) - weekly/monthly (varies by species and life stage) 

2. Status of smoltification for naturally produced fish (silvering, migratory behavior) - weekly

during smoltification 

2. Status of smoltification for naturally produced fish (silvering, migratory behavior) - weekly

during smoltification 

3. ATPase on hatchery ATPase on hatchery fish - fish - every two weeks until pattern is established. weeks until pattern is established. 

4. Cryptic coloration - at release 

Monitoring Criteria for Rearing by Species/Race/Stock: 
D-18 Monitoring & Evaluation Criteria 

RELEASE

a) Genetic Conditions

Evaluation questions applicable to integrated programs and to both conservation and harvest 

programs 

• When does natural out migration occur? 

b) Biological Conditions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• How do the size and growth parameters the cultured fish compare to the natural fish? 

• What are the fish’s energy stores (whole body proximates, liver glycogen, hepatosomatic 

index)? 

• What is the developmental stage of the released fish (fry, pre-smolt, smolt, precocity)? 

• Does the rate of smolt development compare favorably with natural fish in the receiving 

environment? 

• What is the age at release? 

• What is their swimming efficiency (stamina, stride efficiency)? 

Evaluation questions applicable to integrated programs and to both conservation and harvest

programs 

• When does natural out migration occur? 

• When and how are hatchery fish liberated? 

d) Hatchery and Receiving Environment

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the origin of the broodstock (SASI stock, GDU membership; include both major and 

minor sources)? 

• What is the distribution of release sites both in and out of the basin? What is the disease 

history of the juveniles over the last decade? 

• What are the most serious pathogens in terms of pre-release mortality? 

• Are the fish certified and appropriate responsible parties notified? 

Evaluation questions applicable to both integrated and segregated programs and to harvest 

programs 
Monitoring & Evaluation Criteria D-19 

• What are the number and size of fish released by location, time & date? 

• How many fish were marked/tagged? 

• What is the tag type & tag code(s) (cwt, PIT, otolith, etc.)? 

• What is the percent of marked and tagged fish in the fishery? 

• What is the contribution to the fishery? 

f) Ecological Effects

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What pathogens are present and what is their prevalence in the populations? 

• Were diseases present? 

• What drugs and chemotherapeutants were used and what were the treatment protocols? 

• Did the drugs/chemotherapeutants used to trace the disease(s) conform to recommendations of 

the attending fish pathologist? 

• How were the fish released (mass, volitional, staggered)? 

• What are the similarities/dissimilarities between wild and hatchery fish regards size, timing, 

and duration of release period? 

• Is there sufficient attraction water at the hatchery or stream reach to adequately imprint the 

migrants? 

• Are natural fish entering the hatchery facility? 

• What numbers, species and life stages of natural fish bypass hatchery structures? 

• What is the magnitude of fish release (numbers, size, biomass, etc.)? 

• Do these cultured fish exceed the carrying capacity of the receiving stream, and is there excess 

carrying capacity? 

• Are receiving habitats in properly functioning condition? 

• How do the size and growth parameters the cultured fish compare to the natural fish? 

• What are the fish’s energy stores (whole body proximates, liver glycogen, hepatosomatic 

index)? What is the developmental stage of the released fish (fry, pre-smolt, smolt, precocity)? 

• Does the rate of smolt development compare favorably with natural fish in the receiving 

environment? 

• What is the age at release? 

• What is their swimming efficiency (stamina, stride efficiency)? 

• If planted out (trucking, barging, release site, etc.), where are the fish released in the target 

watershed, and what is the distribution and density of natural fish within that watershed? 

• Are fish released into properly functioning habitat? 

• If planted out (trucking, barging, release site, etc.), where are the fish released in the target 

watershed, and what is the distribution and density of natural fish within that watershed? 
D-20 Monitoring & Evaluation Criteria 

• Are acclimation ponds used? 

• If released at the hatchery, what is the manner of release (volitional, staggered, forced, etc)? 

• What is the magnitude of fish release (numbers, size, biomass, etc.)? 

• Do these cultured fish exceed the carrying capacity of the receiving stream, and is there excess 

carrying capacity? 

• If planted out (trucking, barging, release site, etc.), where are the fish released in the target 

watershed? 

• Are acclimation ponds used? 

• If released at the hatchery, what is the manner of release (volitional, staggered, forced, etc)? 

• Is there sufficient attraction water at the hatchery or stream reach to adequately imprint the 

migrants? 

• If planted out (trucking, barging, release site, etc.), where are the fish released in the target 

watershed, and what is the distribution and density of natural fish within that watershed? 

• Are fish released into properly functioning habitat? 

• What is the magnitude of fish release (numbers, size, biomass, etc.)? 

• Do these cultured fish exceed the carrying capacity of the receiving stream, and is there excess 

carrying capacity? 

• What is the magnitude of fish release (numbers, size, biomass, etc.)? Do these cultured fish 

exceed the carrying capacity of the receiving stream, and is there excess carrying capacity? 

• How do the size and growth parameters the cultured fish compare to the natural fish? 

• What are the fish’s energy stores (whole body proximates, liver glycogen, hepatosomatic 

index)? 

• What is the developmental stage of the released fish (fry, pre-smolt, smolt, precocity)? Does 

the rate of smolt development compare favorably with natural fish in the receiving 

environment? 

• What is the age at release? 

• What is their swimming efficiency (stamina, stride efficiency)? 

• What is the prevalence of disease in co-mingling wild and hatchery fish? 

• How do the hatchery fish interact with their natural counterpart (territoriality, displacement, 

foraging ability, etc.)? 

• How are the fish likely to be impacted by water quality and the riparian zone? 

• Is there a management plan for vegetation, herbicide and pesticide use, and surface water 

allocation? 

g) Genetic Interactions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 
Monitoring & Evaluation Criteria D-21

• How are fish released?

• What treatments are used to encourage homing fidelity? 

i) Contribution to Harvest

Evaluation questions applicable to both integrated and segregated programs and to harvest

programs 

• What is the contribution to the fishery?

• (How many fish were marked/tagged? 

• What is the tag type & tag code(s) (cwt, PIT, otolith, etc.)? ) 

Monitoring Criteria for Release by Species/Race/Stock: 

For all programs determine and/or record: 

1. Release method, locations, life stage, length and weight (for individuals in random 100 fish 

sample), and result of required pre-release fish health tests, smoltification - by event 

2. Numbers and types of marks and tags used (to distinguish among segments of the hatchery

populations and between hatchery and natural populations) - by lot

3. Approximate numbers of precocious males - by lot 

4. Health status prior to release or transfer, and disposition of diseased fish -by lot 

5. Disease treatments prior to release (type, date and duration) - by lot 

6. Distribution of naturally-produced and hatchery juvenile fish in the receiving habitat - 

periodically

7. Quantity and quality of the receiving marine and freshwater habitat - annually.

8. Distribution of other potentially affected species 

9. Behavioral characteristics of released fish and their interaction with naturally produced fish 

through feeding behavior, aggressive behavior, group size, territory size, and habitat use 

In addition for integrated programs, determine and record: 

1. Natural outmigration timing (date and duration) - annually

2. For naturally produced fish, length, weight (for 100 fish) - annually

3. For naturally produced fish, timing of smoltification (silvering, migratory behavior) - 

annually

4. For naturally produced fish, nutritional condition (proximate composition, liver glycogen) - 

annually
D-22 Monitoring & Evaluation Criteria 

ADULT RETURN

e) Hatchery Structures

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• Is there unimpeded passage for wild fish through hatchery structures and bypass reaches? 

• What species of salmonids and non-salmonids use the migratory corridor past the hatchery? 

• Are there hatchery structural barriers to upstream passage or entry to hatchery? 

• Is there adequate stream flow below the hatchery water intake and in the by-pass reach to 

allow passage of adults upstream? 

• Are there thermal or odorant barriers that impede or block upstream migration? 

• Is there sufficient upstream spawning habitat to attract adults to the upstream reaches? 

Evaluation questions applicable to integrated and to conservation programs 

• What is stream carrying capacity? 

• Do adults adequately utilize habitat capacity? 

g) Genetic Interactions

Evaluation questions applicable to both integrated and segregated programs and to both 

conservation and harvest programs 

• What is the extent of straying of hatchery fish into natural spawning areas 

• What measures are used to control straying and/or natural spawning of hatchery fish? 

• What is the extent of straying of naturally produced fish into the hatchery? 

• What measures are used to control attraction of wild fish into the hatchery? 
Monitoring & Evaluation Criteria D-23

Monitoring Criteria for Adult Return by Species/Race/Stock:

For all programs determine and/or record: 

1. Potential barriers to upstream migration of adults and movement of adults into and past the 

hatchery - annually

2. The number of HORs from any hatchery program found in spawning areas, and the number 

of NORs attracted into the hatchery - annually

3. Straying rates of individual hatchery populations - periodically

4. Reproductive success of HORs from a particular hatchery program in nature - periodically

5. Abundance and distribution of hatchery- and natural-origin spawners - annually 

Regional Information Key Questions Form E-1 

E. Regional Information Key Questions Form 

This form is provided to regional participants not affiliated with the management agencies, to guide 

them in assembling information for the HSRG’s regional briefing book. 

The HSRG feels it is essential to receive input or knowledge from those who are most familiar with 

the region and its hatchery system. Having been identified as one of these persons, you are requested 

to provide written information for a Regional Briefing Book to be provided to the HSRG. The HSRG 

is requesting information on: 1) regional management goals for conservation, harvest, and other 

priorities; 2) stock status (biological significance and viability of salmonid populations within the 

region); 3) habitat; and 4) hatchery programs. 

The HSRG and regional managers have divided natural and artificially propagated anadromous 

salmonids in the region into appropriate individual stocks (see attached list), reflecting management 

units. It is at this level that the HSRG requests you to provide information. The HSRG will provide 

their evaluations and recommendations based on the stock management goals provided by this same 

grouping. 

Below are a series of questions the HSRG would like you to address. Address any or all questions for 

which you have pertinent information. Please provide this information in memo form, with author, 

affiliation, date, and sources noted. Please provide soft copy in Microsoft Word or Rich Text Format 

to Michael Kern, mkern@lltk.org. 

1. Do you feel that the conservation, harvest, and other goals for the region’s hatchery system 

are appropriate, given current habitat conditions and other factors? If not, what adjustments 

or suggestions do you have to resolve the conflict? 

2. Are monitoring and evaluation programs adequate to determine if goals are being met? 

3. Do you see the quality of the habitat in this region changing for the worse or better in the next 

ten to twelve years? Fifty years? What are the long-term goals for habitat in this region? 

4. Using the definitions given below, what would your overall rating be for the habitat available 

to each sub-regional species? Please provide using the table format below, one table per subregional species. The general habitat ratings are defined as: 

a. High (H) = Healthy: Productivity of the target species is high and the population is 

capable of growth and supporting significant terminal harvest. 

b. Medium (M) = Limiting: The target species is productive enough for the population to 

sustain itself at a low level terminal harvest. 

c. Low (L) = Inadequate: The target species is unproductive and the population will go 

extinct, even without terminal harvest. 
E-2 Regional Information Key Questions Form 

Sub-Region Species: 

Spawning Habitat Freshwater Rearing 

Habitat 

Migration Habitat Estuarine 

Habitat 

Hatchery Wild Hatchery Wild Hatchery Wild 

Rating 

(H/M/L) 

5. Are there exceptions or “islands” of greater or lesser productivity in this sub-region that the 

HSRG should be aware of in reviewing the hatchery programs? 

6. Are there habitat improvement projects that could elevate the rating for this sub-region or that 

could elevate the productivity of “islands” of inferior production within this sub-region? If so, 

what are they and are they in the proposed or planning stages? 

7. How would you rate the stock status (biological significance and population viability) of each 

sub-regional species (high, medium or low)? Please provide using the table format below, one 

set of ratings per sub-regional species. For biological significance, please take into account 

factors such as whether the species is native to the watershed; whether it exhibits any unique 

or distinctive biological attributes that are not shared with other stocks within the GDU; and 

the history of introductions, hatchery fish releases, and hatchery fish strays from other 

watersheds. For population viability, high = healthy, medium = at risk, low = critical. 

Sub-Region Species: Sub-Region Species: Sub-Region Species: Sub-Region Species: 

Biol. 

Sig. 

 Viability Biol. Sig. Viability Biol. Sig. Viability Biol. Sig. Viability 

Rating (H/M/L) 

8. How well are current hatchery programs contributing towards meeting regional goals? In the 

future, could hatchery programs make better or different contributions toward meeting these 

goals? 

9. Are regional hatchery facilities designed and operated to optimize benefits to and reduce 

negative interactions with naturally produced stocks? 

10. In your opinion, what is the most valuable use of these facilities for the future? 
Regional Information Instruction Form F-1 

F. Regional Information Instruction Form 

This form is provided to regional participants from the management agencies, to guide them in 

assembling information for the HSRG’s regional briefing book. 

Purpose 

This document provides information to the co-managers regarding the Hatchery Reform Project and 

the Regional Review Process. This document asks the co-managers questions about hatchery-related 

regional issues. Replies to these questions will be compiled in a briefing book. This book will enable 

the scientists participating in the Hatchery Reform Project to make recommendations for hatchery 

facilities and programs within Washington’s Puget Sound and coastal regions. 

Benefits 

The managers will receive as a result of this review of the hatchery system: 1) independent appraisal 

of the regional hatcheries; 2) documentation of their existing and potential benefits to both salmonid 

conservation and sustainable fisheries; 3) documentation and tools for evaluating potential risks of 

hatchery programs; and 4) recommendations for improvement. These will be in the form of a written 

report. Implementation of these recommendations will be made possible through Washington state and 

US Congressional legislative appropriations and private sector resources. To date, Congress has 

provided $12.6 million for this effort. 

The regional review process involves the following steps: 

1. Managers identify regional and other agency support staff to participate in regional review. 

The facilitation team creates and maintains a regional participant contact list. 

2. Managers and others (such as funding entities) meet with the HSRG and the facilitation team 

to introduce the regional review process and to discuss issues and concerns specific to this 

region. 

3. Managers receive this form; other interested parties receive the HSRG Key Questions form. 

4. Agency staff meet internally and with other regional participants to discuss the best method to 

assemble the information requested on this form. 

5. Managers submit the requested information to the facilitation team who compile it into the 

Regional Briefing Book. 

6. The facilitation team visits and photographs the region and its facilities prior to the regional 

review. 

7. The facilitation team works with regional participants to design a regional tour for the 

beginning of the regional review. 

8. HSRG and facilitation team tour the region’s hatchery and other relevant sites, meeting with 

managers along the way. This regional tour is first day or more of the review. 

9. Managers meet with the HSRG to discuss the regional habitat and goals as they relate to 

hatchery programs. This is primarily to clarify information and gather new data as needed. 
F-2 Regional Information Instruction Form 

10. The HSRG finishes their review and gives regional managers their preliminary 

recommendations verbally in an informal meeting (last day of the schedule review). 

11. Regional managers meet to consider the HSRG’s preliminary recommendations and provide 

feedback prior to the report writing process. 

12. HSRG drafts its report to include recommendations for all regions reviewed. 

13. The draft report is provided to the management agencies to allow them an opportunity to 

include a response to each set of recommendations, including their implementation plans. 

14. Regional review report is provided to the managers, US Congress, Washington state 

legislature and other appropriate parties. 

15. Available funding is prioritized for implementation of recommendations. 

Regional Information Briefing Book – What We Need From You 

The HSRG feels it is essential to receive answers to their questions from the regional managers and 

staff that are most familiar with the region and its hatchery system. Your peers have identified you as a 

regional expert. The HSRG requests your written responses to the questions on this form for a 

Regional Briefing Book. We encourage working together to avoid duplication of efforts and use 

existing documents such as HGMPs, planning documents, etc. as source material (cut and paste as 

needed). The HSRG recognizes that some information may be incomplete, anecdotal, or not well 

documented – it is still important and should be included. If you have little or no information for a 

particular question, please give the information you do have. The HSRG may recognize a lack of 

information, and the corresponding need to learn more as a part of their recommendations. 

 

This Regional Briefing Book will be provided to the HSRG and regional participants in advance of the 

review for your region. You will be provided with due dates and information on where to send the 

material. Please provide the information as soft copy in Microsoft Word or Rich Text Format with 

author(s), affiliation(s), sources, and date noted. You will also be requested to meet with the HSRG to 

participate in the review. 

The HSRG is requesting information on: 

A. Habitat 

B. Salmon and steelhead stock status – both hatchery and wild 

C. Management goals for harvest, conservation and other priorities 

D. Current hatchery programs. 

The HSRG and regional managers will work with you to divide natural and artificially propagated 

anadromous salmonids into appropriate individual stocks. The grouping should reflect management 

units. The HSRG will provide their evaluations and recommendations based on the stock management 

goals provided by this same grouping. 

Questions: WDFW or NWIFC hatchery reform staff members or the facilitation team staff (Kathleen 

Hopper at 206-382-9555 ext. 24, Michael Kern at 206-382-9555 ext. 25, or Michael Schmidt at 206-

382-9555 ext. 26) can be contacted for more information. 
Regional Information Instruction Form F-3 

A. General Description of the Region 

This description is a general overview of the region for the members of the HSRG who are unfamiliar 

with your area. Use existing material if it is available (such as Watershed Lead Entity documents). 

Provide a general narrative description of the regional landscape. This description should include, if 

available: watershed topography, rivers and significant tributaries, land ownership, and land use. 

Feel free to use maps. We ask that this description be as concise as possible. 
F-4 Regional Information Instruction Form 

B. Status of the Habitat by Stock 

Appropriate habitat or other agency policy staff should answer the following questions for each 

hatchery and naturally spawning stock: 

1. Please fill out the table below for each stock using the general definitions provided: 

Stock Name: 

Spawning Habitat Freshwater Rearing 

Habitat 

Migration Habitat Estuarine 

Habitat 

Hatchery Wild Hatchery Wild Hatchery Wild 

Rating 

(H/M/L) 

Three categories of habitat are defined in terms of conditions that support the target stocks, with the 

assumption that these conditions would also provide for the needs of other native stocks of salmonids 

(assume that pre-terminal harvest is part of the environment during the fish’s whole life cycle). 

These habitat ratings are: 

a. High (H) = Healthy: Productivity of the target stocks is high and the population is 

capable of growth and supporting significant terminal harvest. 

b. Medium (M) = Limiting: The target stocks is productive enough for the population to 

sustain itself at a low level terminal harvest. 

c. Low (L) = Inadequate: The target stocks is unproductive and the population will go 

extinct, even without terminal harvest. 

2. Are there exceptions or “islands” of habitat that are in better or worse condition and do not 

correspond with the rating given in question? 

3. What habitat improvement projects could elevate the rating for this sub-region or the “islands” of 

inferior production? If so, please list them and indicate if they are in the proposed or planning stages. 

4. Do you see the quality of the habitat in this region become better or worse in the next ten to twelve 

years? Fifty years? What are the long-term goals for habitat in this sub-region? 

5. What other habitat information should the HSRG consider (for example, salmonid or non-salmonid 

stocks not native to the watershed)? Please describe. 
Regional Information Instruction Form F-5 

C. Status of the Salmonid Stocks 

 

Appropriate management or other agency policy staff should answer the following questions for 

each hatchery and naturally spawning stock: 

I. Trends 

Please answer the following for each stock. 

1. Fill out a table as completely as possible that resembles the template below. We will generate 

a general trend for this stock with this information. 

Y ear S u r v i v a l C a t c h E scap e m e n t

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

1 9___

2 0___

2 0___

F i l l O u t T h i s T e m p l a t e
F-6 Regional Information Instruction Form 

2. What is the age class structure of this stock (by sex) and do historical data exist on potential 

changes over time? For example, five year-old adults may have constituted 20% of returning 

adults 30 years ago, but those fish may now be rare. 

3. Do you know if hatchery origin fish comprise a portion of natural spawning fish? If so, please 

give your estimation of the number of hatchery spawners and a timeline. These numbers can 

be estimated through escapement or carcass counts. 

4. For hatchery stocks - what proportion of hatchery eggs, fry or adults are from wild fish or 

another hatchery? 

5. Is this stock a coded wire tag index stock? If not, which index stock is it most closely aligned 

with? Provide any additional relevant information from previous coded wire tag groups. 
Regional Information Instruction Form F-7 

II. Biological Significance 

Please answer the following for each stock: 

1. Within each watershed, what is the history of introductions (e.g. stock transfers), hatchery fish 

releases, and hatchery fish strays from other watersheds? 

a. Are naturally spawning populations considered “native” with little or no history of 

stock transfers, introductions, or artificial propagation within the watershed? or 

b. Have little or no stock transfers occurred, but the species has been artificially 

propagated within the watershed to some extent (how extensive has artificial 

propagation been?)? or 

c. Have significant stock transfers into the watershed occurred historically, with the 

potential for significant interbreeding between native and introduced fish? or 

d. Was the species extirpated from the watershed historically, but stock introductions 

reestablished the species within the watershed? or 

e. Is the species not native to the watershed, but currently exists as a naturalized 

population resulting from past stock transfers? 

2. Biological Attributes - Does the stock exhibit any unique or distinctive biological attributes 

within the watershed with respect to life history characteristics (e.g. age/size at maturity, run 

timing, freshwater migration distance, morphology, physiology, disease resistance, genetics, 

etc.?) Use the following questions to guide your answer: 

a. Are the distinctive traits potentially irreplaceable or not typical of other stocks within 

the same GDU? Or 

b. Does the stock have no unique, biological attributes but share some unique attributes 

with other stocks in the same GDU? Or 

c. Are all known biological attributes shared with other GDUs? 

3. Population Subdivisions - How diverse is the metapopulation structure within the watershed? 

Use the following questions to guide your answer: 

a. How many distinct spawning aggregations (e.g., tributary creeks) exist within the 

stock under consideration? 

b. What genetic data exist for this stock? Please provide agency reports or publication 

citations that contain these data, or provide summary tables of population allele 

frequencies if such reports or publications do not exist. 

c. What is the total number of stocks within the same GDU as the stock under 

consideration? 

d. What it the mean and range of viabilities (i.e. status) of the other stocks within the 

same GDU? 
F-8 Regional Information Instruction Form 

D. Co-Manager Goals for Salmonid Stocks 

Appropriate management or other agency policy staff should answer the following questions for 

each hatchery and naturally spawning stock: 

1. For each hatchery stock program, is the program goal conservation, harvest or both? 

2. Please list your harvest management goals for each of the following time frames: present day, 

short-term (10 years in the future) and long-term (50 years in the future.) Use the following 

definitions for harvest goals: 

High – harvest opportunity each year, spread over seasons 

Medium – opportunity most years, for some seasons 

Low – occasional opportunity, single run 

0 – no harvest opportunity 

Goals Present Short-Term Long-Term 

Harvest 

Opportunity 

 

3. What are your conservation goals? The answer to this question is typically qualitative. The 

answer should include local as well as regional (i.e., ESU) and/or statewide goals for each 

stock. 

4. For hatchery programs, please summarize the production goals: 

a. How many fish at what size are planned for release? Transferred off-station? 

b. Where are eggs taken and incubated? Where are fish reared and released? 

c. Does this program stay relatively constant or does it change regularly? If it changes, 

what is the process for this change? 

d. Is the duration of this program clearly defined? 

5. Are there other goals for this stock that are important to the co-managers? Some examples 

include: use of a stock as an indicator for survival or fishery contribution, cultural importance 

to tribal members, educational programs, mitigation for lost habitat or access to spawning 

area, scientific research, etc. 

6. Do you have a monitoring and evaluation program that is adequate to determine if the goals 

are being met? If so, please describe. 

7. Are the current goals being achieved? What are the levels of achievements being realized for 

each of these goals? 

8. Is there a conflict between the present goals based upon current management practices or 

habitat conditions? If so, what adjustments or suggestions do you recommend (example: 

hatchery coho production vs. natural chum production)? 

9. Are regional decisions based upon adaptive management? How do you incorporate new 

information to adjust existing programs and goals? 
Regional Information Instruction Form F-9 

E. Current Regional Hatchery Programs 

Appropriate hatchery or hatchery support staff should answer these questions with regard to 

current hatchery programs. 

The first set of questions deals with the general features of each hatchery facility that could affect all 

stocks and activities on station. There should be one set of answers per facility. (Questions 1 through 

9, 20) 

The second set of questions is for each stock that you rear or handle on site. (Questions 10 through 19) 

You can “lump” stocks if the same answer applies. For example, if all your eggs on site are incubated 

in a similar manner, state that the answer will, “Apply To All Stocks.” 

For hatchery stocks that are reared and/or transferred between sites, provide a summary set of answers 

for that stock, rather than splitting up the answers between facilities (include a chart or other graphic to 

express what stage of culture takes place at what site). If a stock released at your site is reared for part 

of the time outside of the region, please include this same information for that facility. 

One answer per facility – questions 1-9 

1. Describe the property location and ownership. Give the funding and operating organization 

names, approximate size of the property (acres), number of buildings, any unique attributes of 

the site worth noting. 

2. What is the primary goal of the facility? (Examples: conservation of Shirley creek summer 

chum because of degraded habitat, harvest augmentation of Michael River coho salmon 

primarily for north Puget Sound commercial fisheries, community education) 

3. What stocks of fish are handled and/or reared at this facility? 

4. Describe the water supply, including the following components: 

a. Each water source: Available flow – stable, increasing, decreasing? Spring, well, 

surface? Normal year’s temperature regime? Pumped or gravity flow? Water 

chemistry profile, if available? 

b. If surface water, is it fish- or specific-pathogen free? Do you experience problems 

with “dirty water” that limits your ability to reach your goals? 

c. Surface water intake structures on station – are they screened or sited in a way that 

excludes fish or other animals from entering the water supply? 

d. If you use surface water, is there adequate water in the by-pass reach throughout the 

year? 

e. Are there unique physical characteristics of the water supply on site or nearby that 

you feel should be noted? 

5. Describe the fish health/pathogen history, including the following components: 

a. How often does a fish health professional visit your site? 
F-10 Regional Information Instruction Form 

b. What is the most significant fish health problem at your facility (this could be a fish 

pathogen, inability to correct a situation, poor water, etc.)? 

c. Have you had any significant epizootics on your facility? Please explain. Were you 

able to isolate the affected containers? Sanitize the effluent? 

d. Do you have a history of viral isolations at your facility in the past five years? This 

excludes epizootics as described above. 

e. Do you disinfect equipment between rearing units or banks of ponds? What method do 

you use? 

f. Are you able to keep distinct lots or stocks of fish physically separated? Please 

answer for each of these life stages – adults, eggs, and juveniles. 

6. Describe the waste removal/pollution abatement system including the following components: 

a. What is the general frequency of pond cleaning? 

b. How is pond waste disposed of (vacuum, brush, dry and remove, etc.)? 

c. Describe pollution abatement pond or settling pond, if one exists. 

d. Status of permits for discharging pollutants? 

e. Any particular challenges you would like to share on this subject? 

7. Other general questions: 

a. What are your predator control methods/facilities (nets, wires, etc)? Do you have 

unresolved predator problems? 

b. Describe how you inventory your fish (frequency, size of weight sample, etc.). 

c. How do you keep your inventory and other data? (Hatpro, spreadsheets of your own, 

agency forms, etc.) 

d. How do you decide which food to use (mandatory contract, fish health 

recommendations, etc.)? 

e. How do you store your feed? 

f. Does your facility have any habitat improvements on site (wetlands, riparian 

improvements, etc.)? 

8. Education – please give details regarding the following: 

a. Is your facility open to the public? 

b. Do you have signs, pamphlets, or other materials for the public to self-tour? 

c. Do hatchery staff or others schedule and conduct tours of the facility? 

d. Are there citizen involvement opportunities such as volunteer programs, student 

interns, etc? 

e. Are hatchery operations visible to facility visitors? 

f. Do other fish and wildlife programs use the facility? 

g. Do you have regular involvement with community or school groups? 

h. Do you give fish or eggs to educational groups? If so, please estimate the amount of 

time this activity takes. 

9. General Administration 

a. Does key staff have a good understanding of the facility goals, budget, and 

expenditures? If not, what tools do you need for correcting this? 
Regional Information Instruction Form F-11 

b. Is new relevant information from research and other sources made available to 

hatchery staff and used for attaining goals? 

c. As fish culture and other related scientific understanding evolves, are you able to 

make changes to your programs? If not, what ideas do you have for changing this?

d. Are there state or federal laws that constrain the program, such as numbers and size 

of smolts produced?

One answer per hatchery stock (Questions 10-19) .The production goals for these stocks are 

summarized under “Co-Manager Goals for Salmonid Stocks”, question 4. 

10. Describe the broodstock as follows: (These may be a repeat of some questions asked under 

stock status - you may refer to those answers or cut and paste.) 

a. How was the broodstock chosen? 

b. Do you consider it an integrated (goal is to maintain a single gene pool and prevent 

divergence) or segregated (isolated in the hatchery ,managed to restrict gene flow) 

population? 

c. Does this broodstock have a history of reportable pathogens? 

d. Are you are able to collect representative samples each year of the population, with 

respect to size, age, sex ratio, and run and spawn timing? If not, please explain the 

limitation. 

e. What has your run size been for the last five years? 

f. What is the sex ratio at spawning? 

g. Do you have any information on the sex ratio by age? If so, please provide. 

11. Describe the broodstock collection process, including the following components. Differentiate 

by Natural Origin Recruit (NOR) and Hatchery Origin Recruit (HOR) if they are collected in 

a different manner: 

a. Describe/give the location of adult collection relative to the physical plant where fish 

are held or spawned? 

b. Describe how fish are collected (ladder, sorter, trap, in river, etc.) 

c. Do you have the ability to handle or sort individual fish? If so, please describe your 

process. 

d. If you transport adults from one site to another, describe method of transport. Have 

you had problems with mortality from handling because of this? 

e. If the fish enter the adult holding structure on their own, describe the process for 

handling and counting. Include details on how and when you pass fish upstream, and 

about your ability to do so. 

f. In what type of container do you hold these adults? Is it covered? Do you use 

overhead sprinklers? Do you have a problem with predation? 

g. Which water supply is used for this purpose? 

h. Are you able to hold these fish within recommended guidelines for temperature, water 

flow, and density? 
F-12 Regional Information Instruction Form 

i. Do you have adequate security? 

j. How do you deal with numbers of fish in excess of your egg take needs? Do you feel 

you have the tools you need for this? 

12. Please describe how you handle adults: 

a. What is the method for choosing and mating your broodstock (include how many 

adults of each sex are used per mating)? 

1. What are the spawner selection protocols (e.g. random, size, ripeness, wild 

or hatchery origin?)? 

2. Record how the gametes are handled (pooling of milt and/or eggs? If so, 

how?). What is the mating scheme (e.g. 1:1, factorial, multiple pooling?) 

b. Do you use anesthesia? 

c. Describe the pathogen-sampling regime. 

d. Describe mark sampling program, if any. 

e. Is there any other biological sampling done on adults? 

f. How do you dispose of spawning waste? 

g. How do you dispose of pre-spawning mortalities? 

h. How do you dispose of spawned adults? 

13. Please describe your method for putting down green eggs: 

a. Do you have adequate “clean” and “dirty” areas for handling eggs? 

b. Describe your water hardening procedure. 

c. Describe your green egg enumeration process. 

d. Where are these eggs incubated (What type of incubator, water supply used)? 

e. Do you incubate in single-family units? If you had the capacity, would that be 

desirable? 

f. How many eggs per incubation unit? 

g. What is the typical flow used? 

 

14. Please describe your methods for handling and putting down eyed eggs: 

a. How do you monitor egg development? (Temperature units, visual check, fish 

pathologist check, etc.) 

b. Have you had any chronic (or difficult to control) losses of eggs to the eyed stage? If 

so, please explain. 

c. How do you dispose of dead eggs? 

d. Do you disinfect eyed eggs prior to putting down to hatch? 

e. What type of container do you use for hatching? 

f. Do you use any type of substrate? 

g. What is your loading density? (eggs per unit) 

15. Other incubation questions: 

a. Is your water temperature regime similar to that in the natural environment? 

b. Are eggs incubated under environmental conditions that tend to maximize individual 

fitness of fry? (e.g. allow volitional ponding of fry, incubate under environmental 

conditions that simulate the natural rearing environment) 
Regional Information Instruction Form F-13 

c. Do you heat or cool your water during incubation? If so, please explain what you do 

and the purpose of the temperature manipulation. 

d. Do you cull eggs during incubation for any purpose? (ELISA results, spawn timing, 

etc.) 

e. Are excess eggs/fry culled randomly when necessary? 

f. How do you deal with eggs in excess of your egg take needs? 

g. Do fry have the ability to emerge volitionally? 

h. If you have to remove fry from rearing units, how do you determine appropriate stage 

of development (Temperature units, visual check, pathologist check, etc.)? 

16. Rearing conditions: 

a. Explain what type of container this stock is rearing in from first ponding to release 

(size and types of each kind of rearing unit). 

b. What water supply is used for rearing this stock (from first ponding to release)? 

c. Are the rearing units covered? 

d. Do you attempt to provide any type of “natural rearing” for this stock (cover, 

substrate, food, etc.)? Please describe. 

e. How do you decide which fish to combine in a rearing unit (individual families, 

results of ELISA, size of fish, etc.)? 

f. What do you use for keeping fish within recommended density and/or poundage 

targets (Flow Index, Density Index, pounds/gallon/minute, etc.)? 

g. Are you typically able to stay at or below this guideline? If not, what are your limiting 

factors? 

h. Are fish produced similar to natural fish in size, growth rate, morphology, behavior 

physiological status, health, etc.? 

17. Stock-specific fish health questions 

a. Do you use any prophylactic treatments? If so, describe drug/chemical used, targeted 

pathogen, life stage treated, and method of delivery. 

b. Do you vaccinate this stock? If so, for what pathogen and with what vaccine? 

c. Are you able to remove and enumerate mortalities easily? If not, what are your 

limitations? 

d. Is this stock sampled for pathogens at spawning? 

e. Do you or your fish health specialist perform any fish health assessments on this 

stock? If so, what sort and at what frequency? 

f. What is your most challenging fish health problem with this stock? If you could, what 

would you do to resolve the problem? 

18. Marking 

a. Is this stock marked or tagged in any way prior to release? Please describe (numbers, 

replications, quality control). 

b. What is the purpose of this mark or tag? 

c. How many years has it been identified in this way? 

d. Are there historic marks or tags we should know about? 

e. Please provide all tag recovery information for this program. 
F-14 Regional Information Instruction Form 

19. Release/transfer of fish 

a. How is time of release decided? 

b. How do you measure the size of fish at release (fish per pound, average length, 

other)? 

c. What is the typical size range in millimeters of these fish at release? If you do not 

know the size range, what is average weight? 

d. What other smolt quality monitoring do you perform, if any (fish pathologist checks, 

on-going research projects, smoltification indicators, etc.)? 

e. Are fish released with adequate imprinting to facility or desired stream reach? 

f. Describe your on-station release procedure for this stock (volitional vs. forced, time 

of day, typical date, length of time of release, etc.). 

g. If you truck this stock off station, where do they go (acclimation pond, stream plant, 

transfer to another facility, etc.)? 

h. Are you or others able to monitor the fish after they enter the river (snorkeling, smolt 

trapping downstream, etc.)? 

i. Do you have any idea if these fish have interactions with other salmonids in the 

receiving environment? If so, what do you know? 

20. Migration of returning adults 

a. Is the straying of hatchery fish into the wild controlled? 

b. Is the attraction of wild fish into the hatchery minimized? 

One answer per facility – question 2 

21. Wish list and other comments 

a. What is the most-needed piece or pieces of equipment for your facility and why? 

b. What capital improvements are most needed at your facility and why? 

c. What do you think would be the most valuable use of your facility? 

d. Is there anything else that we have not covered that you would like to add? 

THANK YOU 
Benefit/Risk Tool G-1 

G. Benefit/Risk Tool 

OVERVIEW

The Hatchery Scientific Review Group’s (HSRG) Benefit/Risk Tool was adapted and simplified 

from a tool developed by the co-managers.63 It allows the HSRG and the managers to evaluate the 

relative benefits and risks associated with specific actions and choices in hatchery management, in 

a scientifically sound, methodical manner. It is the vehicle by which scientists and managers can 

compare the best available science contained in the scientific framework64 and the best operational 

practices in the operational guidelines65 to current hatchery program purposes and operations. As 

such, its use in evaluating hatchery programs is key to meeting the HSRG’s principle that 

hatcheries be operated in a scientifically defensible manner.66

The tool has been used by the HSRG during the regional reviews and contains three worksheets. 

“Generic” (not specific to a region) versions of these worksheets are presented on the following 

pages, after a description of each worksheet and how it is used. 

The HSRG understands that the terms "risk" and "benefit" are sometimes used to convey a specific 

legal or policy status, condition or decision about the results of a particular action, policy or 

program. For the purposes of the HSRG's review and recommendations, these terms are not being 

used in this manner, but rather in the general sense of whether a hatchery program, or some aspect 

of that program, is likely to be affecting one or more regional salmonid stocks in a positive and/or 

negative way. The intent is to provide policy makers with a sense of the trade-offs involved in 

different options or courses of action. 

Part One

The Part One worksheet is titled Summary of Goals for Affected Stocks and Habitat; Description 

of Current Hatchery Programs. It is where the HSRG records the results of working with the 

regional participants to develop a common understanding of the current status of each regional 

hatchery program’s purpose, type and release strategies. The participants also use this worksheet 

to rate current, short-term and long-term goals for each regional stock, in terms of biological 

significance, population viability, habitat and harvest opportunity. Each category is rated as being 

high, medium or low. The following definitions are used for these ratings. 

 

63. Draft Benefit-Risk Assessment Procedure (BRAP) for Washington State Department of Fish and Wildlife Artificial Propagation 

Programs, November 17, 2000.

64 See Appendix A, Scientific Framework for the Artificial Propagation of Salmon and Steelhead. 

65 See Appendix C, Operational Guidelines. 

66 See Applied Hatchery Reform,, Principles and System-Wide Recommendations. 
G-2 Benefit/Risk Tool 

Definition of Population Biological Significance 

Rating criteria and scores for evaluating the biological significance of salmon and steelhead 

populations as part of assessing the benefits and risks of hatchery programs in Puget Sound and 

coastal Washington: 

A. Stock origin (possible scores = 1-5) 

a. Native (Score = 5) 

b. Admixture 

i. >50% native genes (Score = 4) 

ii. <50% native genes (Score = 3) 

c. Reintroduced: species occurred historically in watershed, was extirpated, but stock 

transfers re-established species in watershed (Score = 2) 

d. Introduced: species was historically absent from watershed/habitat (Score = 1) 

[What data/information do we need to obtain a stock origin score?, What/who are the sources 

for that info?] 

B. Biological attributes (Life history, physiological, morphological and behavior characters; 

disease resistance, etc.): How unique are these characters and to what extent are they 

irreplaceable (possible scores = 1-5) 

a. Population has unique, irreplaceable biological attributes that are not shared with other 

SASI stocks within the GDU (Score = 5) 

b. Has no unique biological attributes, but shares some unique attributes with other SASI 

stocks within the GDU that are not shared with other GDUs (Score = 3) 

c. Key biological attributes are shared with other GDUs (Score = 1). 

[What data/information do we need to obtain a biological attributes score? What/who are the 

sources for that info?] 

C. Level of population subdivision or metapopulation structure (scores = 1-7) 

a. Number of distinct spawning aggregations (e.g. tributaries) within the SASI stock under 

consideration: 

i. <5: Score = 2 

ii. >5: Score = 1 

b. Total number of SASI stocks within the same GDU: 

i. < 3: Score = 2 

ii. > 3: Score = 1 

c. Viability of other SASI stocks within the same GDU: 
Benefit/Risk Tool G-3 

i. Mean viability = “High”, Score = 1 

ii. Mean viability = “Medium”, Score = 2 

iii. Mean viability = “Low or no other SASI stocks within GDU, Score = 3. 

[What data/information do we need to obtain a biological attributes score? What/who are the 

sources for that info?] 

Sum of scores and biological significance ratings (A + B + C): 

5-8 = Low 

9-13 = Medium 

14-17 = High 

Definition of Population Viability 

Rating criteria and scores for evaluating the viability of salmon and steelhead populations as part 

of assessing the benefits and risks of hatchery programs in Puget Sound and coastal Washington: 

Ne: Effective population size (estimated from known estimated numbers of spawners per year and 

generation time) Worksheet to be developed. (possible scores = 1-5) 

Ne <100 Score = 1 

100< Ne < 500 Score = 2 

500 < Ne <2,500 Score = 3 

2,500 < Ne <5,000 Score = 4 

Ne > 5,000 Score = 5 

Mean numbers of recruits per spawners (R/S) over preceding 10 years 

a. R/S > 5 Score = 5 

b. 3 < R/S < 5 Score = 4 

c. 2 < R/S < 3 Score = 3 

d. 1 < R/S < 2 Score = 2 

e. R/S < 1 Score = 1 

Proportion of natural spawners comprised of hatchery-origin fish (possible score = 1-4) 

< 1 % Score = 4 

1 – 5 % Score = 3 
G-4 Benefit/Risk Tool 

5-30% Score = 2 

>30% Score = 1 

For hatchery populations, this latter criterion would be chanced to Proportion of eggs, fry or adults 

from wild fish or another hatchery: 

f. <1% Score = 4 

g. 1-5 % Score = 3 

h. 5-30 % Score = 2 

i. > 30% Score = 1 

Sum of scores and population viability ratings: 

3-6 Critical

7-10 At Risk

11-13 Healthy 

Definition of Population Habitat Conditions 

Three categories of environment, habitat (e.g., watershed), are defined in terms of conditions that 

support the target species (i.e., Chinook salmon) with the assumption that these conditions would 

also provide for the needs of other native species of salmonids (these definitions implicitly assume 

that any pre-terminal harvest is part of the environment during the fish’s whole life cycle). 

1. High = Healthy: Productivity of the target species is high, everywhere and at all 

times, and the population is capable of growth and terminal harvest. 

2. Medium = Limiting: The target species is productive enough for the population to 

sustain itself at a low level of harvest. 

3. Low = Inadequate: The target species is unproductive and the population will go 

extinct, even without terminal harvest. 

Habitats are characterized by Quality (HQ1), Quantity (HQ2), and Diversity (HD). An illustration 

of how these categories might be quantified suggests that a characterization of “Healthy” would 

require that HQ1 and HQ2 would combine such that the productivity of the population (recruits 

per spawner uninhibited by density, or some other measure) is greater than 5 and that the 

population has an abundance potential of 5,000 spawners. A categorization of “healthy” would 

require that HD is sufficient to support a variety of life history patterns (e.g., diverse smolt ages, 

emigration timing, a range of run timings, a range of spawning locations.) 

A characterization of “Limiting” would require that HQ1 and HQ2 would combine such that the 

productivity of the population is at least 2, the population has an abundance potential of at least 
Benefit/Risk Tool G-5 

500 spawners, and HD is restricted, supporting only a uniform age and size of smolts, a short 

duration of run timing, and a limited location for spawning. 

Definition of Harvest Goals 

High – harvest opportunity each year, spread over seasons 

Medium – opportunity most year, for some seasons 

Low – occasional opportunity, single run 

0 – no harvest opportunity 

Definition of Other Goals: 

Educational 

Cultural (ceremonial, first fish...) 

Employment 

Research 

Program Purpose and Type 

The purpose of the hatchery program is defined as either conservation, harvest, both and/or 

another purpose (such as education, research or cultural/ ceremonial). 

The type of program is also included. Hatchery programs are classified as integrated if the goal is 

to minimize potential genetic divergence between the hatchery broodstock and the naturallyspawning population in the watershed where fish are released and returning adults trapped for 

broodstock. Segregated programs are classified as those in which the goal is to maintain the 

hatchery population as a distinct, or genetically segregated population. 

Part Two

The Part Two worksheet is entitled How Current Program Operations Compare to HSRG 

Operational Guidelines. It is where the HSRG records the results of working with regional 

hatchery managers to understand current operations at the region’s hatcheries. The HSRG then 

evaluates how these current operations compare to the “best practices” outlined in the HSRG’s 

operational guidelines. The four areas considered in this evaluation are: 1) Culture Methods, 2) 

Accountability/Education, 3) Physical/Morphological/Ecological, and 4) Genetics/Conservation. 
G-6 Benefit/Risk Tool 

Part Three 

The Part Three worksheet is entitled Benefit/Risk Analysis; Recommendations and Alternatives. 

Using the Part Three worksheet, the HSRG assesses the benefits and risks derived from each 

regional hatchery program on both the target stock and every other regional stock. This analysis 

leads to the group’s scientific conclusions, which are recorded on the second half of the 

worksheet. 
Benefit/Risk Tool G-7 

“GENERIC” BENEFIT/RISK TOOL WORKSHEETS

[See following pages] 
Benefit-Risk Tool - Part 1. Summary of Goals for Affected Stocks and Habitat and Description of Current Hatchery Program for Region X

Category Now ShortTerm

LongTerm

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program Description

BioSig

Viabil 

Habitat 

Harvest 

BioSig

Viabil

Habitat 

Harvest

BioSig

Viabil

Habitat 

Harvest

BioSig

Viabil

Habitat 

Harvest

Sub-region

Stock

Goals Current Hatchery Program

Stock B

Stock A

etc.

Stock C

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 G-8
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Genetics and Conservation for Region X. 

Type Purpose Ty

Broodstock Choice

BB 

1. Is the hatchery stock native to the watersheds in which it is released?

I B

3. Have eggs or adults been introduced from outside the watershed since inception of the hatchery program?

Broodstock Collection

BB 4. Are adults randomly selected among all returning adults? BB 

5. Were sufficient numbers of donorscollected from the natural stock to minimize founder effects when the program was initiated? 

B B

6. Are sufficient broodstock collected to maintain an effective population size of 1000 fish per generation? (How many males and females do you typically spawn?)

I B

7. If goal is to minimize genetic divergence, are at least 10% of the broodstock derived from wild fish each year? (How many wild fish do you incorporate into your broodstock each year?)

I C

8. If the wild population has 150 fish or more, is collection of wild broodstock limited to 30% of the population? 

B B 9. Has any backfilling of egg shortages occurred in the recent past?B B 10. Does pre-spawning mortality exceed 10%?B B

11a) Do you have guidelines for acceptable contribution of hatchery origin fish to natural spawning? What do you do with surplus adults?

B B

11b) Are guidelines for hatchery contribution to natural spawning met for all affected naturally spawning populations? What do you do with surplus adults?

I C 13 b) Is a composite of naturally spawned and hatchery-bred fish spawning in the wild?I B

13 d) Is the proportion of naturally spawning fish that are of hatchery origin known? If so, is itcontrolled?

I B 13 e) Is the composition of hatchery and wild fish in the broodstock known and controlled?

B B 14. Is the necessary security of the stocks maintained?

I C 16. Is the duration of the program clearly defined?

Answers to 

( Y = Yes, N = No, I = 

Program A 

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Operations questions derived from conditions for success in HSRG Framework 

Sections 1.1, 2.3 and 3.1 (Genetics and Conservation)

Question applies to:

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Genetics and Conservation for Region X. 

Type Purpose Ty

Answers to 

( Y = Yes, N = No, I = 

Program A 

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Operations questions derived from conditions for success in HSRG Framework 

Sections 1.1, 2.3 and 3.1 (Genetics and Conservation)

Question applies to:

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Spawning

B B 17. Are males and females available for spawning on a given day randomly mated?B B

18. Do fish selected for broodstock have an equal opportunity to make a genetic contribution to the progeny gene pool? (How are eggs fertilized? Pairwise? Overlapping pairwise?, modified matrix? Etc.)

I B 19. Does the hatchery program include any natural spawning?

Incubation

I B

20. Are full sib families incubated separately? (Are eggs from a single female incubated separately?)

I B

23. Are water sources used that match the hatching/emergence timing of naturally produced populations?

Rearing

I B

28. Are fish reared under conditions that maximize the probability that all segments of the population contribute equally to the release population? (Is size grading practiced? If so, are slower growing fish culled?)

B B

29. Are all fish reared under environmental conditions that tend to maximize survival of all segments of the population? (Is growth modulation practiced?)

B B 31. Are excess juveniles culled randomly when necessary?

I B

33. Are the fish produced similar to natural fish in size, growth rate, morphology, behavior, physiological status, health, etc?

B B 34. Are fish reared under conditions that maximize homing fidelity?B C

35. Are fish reared in multiple facilities or with redundant systems to reduce the risk of catastrophic loss?

I C 37. Are fish reared for the shortest period possible?

B C 40. Are families reared individually to maintain pedigrees?

I B 41. If required, are larger families culled to minimize family size variation?

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Genetics and Conservation for Region X. 

Type Purpose Ty

Answers to 

( Y = Yes, N = No, I = 

Program A 

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Operations questions derived from conditions for success in HSRG Framework 

Sections 1.1, 2.3 and 3.1 (Genetics and Conservation)

Question applies to:

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Release

BB 42. Are fish released at life stages and locations that maximize homing fidelity?

I B

43. For a given release date and location, are fish similar to the natural population in size, morphology, behavior, physiological status, health?

I B 44. Is volitional release practiced during the natural out-migration timing?

B B

45. Are marking/tagging techniques used to distinguish among segments of the hatchery population and between the hatchery and natural populations?

I C 46. Are fish identified with nonlethal detectable identification marks or tags?

Adult migration

B H 47. Is the straying of hatchery fish into the wild controlled?

S H 48. Is the attraction of wild fish into the hatchery minimized?

BB 49. Are hatchery fish identified so the status of the natural population is not masked? 

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Physiology, Morphology, and Ecology for Region X. 

Type Purpose Typ

Broodstock Choice

B B SH 1. Is the broodstock local or locally adapting?

I B 2. Does the broodstock chosen for initiating hatchery programs represent populations native or adapted to the watersheds in which they will be released?

S H 3. Does the broodstock chosen minimize negative ecological interactions?

Broodstock Collection

B B SH 4. Are representative samples of the adult population collected with respect to size, age, sex ratio or other traits important to long term fitness?B B SH 5. Are broodstock maintained on natural water temperature profiles to provide optimum maturation and gamete development?B B 6. Does the number of broodstock collected maintain program size within carrying capacity of the natural environment?B B 7. Are adult fish or carcasses provided for upstream planting?

Spawning

None

Incubation

I B 8. Does the program use water sources to match hatching/emergence timing of naturally produced population?

B B 9. Does the number of eggs incubated maintain program size within the carrying capacity of the natural environment?

Rearing

B B SH 10. Does the program use a diet and growth regime that mimics natural growth patterns?

I B 11. Are natural rearing conditions simulated for temperature, photoperiod, hydraulic characteristics, feeding conditions, and predator avoidance?

B B 12. Are adequate flows maintained in the by-pass reach?B B 13. Has a riparian management plan been implemented that incorporates vegetation management, herbicide and pesticide use, and surface water management provisions?B B 14. Does the facility operate within the limitations established in National Pollution Discharge Elimination System permit?BB 15. Has and on or off-site habitat mitigation plan been implemented?B B 16. Does the number of fish reared maintain program size within carrying capacity of the natural environment?

I B 17. Are the fish produced qualitatively similar to natural fish in size, morphology, behavior, physiological status, health, and other attributes?I B

18. Are natural juvenile rearing conditions simulated for rearing density, temperature, hydraulic characteristics, habitat complexity, feeding conditions, and predator avoidance behavior?

B B SC 19. Are fish reared under conditions that maximize homing fidelity?

Operations questions derived from conditions for success in HSRG Framework 

Sections 1.2.1-1.2.3, 2.1, 2.2, 2.2.4 (Physiology, Morphology, and Ecology)

Answers to O

( Y = Yes, N = No, I = 

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program A 

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Question applies to:

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Physiology, Morphology, and Ecology for Region X. 

Type Purpose Typ

Operations questions derived from conditions for success in HSRG Framework Sections 1.2.1-1.2.3, 2.1, 2.2, 2.2.4 (Physiology, Morphology, and Ecology)

Answers to O

( Y = Yes, N = No, I = 

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program A 

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Question applies to:

Release

I B 20. Are fish released within the size range of naturally produced fish from which the hatchery population is derived?I B 21. Are volitional releases during natural out-migration timing practiced? 

Type 1 Interactions – Hatchery/natural fish -- Predation (Inter and intra-specific)

I B SC 22 a. Are fish released at sizes and life history stages similar to those of natural fish of the same species?

B B SC 22 b. Are fish released in areas or at life history stages where they are unlikely to encounter or prey upon natural fish of the same or other species?B B SC 22 c. Are fish released in a manner so they are unlikely to encounter or prey upon natural fish of the same or other species?B B SC 22 d. Are fish released in numbers that do not exceed the carrying capacity for the natural population?B B SC 22 e. Are fish released in stream reaches within the historic range of that species?B B SC 22 f. Are fish released in a manner that simulates natural migratory patterns?B B SC 22 g. Are fish released in areas with adequate imprinting to the facility or desired stream reach?B B SC 23 a. Are fish released at locations where they are unlikely to encounter natural fish that are negatively affected by hatchery fish?B B SC 23 b. Are fish released in numbers that do not exceed the carrying capacity of the natural environment?B B SC 23 c. Are fish released at sizes and life history stages similar to those of natural fish of the same species?

Type 2 Interactions – Adult Returns & offspring of hatchery fish/natural fish

B B SC 24 a. Are fish released in areas with adequate imprinting to facility or desired stream reach?

I B 24 b. Are fish released in numbers that do not exceed the carrying capacity of the natural environment?

B B SC 24 c. Are fish released into properly functioning freshwater, estuarine and marine habitat?

Adult migration

B B SC 25. Is unimpeded passage provided for wild fish through hatchery structures and by-pass reaches?B B SC 26. Does the hatchery operate to allow all migrating species of all ages to pass through hatchery related structures to maximize use of natural habitat?

I B 27. Are adults distributed upstream of hatchery to meet habitat capacity?

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Culture Methods for Region X. 

Type Purpose Type 

Broodstock Choice

S H 1. Does the broodstock chosen have a history of no pathogens?

B B 2. Is the broodstock indigenous to the watershed?

S H 3. Does the broodstock chosen or developed have the desired life history traits to meet harvest goals?

Broodstock Collection

B B

4. If broodstock choice is from another drainage, are eggs preferentially transferred? Are fish or eggs held in quarantine as described in the Salmonid Disease Control Policy of the Fisheries Co-Managers of Washington State (disease control policy). 

B B 5. Are broodstock maintained on pathogen-free and/or fish-free water supply?B B 6. Does attending fish pathologist monitor and recommend treatments to maximize survival as needed?B B 7. Are pre-spawning mortalities disposed of in a manner that prevents pathogen transmission to the receiving watershed?B B 8. Are disinfection procedures implemented that prevent pathogen transmission between stocks of fish on site?B B 9. Are species-specific holding recommendations followed for water quality, flows, temperature, and density?B B 10. Is the broodstock collected and held in a manner that minimizes prespawning mortality?

Spawning

B B SC 11. Is a minimum effecitive population size of 1000 fish per generation maintained?B B

12. Is pathogen sampling at spawning sufficient to provide quantitative and qualitative information for needed pathogen control measures that may be necessary for resultant transfers or rearing of progeny?

B B 13. Are eggs water-harden in iodophor solution as described in the disease control policy?B B 14. Are carcasses disposed of in a manner that prevents pathogen transmission to the receiving watershed?B B 15. Is spawning waste collected and disinfected prior to discharge to receiving water?B B 16. Are disinfection procedures implemented that prevent pathogen transmission between stocks of fish on site?

Operations questions derived from conditions for success in HSRG Framework 

Sections 1.2.4, 1.3, and 3.2 (Culture Methods)

Answers to Oper

( Y = Yes, N = No, I = Insuf

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program A Prog

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Question applies to:

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Culture Methods for Region X. 

Type Purpose Type 

Operations questions derived from conditions for success in HSRG Framework Sections 1.2.4, 1.3, and 3.2 (Culture Methods)

Answers to Oper

( Y = Yes, N = No, I = Insuf

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program A Prog

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Question applies to:

Incubation

B B 17. Does incubation occur on pathogen-free and/or fish-free water supply?B B

18. Are species-specific incubation recommendations followed for water quality, flows, temperature, substrate, or density parameters to prevent syndromes such as “gas bubble disease”, “cold water disease”, “blue sac”, etc.)?

B B 19. Are eggs monitored when needed to determine fertilization efficiency and embryonic development?B B 20. Are incubating eggs treated when recommended by attending fish pathologist?B B 21. Following eye-up stage, are eggs inventoried, dead or undeveloped eggs removed, and disinfected as described in the disease control policy?B B 22. Are eggs (dead or culled) discarded in a manner that prevents pathogen transmission to the receiving watershed?B

H 23. Are fry removed from incubation units when 80-90% of observed fry have yolk-sac material that is 80-90% utilized and contained within body cavity (“button-up”)

B B 24. Are disinfection procedures implemented that prevent pathogen transmission between stocks of fish on site?B B 25. Are appropriate water temperature profiles maintained to provide optimum embryo development?B B 26. Are incubator loading and densities maintained at levels that ensure optimum survival of eggs and fry?B B 27. Is substrate used to promote suitable fry distribution, optimum size, and appropriate emergence timing?

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Culture Methods for Region X. 

Type Purpose Type 

Operations questions derived from conditions for success in HSRG Framework Sections 1.2.4, 1.3, and 3.2 (Culture Methods)

Answers to Oper

( Y = Yes, N = No, I = Insuf

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program A Prog

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Question applies to:

Rearing

B B 28. Does rearing occur on pathogen-free and/or fish free water supply?B B

29. Are species-specific recommendations followed for water quality, flows, temperature, or density parameters to reduce adverse stress and related pathogens and/or disease syndromes?

S H 30. Are facility and species-specific recommendations for water quality, temperature, loading, and density followed to maximize recruitment to fisheries?

B B 31. Are settleable solids, unused feed and feces periodically removed to ensure proper cleanliness of rearing container?B B 32. Are mortalities removed daily and disposed of in a manner that prevents pathogen transmission to the receiving watershed?B B 33. Are fish health examinations performed at a minimum of once per month and more frequently when required?B B 34. Whenever possible, are vaccines used to minimize the use of antimicrobial compounds?B B 35. Are fish treated with appropriate chemicals or drugs as recommended by fish pathologist?B B 36. Does the operator follow proper feeding rates, conduct periodic feed quality analysis, and store feed under proper conditions to prevent nutritional disorders?B B 37. Are disinfection procedures implemented that prevent pathogen transmission between stocks of fish on site?

S B 38. Are predators excluded from ponds to prevent the spread of pathogens between containers?

B B 39. In the event of an epizootic, are: Treatment recommendations of attending pathologist followed? Are affected containers isolated? Is effluent sanitized if possible?B B

40. Are appropriate physical and chemical characteristics of water inflow and effluent (suspended solids, temperature, dissolved gases, pH, mineral content, and potential toxic metals) maintained to promote growth and survival?

B B 41. Are accurate fish inventory data maintained (e.g. Hat-Pro) with a minimum of handling stress?B B 42. Are appropriate flow and density indexes maintained for the species and life stage being reared?B B 43. Is the correct amount and type of food provided to achieve the desired growth rate, body composition, and condition factors for the species and life stage being reared?

I B 44. Do the hatchery populations exhibit growth rates, body composition and condition factors similar to natural populations?

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Culture Methods for Region X. 

Type Purpose Type 

Operations questions derived from conditions for success in HSRG Framework Sections 1.2.4, 1.3, and 3.2 (Culture Methods)

Answers to Oper

( Y = Yes, N = No, I = Insuf

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program A Prog

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Question applies to:

Release

B B SC

45. Are all fish examined for presence of “reportable pathogens” as defined in the disease control policy at the assumed pathogen prevalence Level (APPL) of 5% no less than 3 weeks prior to release?

B B SC 46. Are attending fish pathologist recommendations followed for treatments prior to release?B B SC 47. Are fish released in same drainage as rearing facility? B B 48. Are transfers out of drainage inspected as above and accompanied by appropriate notifications to responsible/regulatory parties as described in the disease control policy?B B SC 49. Are fish released at times of the year and sizes to allow adoption of multiple life history strategies?

S H 50. Are fish released at a time, size, location, and in a manner that maximizes recruitment to fisheries?

B B SC 51. Are releases consistent with the ability of the habitat (freshwater, estuarine, and marine near-shore and off-shore) to support the number and life stage being released?

Post Release and Adult migration

B B SC 52. Are fish released into properly functioning habitats?B B SC 53. Are the number of fish released compatible with habitat carrying capacity?B

H 54. Is sufficient water flow provided to attract and separate adults into hatchery?

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 2: Operational Guidelines Questions Related to Accountability and Education for Region X. 

Type Purpose Type 

Accountability

B B

1. Are all hatchery personnel aware of the goals for the hatchery with respect to conservation, harvest and other purposes?

B B

2. Are expenditures tracked to assure that funds are expended as intended for the hatchery program?

B B

3. Are KEY staff aware of the funding available for carrying out the various activities in the production cycle so that it can be done the most cost effective manner?

B B

4. Is all new relevant information from research or other sources made available to hatchery staff and others and used for attaining goals?

B B

5. Is the most recent information obtained from monitoring and evaluation programs for the production cycle, including performance indicators and progress toward goals, taken into consideration when determining whether hatchery operations should be changed or not?

B B

6. Is there a management program in place that assures that information pertaining to items 1-4 is available on a “real-time” basis and that changes warranted by that information are implemented?

B B

7. Are standards specified for in-culture and post release performance of hatchery fish and their offspring?

B B?

8. Are there state or federal laws that constrain the program by specifying objectives, such as numbers and size of smolt produced? 

EducationHatchery Operations

B B 9. Is the hatchery facility open to the public during hours of operation?B B 10. Are the hatchery operations visible to facility visitors?B B 11. Are hatchery operations (egg take, incubation, rearing) demonstrated to the public?B B

12. Does the facility have a fish ladder and/or adult holding facilities that are open to the public?

Hatchery Physical Plant

B B

13. Does the hatchery have signage describing the facility, fish production goals, ties to management goals, ecosystem function?

B B 14. Is there a visible link to riparian zone such as viewing boardwalk or bridge?B B 15. Is the facility used by other fish and wildlife programs?B B 16. Does the hatchery schedule tours for groups?

Educational Outreach Programs

B B 17. Does the program provide opportunities for student interns?B B 18. Does the program provide opportunities for citizen volunteer involvement?B B 19. Does the agency maintain a web page describing the hatchery program?B B 20. Is a pamphlet or brochure describing agency or hatchery programs available?

Hatchery Program

B B 21. Are eggs or fish provided to volunteer groups?B H? 22. Are eggs or fish provided to educational groups i.e. “Salmon in the Classroom”?

Hatchery Staff

B B 23. Is hatchery staff involved in community/volunteer meetings or outreach programs?B B 24. Does hatchery staff regularly give classroom presentations?B B 25. Does hatchery staff participate in formal professional presentations/seminars?

Formal Research

B B 26. Is the facility used or does staff participate in agency research projects?B B

27. Is the facility used or does staff participate in university or other cooperative research projects?

B B 28. Are data and information pertaining to the program accessible to interested researchers?

Operations questions derived from conditions for success in HSRG Framework 

Sections 3.3, and 4 (Accountability and Education)

Answers to Operati

( Y = Yes, N = No, I = Insuf. In

Program Type

(S = Segregated,

 I = Integrated, 

B = Both)

Program Purpose

(C = Conservation, 

H = Harvest, 

B = Both)

Program A Program 

 Not Applicable To:

(SH =Segregated/ 

Harvest, SC = 

Segregated/ 

Conservation)

Question applies to:

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 
Benefit-Risk Tool - Part 3. Benefit/Risk Analysis; Recommendations and Alternatives for Pr

Benefits Risks

Sub-regionStock AStock BStock Cetc.

Operations Monitoring

Broodstock ChoiceBroodstock CollectionSpawningIncubationRearingReleasePost ReleaseAdult Migration

Monitoring

Operations Accountability

Life Stage Hatchery Program Recommendations: Program Y, Region X

General Comments - Alternative Programs for Consideration – Different Facility and Production Solu

Program and Facilities

Potentially 

Affected 

Stocks

Benefits/Risks Evaluated: Program Y, Region X

For each potentially affected stock, identify a) significant benefits to, and b) major conflicts with...

Benefit/Risk Tool Hatchery Reform: Principles and Recommendations - April 2004 

Research Grants H-1 

H. Research Grants 

Funded Grants - 2000 Project Descriptions

Category A: Sustainable Fisheries 

Development of Field Methods to Determine the Effects of Hatchery 

Release Methods on Residualism and Interactions Between Hatchery 

and Wild Juvenile Salmonids in Relation to Stream Carrying Capacity 

Project Sponsor: NMFS and WDFW 

Principal Investigators: Stephen Riley, HSRG + Sponsor Share = Total Cost:

NMFS; Howard Fuss, WDFW $91,941 + $102,067 = $194,008

Associate Investigators: Todd Pearsons, 

Geraldine VanderHaegen, WDFW; Barry 

Berejikian, Walt Dickoff, NMFS 

Project Summary: The objective of this project is to develop a cost-effective method to evaluate 

the effects of hatchery releases on wild juvenile salmonids. We propose to develop field methods 

designed to determine how hatchery releases affect the abundance, behavior, habitat use, growth, 

stomach fullness, and condition of wild juvenile salmonids. Field methods will be applied in areas 

upstream and downstream of hatchery release sites before and after releases, and will involve three 

levels of effort: a) underwater observation of numbers and behavior of wild and hatchery 

juveniles; b) estimation of territory size and habitat use of wild juveniles; and c) estimation of the 

growth, stomach content volume, and physiological status of wild and hatchery juveniles captured 

by electrofishing or angling. Comparisons between upstream and downstream sites will be used to 

determine the degree to which wild fish are affected by hatchery releases and the extent of 

redistribution of hatchery residuals. We will also use these data to estimate the sample size 

necessary to obtain adequate statistical power of all comparison, and the costs associated with 

each component of the study will be determined. Similar procedures could be used to evaluate 

hatchery releases in a variety of streams coast wide. Underwater observations will also be used to 

assess the level of residualism related to certain hatchery practices such as flush and volitional 

releases and outplanting. Ultimately, these methods could be routinely applied as part of hatchery 

evaluations that are likely to be required under the ESA. 

Test Commercial Selective Harvest Gears 

Project Sponsor: Willapa Alliance 

Principal Co-Investigators: Mark Heckert, HSRG + Sponsor Share = Total Cost:
H-2 Research Grants 

Willapa Alliance; Geraldine VanderHaegen, $49,260 + $53,374 = $102,634 

WDFW 

Associate Investigators: WDFW regional staff

Project Summary: On the Naselle River, Willapa Bay, the Willapa Alliance and WDFW propose 

to test two commercial live capture gears to selectively remove adult hatchery fish from 

commingled wild stocks. Removing returning adult hatchery salmon will reduce the number of 

hatchery adults on the spawning grounds, and thereby reduce gene flow and ecological 

interactions between hatchery and natural spawners. We will also install an adult trap at Naselle 

Hatchery to collect hatchery broodstock. We will use a series of mark and recapture experiments 

to estimate long-term survival of released fish, the proportion of hatchery fish that could be 

removed with these gears and to collect data characterizing the run. If successful, the project will 

assist Naselle Hatchery in meeting its Chinook egg take goals, will remove hatchery fish from the 

spawning grounds, and will provide fishing opportunity for commercial fishermen and will 

evaluate the impacts of selective commercial fishing gear on released fish. This method of 

removing hatchery adults would be applicable throughout Washington. Our progress and results 

will be shared at community meetings, by mailings, through annual reports and by publication in a 

peer-reviewed journal. During the fishing season our progress will be posted daily on the internet. 

Impacts of Size Selective Gillnet Fisheries on Puget Sound Coho 

Salmon Populations 

Project Sponsor: WDFW 

Principal Investigators: Curtis Knudsen, HSRG + Sponsor Share = Total Cost:

Craig Busack, WDFW $11,427 + $3,720 = $15,147 

Project Summary: We will document historical trends in size selectivity of terminal Puget Sound 

and coastal gillnet fisheries by comparing coded-wire tagged recoveries from the fishery to 

recoveries from the terminal spawning areas (trap or hatchery). Utilizing the coded-wire tag 

database allows us to focus on specific marked populations of coho caught within terminal area 

fisheries rather than having to deal with aggregations of mixed populations making estimates of 

size selectivity much more accurate. Reduced body size impacts a population’s productivity and 

the reproductive fitness of returning adults. We will describe the demographic and genetic impacts 

to these populations caused by reduced body size selective fisheries. The rates of decline in 

populations experiencing different intensities of size selection will be compared to determine if 

they are correlated with the magnitude of size selectivity and fishing intensity and what the 

background level of size decline may be from other sources such as reduced ocean productivity. 

Understanding the consequences of size selective fisheries will allow management decisions to be 

made that take into account the impacts on hatchery and wild population’s productivity and 

reproductive fitness. 
Research Grants H-3 

Category B: Recover and Conserve Natural Spawning 

Populations 

Genetic Characterization of Lake Ozette Sockeye Salmon 

Project Sponsor: Makah Fisheries Management 

Principal Investigators: Ken Currens, NWIFC; HSRG + Sponsor Share = Total Cost: 

Jim Shaklee, WDFW; Michael Crewson, Makah $22,000 + $45,920 = $67,920 

Tribe 

Associate Investigator: Jeffrey Grimm, WDFW 

Project Summary: This project provides baseline genetic and demographic information for 

testing 1) whether sockeye salmon and be successfully reintroduced into tributaries of Lake 

Ozette, where they were extinct, and 2) whether distribution and abundance of beach spawning 

populations can be rebuilt through supplementation. Genetic profiles of Lake Ozette sockeye 

salmon, which are protected under the ESA, and kokanee salmon, which are not, are necessary to 

guide brood stock selection and to monitor hybridization and gene flow. Profiles will be developed 

from 6-8 microsatellite DNA loci. The ability to mark and identify hatchery is also essential to 

monitor recovery efforts, but most hatchery-produced sockeye salmon will be released before 

external marking are possible. Consequently, this project tests eolith marking as a tool. The 

combination of genetic data and otolith marking will allow the co-managers to develop effective 

strategies to monitor abundance, distribution, and interactions among natural and hatchery 

populations. Project results will be summarized in a final technical report to the funding agency, 

co-managers, and National Marine Fisheries Service (NMFS) and will be incorporated into the 

Hatchery Genetic Management Plan and recovery plan for Lake Ozette sockeye salmon. 

White River Acclimation Pond Evaluation 

Project Sponsor: WDFW 

Principal Investigators: Chuck Baranski, HSRG + Sponsor Share = Total Cost:

WDFW; Blake Smith, Puyallup Tribe; $40,508 + $154,368 = $194,876 

Richard Johnson, Muckleshoot Tribe 

Associate Investigator: Curt Knudsen, WDFW 

Project Summary: One strategy employed to increase natural spring Chinook spawning in the 

upper White River is to release smolts from three upriver acclimation sites (Huckleberry Cr., 

Cripple Cr., Clearwater R.). Survival from smolt to spawner and the distribution of pond-origin 

spawners have not been adequately evaluated. If survivals are low or if returning adults are widely 

distributed in the Puyallup basin (particularly into fall Chinook production areas), alternative 

strategies will need to be developed. Standard CWT tagging is not a suitable took in this case 
H-4 Research Grants 

because all nose tagged fish are removed from the upriver population. This proposal would utilize 

“body tagging” as a means of identifying and evaluating these smolt releases. The SSSCTC 

proposes that WDFW “body tag” (no marks) a total of 400,000 White River Chinook fry at Hupp 

Springs and White River hatcheries prior to their transfer to the acclimation sites. Tag retention 

will be estimated at release. Survival and spawning distribution will be quantified by sampling 

unmarked Chinook returns to White River Hatchery (Muckleshoot Tribe), the Buckley trap and 

haul facility (Muckleshoot and Puyallup Fisheries staff), Voights Creek Hatchery (WDFW) and 

Puyallup basin natural spawning grounds (WDFW, Muckleshoot and Puyallup staffs). SSSCTC 

proposes to tag a complete brood cycle (5 years). Results will be presented annually in the 

Northwest Fishery Resource Bulletin’s Project Report Series. 

Differences in Natural Production between Hatchery and Wild Coho 

Salmon: A Proposal to Measure the Influence of the Degree of 

Hatchery Ancestry on Natural Production Success 

Project Sponsor: WDFW and NMFS 

Principal Investigators: Howard Fuss, HSRG + Sponsor Share = Total Cost

Patrick Hulett, Cameron Sharpe, WDFW; $146,973 + $96,496 = $243,469 

Ken Currens, NWIFC; Michael Ford, 

Jeffrey Hard, NMFS 

Project Summary: Natural production of coho will be evaluated to measure (and identify causal 

factors for) differences in reproductive competence between hatchery and wild fish. Analyses of 

morphological (size/age/fecundity/body shape), behavioral (run-time/spawning/rearing), and 

genetic (msDNA) data will be used to carry out two phases of work. Phase 1 (from 2000 to 2005) 

will examine reproductive success of hatchery and wild coho spawning together. Phase 2 (from 

2006 to 2011) will examine reproductive success of the adult offspring of the Phase 1 fish. Those 

fish are wild but individually will have varying degrees of hatchery ancestry. Phase 1 will directly 

measure the ability of hatchery coho to reproduce in the natural environment relative to wild fish 

of similar genetic backgrounds n the same basin. Phase 2 will allow a determination of the genetic 

basis for differences in reproductive success between hatchery and wild fish. To facilitate this 

research it is essential to modify the existing barrier at Minter creek Hatchery in south Puget 

Sound to control access of salmonids to Minter Creek spawning grounds. The project will be 

conducted as a partnership between WDFW, NMFS, and the NWIFC. In addition to annual 

progress reports, final reports or peer-reviewed publications will be produced at the end of each 

major research phase. The work will increase understanding of differences in reproductive fitness 

between hatchery and wild fish and, further, will demonstrate how a large hatchery program can 

be managed without conflicting with natural production objectives in the same watershed. 

Snow Creek Coho Recovery Program 

Project Sponsor: WDFW 
Research Grants H-5 

Principal Investigators: Steve Schroder, HSRG + Sponsor Share = Total Cost

Thom Johnson, WDFW $10,000 + $46,208 = $56,208 

Collaborators: Wild Olympic Salmon,

North Olympic Salmon Coalition 

Project Summary: In the mid-nineteen seventies, as many as 1,400 adult coho and thousand of 

coho smolts were observed in Snow Creek, a Discovery Bay stream. However, drastic reductions 

in adult (often<100 and as few as three) and smolt abundance have occurred since 1991. 

Beginning in the fall of 1998, WDFW and local volunteer groups began an effort to recover this 

stock. Every returning adult was captured at a permanent weir located near the mouth of the 

stream. The fish were artificially spawned and their eggs were incubated at the Hurd Creek 

Hatchery. Eggs from each female were split into three portions, and each group received a unique 

thermal otolith mark for later identification. Eggs from two of the groups were placed into remote 

site incubators that were established in Snow Creek and its main tributary, Andres Creek. The 

remaining eggs were left in the hatchery and the fish produced form them were cultured for either 

seven or ten months. The reared fish received CWTs. Those fed for seven months had tags placed 

in their snouts while those reared for ten months had tags placed in their adipose fins. The fish 

reared for seven months were released into Crocker Lake in November. The second group of 

reared fish will be place into Crocker Lake in late February. They are expected to over-winter in 

the lake and emigrate out of system in the spring of 2000. This approach will be continued 

annually until 2006 and if abundance increases, coho will be allowed to spawn naturally in the 

system to produce another type of treatment. The objectives of this study are to assess how many 

smolts are produced from each type of release, to see if size and out-migration timing differ 

because of treatment origin, to compare the marine survival of smolts originating from each type 

of release, to determine how differing rearing treatments may have affected adult attributes (e.g. 

incidence of precocious maturity, size, fecundity, egg size, reproductive effort) and to examine 

how annual variation in environmental condition may affect fish from each treatment. Results will 

be presented in the peer-reviewed literature, and annual reports describing project accomplishment 

will be produced. Data obtained from this work will be used to refine coho recovery efforts 

throughout Puget Sound and the Washington coast. 

Hamma Hamma River Steelhead Supplementation Evaluation 

Project Sponsor: NMFS 

Principal Investigators: Barry Berejikian, HSRG + Sponsor Share = Total Cost 

NMFS; Thom Johnson, WDFW; Rick Endicott, $34,000 + $58,562 = $92,562 

LLTK; Al Adams, HCSEG 

Associate Investigators: Chris Weller, PNPTC; Collaborators: Point No-Point Treaty

Kathy Hopper, LLTK; Steve Schroder, WDFW Council 

Project Summary: Conservation hatcheries are playing an increasing role in recovery efforts for 

imperiled salmonid populations in the Pacific Northwest. This research will be carried out through 
H-6 Research Grants 

a cooperative partnership between non-profit organizations (Hood Canal Salmon Enhancement 

Group and Long Live the Kings), Washington Department of Fish and Wildlife, National Marine 

Fisheries Service, and the Point No Point Treaty council, established to apply conservation 

hatchery strategies to salmon recovery in Hood Canal. The project will evaluate the contribution 

of a steelhead (Oncorhynchus mykiss) supplementation program, implementing conservation 

hatchery protocols, to changes in the abundance of steelhead in the Hamma Hamma River, WA, 

and will determine the program’s impact by comparing changes in steelhead abundance to other 

Hood Canal Rivers. Recent research suggests that culturing salmonids under more natural 

conditions, or implementing alternative release strategies may reduce genetic divergence and 

harmful effects on target wild populations. The project has an excellent opportunity to succeed in 

empirically testing the merits of using artificial propagation for conservation purposes. Results of 

the project will be reported annually to the funding agency and published in peer-reviewed 

scientific literature. 

Category C: Improve Quality and Cost-Effectiveness of Hatchery 

Programs 

Development of Engineered Streams for Salmon Production 

Project Sponsor: University of Idaho 

Principal Investigators: Ernest Brannon, HSRG + Sponsor Share = Total Cost

WSU/UI; Bill Kinsel, WSU; Howard Fuss, $48,301 + $20,290 = $68,591 

WDFW 

Project Summary: Development of an engineered stream is proposed as a new concept in 

hatchery supplementation. In collaboration with WDFW development of engineered streams is 

proposed by UI/WSU as a long-range alternative to hatcheries for supplementation of weak or 

failing wild salmonids populations. The objectives are to provide natural-type engineered streams 

for coho salmon production that result in wild smolt quality and to monitor performance as a 

demonstration project for the new hatchery concept. The approach is to develop artificial streams 

for use as salmon habitat with engineering specification based on biological criteria of the species 

targeted, while maintaining genetic specificity, diversity, and natural smolt quality. The artificial 

stream will substitute for, or be used in conjunction with, standard hatcheries. Natural feed with 

supplemental artificial feed will be the source of food. The site selected is Hatchery Creek located 

immediately behind the WDFW hatchery on the Dungeness River. The present upper creek 

channel will be enhanced with habitat structures, pools and riffles, and cover to mimic natural 

coho habitat. Coho stock will be introduced from the Dungeness by planting eyed eggs to provide 

the determined ultimate density of fish/m2. Performance will be based on monitoring of fish 

condition at migration, residence time, and biomass sustained. Quality will be based on residence 

time and fish condition monitored over the residence period. Post-migration monitoring will 

involve adult return success based on thermal marks compared to hatchery fish. Results will be 

published and implemented through application at other sites. 
Research Grants H-7 

Increase Post-Release Survival by Rearing Coho with NATURES SemiNatural Raceway Habitat 

Project Sponsor: NMFS 

Principal Investigators: Desmond HSRG + Sponsor Share = Total Cost

Maynard, Thomas Flagg, John Colt, NMFS; $80,000 + $75,115 = $155,115 

Geraldine VanderHaegen, WDFW 

Project Summary: It has been repeatedly demonstrated that rearing Chinook salmon in 

NATURES semi-natural raceway habitat increases their instream survival. Here, WDFW and 

NMFS are proposing research to determine if NATURES rearing also increases the number of 

coho salmon recruiting to the fishery and spawning population. The research will be conducted 

with salmon grown in standard concrete raceways at Puget Sound hatcheries. At each hatchery, 

there will be control and semi-natural habitat raceways. The experimental habitat will be created 

by fitting the raceways with: 1) gravel pavers, 2) fir tree instream structure, and 3) camouflage net 

overhead covers. Salmon will be reared in the raceways for at least 90 days before release. Fish 

growth, color development, and health will be routinely monitored and compared. Experimental 

and control fish will be coded-wire-tagged to measure their contribution to the fishery and 

spawning population. NATURES semi-natural raceway habitat rearing is expected to increase the 

relative number of fish recruiting to the fishery and spawning population by 25%. Resource 

managers can use this increased survival to: 1) increase the number of recruits per smolt released, 

2) reduce the number of broodstock salmon culture programs must use to produce a given number 

of recruits to the next generation, and 3) enhance the operational efficiency of mitigation and 

salmon enhancement programs. We will submit all of our results to peer-reviewed journals for 

publication. 

Using Semi-Natural Rearing Habitat to Improve Smolt-Adult Survival 

of Chinook Salmon 

Project Sponsor: WDFW 

Principal Investigators: Geraldine Vander- HSRG + Sponsor Share = Total Cost

Haegen, WDFW; John Barr, Bill St. Jean, $19,092 + $20,150 = $39,242 

Nisqually Tribe 

Collaborator: Northwest Indian Fisheries 

Commission 

Project Summary: WDFW and the Nisqually Tribe are cooperating to test the hypothesis that the 

addition of artificial structures to a large rearing pond will increase the smolt-to-adult survival of 

Chinook salmon. At Clear Creek Hatchery on the Nisqually River (Pierce County), floating and 

bottom structures will be installed into a large Chinook rearing pond. A second pond identical to 

the first will be used as a control. Fish in both ponds will be reared identically except for the 
H-8 Research Grants 

addition of the artificial structures. Growth and health of fish form each pond will be compared 

during rearing. Fish from each pond will be coded-wire-tagged and recoveries of tagged adults in 

fisheries and at the hatchery will be used to compare survival of each group of fish. If the addition 

of artificial structures to the Clear Creek rearing ponds increases the smolt-to-adult survival, more 

hatchery adults will be available for harvest, and the techniques will be directly applicable to the 

Nisqually Tribe’s supplementation plan for recovering Chinook. The increased smolt-to-adult 

survival may reduce the number of wild broodstock need to produce a given number of recruits in 

the next generation and reduce the number of fish that must be released to provide the desired 

number of adults. The study will be repeated over three brood years and the final results will be 

published in a peer-reviewed journal. Annual report will be made available to all interested 

parties. 

Category D: Protect Genetic Resources 

Interactions between Wild and Hatchery Steelhead: Evaluating Key 

Assumptions 

Project Sponsor: University of Washington 

Principal Investigators: Thomas Quinn, UW HSRG + Sponsor Share = Total Cost

$24,000 + $34,428 = $58,428 

Associate Investigator: Paul Bentzen, UW

Collaborators: Weyerhaeuser, NMFS, 

LLTK, Willapa Bay Alliance

Project Summary: Natural resource agencies are challenged to not only maintain the overall 

abundance of salmon and steelhead but also to maintain their genetic and ecological diversity. 

Hatchery production, designed to achieve the first objective, sometimes conflicts with the second. 

To prevent deleterious interactions, steelhead in Washington have been bred to return early in the 

year with the hope that genetic, ecological and fisheries interactions with wild fish can be 

minimized. The recent establishment of hatchery steelhead at Forks Creek presents a unique 

opportunity to examine the assumptions underlying this innovative approach. We request funds to 

supplement an ongoing study, supported by the Weyerhaeuser Foundation and with cooperation 

form Long Live the Kings, to sample hatchery and naturally produced steelhead at discrete 

juvenile and adult life history stages. We will sample all adults spawned at the hatchery, and also 

naturally-produced fish returning to the river to spawn, as well as naturally produced juveniles in 

the river, smolts, and hatchery pre-smolts. Analysis of DNA microsatellites form fin-clip samples 

will reveal the parentage and origin of juveniles and returning adults. From this we will determine 

the relative production and survival of wild, hatchery, and naturally-spawning hatchery origin 

steelhead, and the extent of interbreeding between groups. The results will be conveyed to agency 

management staff, contributing sponsors and regional organization, and the scientific community. 
Research Grants H-9 

Funded Grants - 2001 Project Descriptions

Category A: Sustainable Fisheries 

Development of Field Methods to Determine the Effects of Hatchery 

Release Methods on Residualism and Interactions between Hatchery 

and Wild Juvenile Salmonids in Relation to Stream Carrying Capacity 

Project Sponsor: WDFW and NMFS 

Principal Investigators: Howard Fuss, WDFW; HSRG Share + Sponsor Share = Total Cost:

Steve Riley, NMFS $102,500 + $110,261 = $212,761 

Collaborators: University of Washington, 

Weyerhaeuser Co. 

Project Summary: There is currently a great deal of uncertainty regarding the effects of hatchery 

practices on wild salmonids, and it is important to develop standard methods to estimate the 

effects of hatchery releases on wild juvenile salmonids, particularly for listed stocks. This study is 

designed to estimate the effects of hatchery releases on wild juvenile salmonids using underwater 

observation and sampling for growth and condition. We will evaluate several important fitness 

parameters, including abundance, behavior, habitats use, growth and physiological condition. We 

will estimate the sample sizes and effort required to obtain adequate statistical power to determine 

significant differences between treatment (hatchery fish released) and control (no release) sites, 

and we will determine the cost effectiveness of all techniques applied. This project will result in 

the development of a cost-effective method to evaluate the impacts of hatchery releases on wild 

juvenile salmonids, including estimates of required sample sizes and costs. We will provide 

estimates of the ecological effects of hatchery releases on selected wild salmonids populations in 

western Washington, information that is needed to assess risks to ESA-listed wild salmonid stocks 

that are associated with hatchery operations. Ultimately, if standardized methods are applied 

widely, the resulting database will be useful in assessing the effects of different hatchery rearing 

and release practices on wild salmon population. 

Test Commercial Selective Harvest Gears 

Project Sponsor: WDFW 

Principal Investigator: Geraldine Vander- HSRG Share + Sponsor Share = Total Cost:

Haegen $75,000 + $80,870 = $155,870 

Co-investigators: Michael Johnson, Pat Verhey Collaborators: Columbia-Pacific Resource

 Conservation and Development, Willapa Bay 

 Gillnetters Association, Willapa Bay Regional 

 Fisheries Enhancement Group 
H-10 Research Grants 

Project Summary: On the Willapa River, WDFW and the Pacific Conservation District will 

evaluate the effectiveness of tangle nets and a floating trap for live capture, selective harvesting of 

coho. Our objectives are to compare the number and condition of coho caught in the tangle net to 

the conventional gill net, to enumerate the catch of non-target species in each net, to compare the 

long-term survival of coho released from each net, to estimate the frequency and short-term 

survival rate of coho recaptured during the fishery, to compare the fork lengths of fish caught in 

each net to those spawned at Forks Creek Hatchery, and to evaluate a floating trap for capturing 

coho. Five fishers will simultaneously fish a net that is half tangle net and half conventional gill 

net in Sept 2001 and will tag and release coho. Fish recaptured during the test fishery will be held 

for 24 hours to observe the effects of multiple recaptures. Extensive tag recovery efforts in the 

sport and commercial fisheries, on the spawning grounds and from area hatcheries will continue 

through January 2002 to compare the long-term survival of fish released from the tangle net to 

those released from the gill net. A floating trap will also be deployed to target coho. We expect to 

collect information that will allow for science based implementation of commercial selective 

fisheries to provide access to more hatchery fish and to reduce the number of surplus fish 

returning to the hatcheries. 

Salmon Marine Trophic Demand-Distribution 

Project Sponsor: University of Washington 

Principal Investigator: David Beauchamp, HSRG Share + Sponsor Share = Total Cost:

UW 60,000 + $31,285 = $91,285 

Co-investigators: WDFW, Washington Collaborators: WDFW, NMFS 

Cooperative Fisheries and Wildlife Research 

Unit, USGS, King County Department of 

Natural Resources 

Project Summary: WDFW, USGS/BRD and UW will examine temporal distribution, diet and 

size patterns of juvenile salmon at selected estuarine and nearshore marine areas on northern and 

southern Puget Sound associated with significant production of wild and hatchery salmon. 

Chinook, coho and chum salmon will be targeted by this study, but all salmonids and potential 

predator and competitor species will be examined in a food web context. By combining field data 

on diet, distribution and growth from beach seining and fine-mesh purse seining with 

bioenergetics modeling, we will produce first-cut estimates of temporal feeding rates by juvenile 

salmon on their major prey, thus evaluating whether food limitation, predation or competition 

reduce survival or growth of juvenile salmon in these areas. This effort will provide a first look at 

current distribution and feeding conditions for juvenile salmon, establish the foundation for 

expanded studies, identify key processes that influence interactions among species and size classes 

of hatchery and wild salmonids and with other marine species. This project will provide the 

rationale for prioritizing and focusing subsequent research and management activities by 

identifying and quantifying processes that limit survival and growth of juvenile salmon during 

their critical early life stages in Puget Sound. We will coordinate with King County's sampling in 

central Puget Sound to provide the broadest possible spatial coverage using standardized methods. 
Research Grants H-11 

Category B: Recover and Conserve Natural Spawning 

Populations 

Snow Creek Coho Recovery Program 

Project Sponsor: WDFW 

Principal Investigator: Steve Schroder, HSRG Share + Sponsor Share = Total Cost: 

WDFW $36,000 + $16,290 = $52,290 

Collaborators: Wild Olympic Salmon, 

North Olympic Salmon Coalition, PointNo-Point Treaty Council, Jamestown 

S’Klallam Tribe

Project Summary: Beginning in 1998, WDFW, Wild Olympic Salmon and the North Olympic 

Salmon Coalition began an effort to recover a threatened coho population native to Snow Creek, a 

Northeast Olympic Peninsula stream. Since then, every adult coho returning to Snow Creek has 

been captured at a permanent weir. The fish are artificially spawned and their eggs are incubated 

at the nearby Hurd Creek Hatchery. Offspring from each fish are placed into three alternative 

recovery strategies. One involves placing eyed-eggs into remote site incubators located throughout 

the Snow Creek Basin. In the other two, fish are reared for either seven- or ten-months before 

being liberated as pre-smolts into Crocker Lake, a 25-hectare body of water that is used as a 

rearing and over-wintering location by Snow Creek coho. Fish placed into each treatment group 

have their otoliths thermally marked and the reared fish are also tagged. The otolith marks and 

tags are used to determine: 1) how many smolts are produced from each treatment, 2) if treatment 

origin affects size and out-migration timing of smolts, and 3) whether a recovery strategy affects 

overall survival, size, age, fecundity, egg size, and reproductive effort at maturation. This 

approach will be continued annually until 2006 and if abundance allows, coho will be allowed to 

reproduce naturally to create a fourth treatment type. Results from this study will be used to help 

refine coho recovery efforts throughout Puget Sound and the Washington Coast.

Differences in Natural Production Between Hatchery and Wild Coho 

Salmon 

Project Sponsor: WDFW and NMFS 

Principal Investigator: Howard Fuss, WDFW; HSRG Share + Sponsor Share = Total Cost:

Michael Ford, NMFS $100,500 + $76,058 = $176,608 

Co-investigators: Jeff Hard, Barry Berejikian, Collaborators: WDFW, NWIFC 

NMFS 
H-12 Research Grants 

Project Summary: A key question facing salmon managers is how successful hatchery 

propagated fish and their offspring are at surviving and reproducing in the wild. This is critical for 

assessing both risks and benefits of hatchery supplementation. 

In this collaborative federal, state and tribal project, we are using state-of-the-art genetic 

techniques to evaluate the spawning success and survival in the wild of hatchery propagated and 

naturally-spawning coho salmon. The results of this project will, for the first time, provide 

information on the rate at which hatchery fish can readapt to the wild environment. 

The project works like this: For three years, starting in the fall of 2000, we will intercept all adult 

coho salmon returning to spawn in Minter Creek, WA. The run consists of naturally produced and 

hatchery propagated coho salmon. Before being passed upstream to spawn naturally, we measure, 

photograph and tag each fish; determine its origin (hatchery or natural); and take a small nonlethal fin clip for later DNA analysis. Over the next 6 years, starting this spring, we will sample 

the progeny of these fish and use microsatellite DNA fingerprinting to determine their parentage. 

From these data, we will estimate the relative fitness of naturally spawning hatchery- and naturalorigin salmon. In the years 2003-2008, we will measure the relative fitness of natural-origin fish 

with varying hatchery ancestry, providing data on the rate hatchery coho readapt to the wild. 

Hamma Hamma River Steelhead Supplementation Evaluation 

Project Sponsor: NMFS 

Principal Investigator: Barry Berejikian, HSRG Share + Sponsor Share = Total Cost: 

NMFS $62,500 + $70,659 = $133,159 

Collaborators: Long Live the Kings, Hood 

Canal Salmon Enhancement, WDFW, 

Point-No-Point Treaty Council 

Project Summary: This project addresses several aspects of the conservation hatchery paradigm 

including: natural growth profiles, enriched hatchery rearing habitats, release strategies and 

experimentation to improving captive broodstock technologies. It also evaluates the impacts of a 

supplementation program on changes in spawner abundance in the Hamma Hamma River where 

confounding variables (e.g., habitat degradation, harvest) will have minimal influence. The 

specific research objectives are as follows: 

1. Determine whether the supplementation program affects the abundance of naturally spawning 

steelhead in the Hamma Hamma River. 

2. Determine the relative reproductive success of female steelhead from two different 

reintroduction strategies (smolt vs. adult release). 

3. Estimate the relative abundance of steelhead spawners produced from a) wild smolts, b) 

smolts reared in 'conservancy' ponds and c) smolts reared in hatchery tanks. 
Research Grants H-13 

4. Develop rearing protocols to produce steelhead smolts with a two-year freshwater rearing 

history, such that growth profiles mimic those of wild fish. 

5. Compare the reproductive behavior and breeding success of captively reared steelhead grown 

in high vs. low water velocity environments. 

Category C: Improve Quality and Cost-Effectiveness of Hatchery 

Programs 

Development of BKD Vaccine 

Project Sponsor: WDFW 

Principal Investigator: Jed Varney, HSRG Share + Sponsor Share = Total Cost:

WDFW $40,000 + $81,235 = $121,235 

Collaborators: USGS Western Fisheries 

Research Center, WDFW, NMFS 

Project Summary: State, tribal and federal fish health specialists in Washington state believe that 

bacterial kidney disease (BKD) is a major disease-of-concern for wild and cultured salmonids. 

Despite significant improvements in fish culture practices and the use of chemotherapeutants such 

as erythromycin, BKD continues to be a major factor in the propagation of many salmonid stocks 

in the Pacific Northwest. Because avoidance or treatment is not completely effective, vaccination 

may represent the most promising control method. This project is a collaborative investigation 

between the WDFW and researchers at the Western Fisheries Research Center (USGS) in Seattle, 

WA in which the relative efficacies of one commercial bacteria and five experimental vaccines for 

BKD, will be compared under laboratory conditions. The final objective of this study is to 

evaluate the potential for each vaccine to protect juvenile Chinook salmon from infection by the 

kidney disease bacterium. Groups of vaccinated fish will be exposed under strictly controlled 

environment conditions to a waterborne BKD challenge specifically designed to resemble what 

occurs in the natural environment. When complete, this study will provide fish health specialists 

with an accurate assessment of the feasibility of using any of the six vaccines for the control of 

BKD in cultured salmonids. If one, or more, vaccines show promise for controlling BKD, they 

will be evaluated in further laboratory and production-scale trials. 

Increase Post Release Survival by Rearing Coho with Natures SemiNatural Raceway Habitat 

Project Sponsor: NMFS and WDFW 

Principal Investigator: Desmond Maynard, NMFS 
H-14 Research Grants 

Co-Investigators: Geraldine VanderHaegen, HSRG Share + Sponsor Share = Total Cost:

WDFW $72,380 + $103,885 = $176,265 

Project Summary: It has been repeatedly demonstrated that rearing Chinook salmon in 

NATURES semi-natural raceway habitat increases their instream survival. In the current study, 

WDFW and NMFS are conducting a 4-year experiment to determine if NATURES rearing also 

increases the number of coho salmon recruiting to the fishery and spawning population. The 

research is being conducted with salmon grown in standard concrete raceways at Puget Sound 

hatcheries. At each hatchery, there are control and semi-natural habitat raceways. The semi-natural 

habitat was created by fitting the raceways with: (1) gravel pavers (2) fir tree instream structure 

and (3) camouflage net overhead covers. Fish growth, color development and health are being 

routinely monitored and compared. Experimental and control fish are coded-wire-tagged to 

measure their contribution to the fishery and spawning population. NATURES semi-natural 

raceway habitat rearing is expected to increase the relative number of fish recruiting to the fishery 

and spawning population by 25%. Managers can use the increased survival offered by NATURES 

salmon culture practices to restore natural spawning runs, maintain sustainable fisheries, promote 

economically efficient salmon culture, and reduce ecological interactions with ESA listed wild 

salmon populations. 

Nature vs. Nurture: Do Hatchery Practices Impair Brain Development? 

Project Sponsor: NMFS 

Principal Investigator: Penny Swanson HSRG Share + Sponsor Share = Total Cost:

 $30,000 + $15,800 = $45,800 

Project Summary: Fish reared in hatcheries are generally less fit to survive in the wild than 

naturally-reared fish, but the underlying causes (genetic selection or rearing environment) are not 

known. Numerous studies have demonstrated behavioral differences between fish reared in 

conventional hatcheries and wild fish. More recently it has been shown that various regions of the 

brains of hatchery and wild trout differ considerably in size, but the underlying causes of the brain 

differences are unknown because fish from this study were from different genetic stocks. The 

observations on behavior and brain size in salmon and trout are not surprising in view of the recent 

work in mammals demonstrating that environment can directly impact neural plasticity, 

development and behavior. In the proposed research, we will determine the effects of rearing 

environment on brain development in juvenile steelhead reared at the UW, Big Beef Creek Field 

Station as part of another study funded by Bonneville Power Administration and NMFS. We will 

compare the size and volume of various brain regions of fish reared in conventional hatchery 

raceways, raceways enriched with substrate or natural streams. We expect that this technique will 

be a more direct measure of fitness and could be used as a simple index by which to evaluate wild 

and hatchery fish, and fish reared in semi-natural rearing systems as proposed for conservation 

hatcheries. 
Research Grants H-15 

Development of Engineered Streams for Salmon Production 

Project Sponsor: University of Idaho 

Principal Investigator: Ernest Brannon, UI HSRG Share + Sponsor Share = Total Cost:

 $33,000 + $0 = $33,000 

Collaborators: WDFW 

Project Summary: This project is a demonstration of a new concept that combines the benefits of 

hatcheries and natural habitat to improve salmon populations. In collaboration with the WDFW 

development of engineered streams is proposed by UI/WSU as a long-range alternative to 

hatcheries for supplementation of weak or failing wild salmonid populations. The objectives are to 

provide natural-type engineered streams for coho salmon production that result in wild smolt 

quality and to monitor performance as a demonstration project for the new hatchery concept. The 

approach is to develop artificial streams for use as salmon habitat with engineering specifications 

based on the biological criteria of the species targeted, while maintaining genetic specificity, 

diversity, and natural smolt quality. The artificial stream will substitute for, or be used in 

conjunction with, standard hatchery raceways. Natural feed with supplemental artificial diets will 

be the source of food. The site selected is Hatchery Creek located immediately behind the WDFW 

hatchery on the Dungeness River. A channel was constructed with habitat structures, pools, riffles, 

and cover to mimic natural coho habitat. Approximately 50,000-eyed eggs will be introduced in 

the spring of 2001 and fish use of the channel will be quantified through snorkel surveys 

throughout the summer and fall. Post-migration monitoring will involve adult return success based 

on thermal marks applied to the eyed eggs. 

Category D: Protect Genetic Resources 

Residualism in Wild Broodstock Steelhead 

Project Sponsor: WDFW 

Principal Investigator: Cameron Sharpe, HSRG Share + Sponsor Share = Total Cost:

WDFW $50,000 + $36,893 = $86,893 

Co-investigators: Brian Beckman, Pat 

Hulett, Walt Dickhoff, NMFS Collaborators: WDFW, NMFS 

Project Summary: Some hatchery steelhead and other salmonid smolts become residuals (i.e. fail 

to out migrate) after release. The problem appears to be particularly acute in hatchery programs 

that use wild broodstock - a practice that is becoming increasingly popular as a means to limit 

genetic risk to wild salmonids. Ironically, high rates of residualism increase genetic and ecological 

risks to wild fish. 

Our objectives are to: (1) Develop a method to reduce residualism of hatchery-reared wildbroodstock steelhead, (2) Assess growth, physiological status, and migration/residualism to 
H-16 Research Grants 

determine mechanisms promoting residual behavior and (3) Compare growth, physiological status, 

migration pattern, and residualism among offspring of wild and domesticated broodstock. 

The project is a collaboration between WDFW and NMFS. The work will be conducted in the 

Kalama River and will coordinate closely with the existing federally funded wild steelhead 

broodstock project in that basin. 

The experimental approach will be to control growth patterns to simultaneously reduce the 

numbers of (1) small fish that residualize because they fail to reach smolt size and (2) large male 

fish that residualize because they become precociously mature. 

Our goal is to develop a practical and effective method to reduce residualism of cultured 

salmonids. We expect that the results will be "exportable" to steelhead and other salmonid culture 

programs region wide. 

Olfactory Imprinting in Hatchery Salmon 

Project Sponsor: National Marine Fisheries 

Service 

Principal Investigator: Andrew Dittman, HSRG Share + Sponsor Share = Total Cost: 

NMFS $32,000 + $78,100 = $110,100 

Project Summary: Exposure to home-stream water during appropriate juvenile stages is critical 

for olfactory imprinting in salmon and ultimately for successful completion of the adult homing 

migration. Inappropriate hatchery rearing conditions and juvenile release practices that interfere 

with the imprinting process can dramatically increase straying. Straying hatchery fish may in turn 

have negative ecological and genetic effects on endangered and/or wild populations. The overall 

goal of this project is to identify the critical developmental periods and environmental conditions 

required for olfactory imprinting in hatchery-reared Pacific salmon. Experimentally assessing 

successful imprinting is difficult and currently the only effective measures of imprinting involve 

expensive large-scale tag-recapture studies or behavioral assessments of captively-reared mature 

adults. This project has two major components: 1) develop and validate new molecular and 

electrophysiological tools for assessing imprinting that will not require large-scale adult rearing 

experiments; 2) determine the critical periods for imprinting for Puget Sound coho salmon by 

exposing juvenile salmon to imprinting odorants during key developmental periods under different 

environmental conditions. Ultimately, the imprinting assays developed for this project should be 

useful for studying homing in all salmonids and the findings of this study will be used to improve 

hatchery rearing and release strategies to minimize straying. 

Interactions between Wild and Hatchery Steelhead: Evaluating Key 

Assumptions 

Project Sponsor: University of Washington 
Research Grants H-17 

Principal Investigator: Thomas Quinn, HSRG Share + Sponsor Share = Total Cost: 

UW $23,700 + $11,156 = $34,856 

Collaborators: Weyerhaeuser Company, NMFS, 

WDFW

Project Summary: Natural resource agencies are challenged to maintain both the abundance of 

salmonids and their genetic and ecological diversity. Hatchery production, designed to achieve the 

first objective, sometimes conflicts with the second. In Washington, steelhead have been bred to 

return early in the year. This selection was initially done to help produce yearling smolts but it 

now permits selective fisheries on hatchery and wild fish, and provides a measure of genetic 

separation between the stocks. The extent to which timing differences minimize genetic and 

ecological interactions between hatchery and wild fish depends on the heritability of spawning 

date, the reproductive success of the stocks, and the extent of interbreeding. The recently 

established hatchery steelhead program at Forks Creek Hatchery presents a unique opportunity to 

examine the assumptions underlying this approach. We request renewal of funds to sample 

hatchery and naturally produced adults returning to spawn, naturally produced juveniles in the 

river and smolts, and hatchery pre- smolts. Analysis of DNA microsatellites from fin-clip samples 

will reveal the parentage and origin of juveniles and returning adults. This will allow us to 

determine the relative production and survival of wild, hatchery and naturally spawning hatchery 

origin steelhead, and the extent of interbreeding. The results will be conveyed to agency staff, 

contributing sponsors and regional organizations and the scientific community. 

Funded Grants - 2002 Project Descriptions

Category A: Sustainable Fisheries 

Salmon Marine Trophic Demand-Distribution 

Project Sponsor: University of Washington 

Principal Investigator: David Beauchamp, HSRG Share + Sponsor Share = Total Cost: 

UW $69,445 + $33,672 = $103,117 

Associate Investigator: Raymond Buckley, Collaborators: WDFW, UW-Wetland

 WDFW, Ecosystem Team, USGS, King 

 County Department of Natural Resources, 

 NOAA, NMFS 

Project Summary: UW, WDFW, and USGS/BRD will examine temporal distribution, diet and 

size patterns of juvenile salmon at selected estuarine and nearshore marine areas on northern and 

southern Puget Sound containing significant numbers of wild and hatchery salmon in a year with 

high juvenile pink salmon densities. Chinook, coho and chum salmon will be targeted by this 
H-18 Research Grants 

study, but all potential predator and competitor species will be examined in a food web context. 

Diet, growth, and timing of nearshore use will be compared among species, between hatchery and 

wild salmon, between northern and southern sites, and to historic data. By combining field data on 

diet, distribution and growth from beach seining and tow netting with bioenergetics modeling, we 

will estimate temporal feeding rates by juvenile salmon to evaluate whether food limitation, diet, 

environmental conditions, predation or competition reduce survival or growth of juvenile salmon 

in these areas. Changes in body size and growth conditions will be related to timing of declines of 

salmon in nearshore and the offshore transition. This project will provide the foundation for 

prioritizing and focusing subsequent research and management activities by identifying and 

quantifying processes that potentially limit survival and growth of juvenile salmon during critical 

early life in Puget Sound. Activity will be coordinated with King County, Seattle, NMFS, Army 

Corps to broaden spatial and topical coverage using standardized methods. 

Category B: Recover and Conserve Natural Spawning 

Populations 

Differences in Natural Production between Hatchery and Wild Coho 

Salmon 

Project Sponsor: WDFW and NMFS 

Principal Investigator: Howard Fuss, WDFW HSRG Share + Sponsor Share = Total Cost:

and Michael Ford, NMFS $107,567 + $74,637 = $182,204 

Collaborators: NWIFC 

Project Summary: A key question facing salmon managers is how successful hatchery 

propagated fish and their offspring are at surviving and reproducing in the wild. This is critical for 

assessing both risks and benefits of hatchery supplementation. In this collaborative federal, state, 

and tribal project, we are using state of the art genetic techniques to evaluate the spawning success 

and survival in the wild of hatchery propagated and naturally produced coho salmon. The results 

of this project will, for the first time, provide information on the rate at which hatchery fish can 

readapt to the wild environment. The project works like this: For three years, starting in the fall of 

2000, we will intercept all adult coho salmon returning to spawn in Minter Creek, WA. The run 

consists of naturally produced and hatchery propagated coho salmon. Before being passed 

upstream to spawn naturally, we measure, photograph, and tag each fish; determine its origin 

(hatchery or natural); and take a small non-lethal fin clip for later DNA analysis. Over the next six 

years, we will sample the progeny of these fish as fry and as smolt and use microsatellite DNA 

fingerprinting to determine their parentage. From these data, we will estimate the relative fitness 

of naturally spawning hatchery and natural-origin salmon. In the years 2003-2008, we will 

measure the relative fitness of natural-origin fish with varying hatchery ancestry, providing data 

on the rate hatchery coho readapt to the wild. 
Research Grants H-19 

Snow Creek Coho Recovery Program 

Project Sponsor: WDFW 

Principal Investigator: Steve Schroder, HSRG Share + Sponsor Share = Total Cost: 

WDFW $28,130 + $10,000 = $38,130 

Collaborators: Wild Olympic Salmon, 

North Olympic Salmon Coalition, PointNo-Point Treaty Council, Jamestown 

S’Klallam Tribe 

Project Summary: Beginning in 1998, WDFW, Wild Olympic Salmon and the North Olympic 

Salmon Coalition began an effort to recover a threatened coho population native to Snow Creek, a 

Northeast Olympic Peninsula stream. Since then, every adult coho returning to Snow Creek has 

been captured at a permanent weir. The fish are artificially spawned and their eggs are incubated 

at the nearby Hurd Creek Hatchery. Offspring from each fish are placed into three alternative 

recovery strategies. One involves placing eyed-eggs into remote site incubators located throughout 

the Snow Creek Basin. In the other two, fish are reared for either seven or ten months before being 

liberated a pre-smolts into Crocker Lake, a 25-hectare body of water that is used as a rearing and 

over-wintering location by Snow Creek coho. Fish placed into each treatment group have their 

otolith thermally marked and the reared fish are also tagged. The otolith marks and tags are used 

to determine: 1) how many smolt are produced from each treatment, 2) if treatment origin affects 

size and out-migration timing of smolt, and 3) whether a recovery strategy affects overall survival, 

size and age at maturation. This approach will be continued annually until 2006 and if abundance 

allows, such as in 2001, coho will be allowed to reproduce naturally to create a fourth treatment 

type. Results from this study will be used to help refine coho recovery efforts throughout Puget 

Sound and the Washington Coast. 

Hamma Hamma River Steelhead Supplementation Evaluation 

Project Sponsor: NMFS 

 

Principal Investigator: Barry Berejikian, HSRG Share + Sponsor Share = Total Cost:

NMFS $68,554 +$124,440 = $192,994 

Collaborators: Long Live the Kings, 

Hood Canal Salmon Enhancement, 

WDFW, Point-No-Point Treaty Council 

Project Summary: This project addresses several aspects of the conservation hatchery paradigm 

including: natural growth profiles, enriched hatchery rearing habitats, release strategies, and 

experimentation to improving captive broodstock technologies. It also evaluates the impacts of a 

supplementation program on changes in spawner abundance in the Hamma Hamma River where 
H-20 Research Grants 

confounding variables (e.g., habitat degradation, harvest) will have minimal influence. The 

specific research objectives are as follows: 

1. Determine whether the supplementation program affects the abundance of naturally spawning 

steelhead in the Hamma Hamma River. 

2. Determine the relative reproductive success of female steelhead from two different 

reintroduction strategies (smolt vs. adult release). 

3. Estimate the relative abundance of steelhead spawners produced from i) wild smolt, ii) smolt 

reared in 'conservancy' ponds, and iii) smolt reared in hatchery tanks. 

4. Develop rearing protocols to produce steelhead smolt with a two-year freshwater rearing 

history, such that growth profiles mimic those of wild fish. 

5. Compare the reproductive behavior and breeding success of captively reared steelhead grown 

in high vs. low water velocity environments. 

Category C: Improve Quality and Cost-Effectiveness of Hatchery 

Programs 

Increase Post-Release Survival by Rearing Coho with NATURES SemiNatural Raceway Habitat 

Project Sponsor: NMFS 

Principal Investigator: Des Maynard, HSRG Share + Sponsor Share = Total Cost:

NMFS $84,962 + $84,209 = $169,171 

Associate Investigator: Geraldine Vander- Collaborators: WDFW, Tribes 

Haegen, WDFW 

Project Summary: It has been repeatedly demonstrated that rearing Chinook salmon in 

NATURES semi-natural raceway habitat increases their instream survival. In the current study, 

WDFW and NMFS are conducting a 4 (four) year experiment to determine if NATURES rearing 

also increases the number of coho salmon recruiting to the fishery and spawning population. The 

research is being conducted with salmon grown in standard concrete raceways at Puget Sound 

hatcheries. At each hatchery, there are control and semi-natural habitat raceways. The semi-natural 

habitat was created by fitting the raceways with: 1) gravel pavers, 2) fir tree instream structure, 3) 

camouflage net overhead covers. Fish growth, color development, and health are being routinely 

monitored and compared. Experimental and control fish are coded-wire-tagged to measure their 

contribution to the fishery and spawning population. NATURES semi-natural raceway habitat 

rearing is expected to increase the relative number of fish recruiting to the fishery and spawning 

population by 25%. Managers can use the increased survival offered by NATURES salmon 

culture practices to restore natural spawning runs, maintain sustainable fisheries, promote 
Research Grants H-21 

economically efficient salmon culture, and reduce ecological interactions with ESA listed wild 

salmon populations. 

Development of Engineered Streams for Salmon Production 

Project Sponsor: University of Idaho 

Principal Investigator: Ernest Brannon, UI HSRG Share + Sponsor Share = Total Cost:

 $18,819 + $0 = $18,819 

Collaborators: WDFW, NMFS 

Project Summary: The project is a demonstration of a new concept that combines the benefits of 

hatcheries and natural habitat to improve salmon populations. In collaboration with the WDFW 

development of engineered streams is proposed by UI/WSU as long-range alternative to hatcheries 

for supplementation of weak or failing wild salmonid populations. The objectives are to provide 

natural-type engineered streams for coho salmon production that result in wild smolt quality and 

to monitor performance as a demonstration project for the new hatchery concept. The approach is 

to develop artificial streams for use as salmon habitat with engineering specifications based on the 

biological criteria of the species targeted, while maintaining genetic specificity, diversity, and 

natural smolt quality. The artificial stream will substitute for, or be used in conjunction with, 

standard hatchery raceways. Natural feed with supplemental artificial diets with be the source of 

food. The site selected is Hatchery Creek located immediately behind the WDFW hatchery on the 

Dungeness River. A channel was constructed with habitat structures, pools, riffles, and cover to 

mimic natural coho habitat. Approximately 25,000-eyed eggs will be introduced in the spring of 

2002 and fish use of the channel will be quantified through snorkel survey throughout the summer 

and fall. Post-migration monitoring will involve adult return success based on the thermal marks 

applied to the eyed eggs. 

Funded Grants - 2003 Project Descriptions

Category A: Sustainable Fisheries 

Salmon Marine Trophic Demand-Distribution 

Project Sponsor: University of Washington 

Principal Investigator: David Beauchamp, HSRG Share + Sponsor Share = Total Cost: 

UW $60,871 + $0 = $60,871 

Associate Investigator: Raymond Buckley, Collaborators: WDFW, UW-Wetland

WDFW Ecosystem Team, USGS, King County 

 Department of Natural Resources, 

 NOAA Fisheries 
H-22 Research Grants 

Project Summary: Predation rates will be estimated on nearshore-offshore distribution of 

juvenile hatchery and wild salmon during their early life history in northern and southern Puget 

Sound. Previous results revealed significant predation by small sea-run cutthroat trout. Larger searun cutthroat trout and other salmonids also forage in these habitats, but are not captured 

effectively with the standard beach seining methods. It is hypothesized that these larger predators 

represent a larger and prolonged source of mortality for juvenile salmon in Puget Sound, because 

the per capita consumption rates are higher, they can consume larger prey, and can forage more 

effectively for juvenile in both nearshore and offshore habitats. Larger seines will be used, tow 

netting, angling, gillnetting, and hydroacoustics to determine the distribution of predators and 

juvenile salmon, and to provide samples for diet analysis of predators. Differential predation rates 

between hatchery and wild origin salmon will be recorded. The transition from nearshore to 

offshore habitats and offshore distribution of juvenile salmon will determine both their growth 

potential and exposure to predators. This information will help managers identify the timing and 

location of critical factors limiting survival of juvenile salmon during residence and migration in 

Puget Sound. This will be a joint project between University of Washington, United States 

Geological Service, and WDFW and will coordinate with complementary efforts of Army Corps, 

NOAA Fisheries, tribes, and city and county agencies. 

Category B: Recover and Conserve Natural Spawning 

Populations 

Differences in Natural Production between Hatchery and Wild Coho 

Salmon: A Proposal to Measure the Influence of the Degree of 

Hatchery Ancestry on Natural Reproductive Success 

Project Sponsor: WDFW and NOAA Fisheries 

Principal Investigator: Howard Fuss, WDFW HSRG Share + Sponsor Share = Total Cost:

and Michael Ford, NOAA Fisheries $106,627 + $57,872 = $164,499 

Collaborators: NWIFC 

Project Summary: A key question facing salmon managers is how successful hatchery 

propagated fish and their offspring are at surviving and reproducing in the wild. This is critical for 

assessing both risks and benefits of hatchery supplementation. In this collaborative project 

National Marine Fisheries Service (NMFS) and Washington Department of Fish and Wildlife 

(WDFW), are using state-of-the art genetic techniques to evaluate the spawning success and 

survival in the wild of hatchery propagated and naturally produced coho salmon. The results of 

this project will, will for the first time, provide information on the rate at which hatchery fish 

readapt to the wild environment. 

Since the fall of 2000, all adult coho salmon returning to spawn in Minter Creek, Washington have 

been intercepted. The run consists of naturally produced and hatchery propagated coho salmon. 
Research Grants H-23 

Before being passed upstream to spawn naturally, each adult is measured, photographed, and 

tagged, its’ origin (hatchery or natural) determined, and a small non-lethal fin clip taken for later 

DNA analysis. Over the subsequent six years, the progeny of these fish are being sampled as fry 

and as yearling smolts and microsatellite DNA fingerprinting used to determine their parentage. 

From these data, the relative fitness of naturally spawning hatchery and natural-origin salmon will 

be estimated. In the years 2003-2008, the relative fitness of natural-origin fish with varying 

hatchery ancestry will be estimated, providing data on the rate hatchery coho readapt to the wild. 

Snow Creek Coho Salmon Recovery Program 

Project Sponsor: WDFW 

Principal Investigator: Steve Schroder, HSRG Share + Sponsor Share = Total Cost: 

WDFW $32,972 + $10,000 = $42,972 

Collaborators: Wild Olympic Salmon, 

North Olympic Salmon Coalition, PointNo-Point Treaty Council, Jamestown 

S’Klallam Tribe 

Project Summary: Beginning in 1998, WDFW, North Olympic Salmon Coalition, and Wild 

Olympic Salmon began an effort to recover a threatened coho salmon population native to Snow 

Creek, a Northeast Olympic Peninsula stream. Since then, every adult coho salmon returning to 

Snow Creek has been captured at a permanent weir. The fish are artificially spawned and their 

eggs are incubated at nearby Hurd Creek Hatchery. Offspring from each fish are placed into three 

alternative recovery strategies. One involves placing eyed-eggs into Remote Site Incubators 

located throughout the Snow Creek Basin. In the other two, fish are reared for either seven or ten 

months before being liberated as pre-smolts into Crocker Lake, a 25 hectare body of water that is 

used as a rearing and over-wintering location by Snow Creek coho salmon. Fish placed into each 

treatment group have their otoliths thermally marked and the reared fish are also tagged. The 

otolith marks and tags are used to determine: 1) how many smolts are produced from each 

treatment, 2) if treatment origin affects size and out-migration timing of smolts, and 3) whether a 

recovery strategy affects overall survival, size, age, fecundity, egg size, and reproductive effort at 

maturation. This approach will be continued annually until 2006. In 2001 and 2002 adult coho 

were allowed to reproduce naturally in Snow Creek to create a fourth treatment type. Results from 

this study will be used to help refine coho recovery throughout Puget Sound and the Washington 

Coast. 

Hamma Hamma River Steelhead Supplementation Evaluation 

Project Sponsor: NOAA Fisheries 

 

Principal Investigator: Barry Berejikian, HSRG Share + Sponsor Share = Total Cost:

NOAA Fisheries $68,226 + $105,660 = $173,886 
H-24 Research Grants 

Collaborators: Long Live the Kings, 

Hood Canal Salmon Enhancement, 

WDFW, Point-No-Point Treaty Council 

Project Summary: This project evaluates the impacts of a steelhead supplementation program on 

changes in spawner abundance in the Hamma Hamma River, where confounding variables (e.g., 

habitat degradation, harvest) will have minimal influence. Collaborators include Long Live the 

Kings, Hood Canal Salmon Enhancement Group, NOAA Fisheries. WDFW, and Point No Point 

Treaty Council The project addresses several aspects of the conservation hatchery paradigm 

including: natural growth profiles, enriched hatchery rearing habitats, alternative release strategies, 

and experimentation to improving captive broodstock technologies. The specific research 

objectives are as follows: 

1) Determine whether the supplementation program affects the abundance of naturally spawning 

steelhead in the Hamma Hamma River; 2) Determine the relative reproductive success of female 

steelhead from two different reintroduction strategies (smolt vs. adult release); 3) Estimate the 

relative abundance of steelhead spawners produced from i) wild smolts, ii) smolts reared in 

'conservancy' ponds, and iii) smolts reared in hatchery tanks; 4) Develop rearing protocols to 

produce steelhead smolts with a two-year freshwater rearing history, such that growth profiles 

mimic those of wild fish; and 5) Compare the reproductive behavior and breeding success of 

captively reared steelhead grown in high versus low water velocity environments. 

Category C: Improve Quality and Cost-Effectiveness of Hatchery 

Programs 

Increase Post-Release Survival by Rearing Coho with NATURES SemiNatural Raceway Habitat 

Project Sponsor: NOAA Fisheries 

Principal Investigator: Des Maynard, HSRG Share + Sponsor Share = Total Cost:

NOAA Fisheries $82,172 + $126,580 = $208,752 

Associate Investigator: Geraldine Vander- Collaborators: WDFW, Tribes 

Haegen, WDFW 

Project Summary: It has been repeatedly demonstrated that rearing Chinook salmon in 

NATURES semi-natural raceway habitat increases their instream survival. In the current study, 

WDFW and NMFS are conducting a 4 year evaluation to determine if NATURES rearing in a 

production environment increases the number of coho salmon recruiting to the fishery and 

spawning population. The research is being conducted with salmon grown in standard concrete 

raceways at Puget Sound hatcheries. At each hatchery, there are control and semi-natural habitat 

raceways. The semi-natural habitat was created by fitting the raceways with: 1) gravel pavers, 2) 
Research Grants H-25 

fir tree instream structure, and 3) camouflage net overhead covers. Fish growth, color 

development, and health are being routinely monitored and compared. Experimental and control 

fish are coded-wire-tagged to measure their contribution to the fishery and spawning population. 

NATURES semi-natural raceway habitat rearing is expected to increase the relative number of 

fish recruiting to the fishery and spawning population by 25%. Managers can use the increased 

survival offered by NATURES salmon culture practices to restore natural spawning runs, maintain 

sustainable fisheries, promote economically efficient salmon culture, and reduce ecological 

interactions with ESA listed wild salmon populations. 

Development of Engineered Streams for Salmon Production 

Project Sponsor: University of Idaho 

Principal Investigator: Ernest Brannon, UI HSRG Share + Sponsor Share = Total Cost:

 $30,464 + $0 = $30,464 

Collaborators: WDFW, NOAA Fisheries 

Project Summary: This project is a demonstration of a new concept that combines the benefits of 

hatcheries and natural habitat to improve salmon populations. In collaboration with the WDFW 

development of engineered streams is being investigated by the University of Idaho as a longrange alternative to hatcheries for supplementation of weak or failing wild salmonid populations. 

The objectives are to provide natural-type engineered streams for coho salmon production that 

result in wild smolt quality and to monitor performance as a demonstration project for this new 

hatchery concept. The approach is to develop artificial streams for use as salmon habitat with 

engineering specifications based on the biological criteria of the species targeted, while 

maintaining genetic specificity, diversity, and natural smolt quality. The artificial stream will 

substitute for, or be used in conjunction with, standard hatchery raceways. Natural feed with 

supplemental artificial diets will be the source of food. The site selected is Hatchery Creek located 

immediately behind the WDFW hatchery on the Dungeness River. A channel was constructed 

with habitat structures, pools, riffles, and cover to mimic natural coho habitat. Production levels 

were comparable to natural habitat at 1.5 smolt/m2

. Based on the previous two years of data, the 

channel will be modified to increase volitional rearing densities and increase smolt production to 

levels above natural production while still maintaining wild fish characteristics. 
A Scientific and Systematic Redesign of Hatcheries Programs to 

Help Recover Wild Salmon and Support Sustainable Fisheries 

HATCHERY REFORM

RECOMMENDATIONS

Eastern Strait of Juan de Fuca, South Puget 

Sound, Stillaguamish and Snohomish Rivers 

Prepared By, 

The Hatchery Scientific Review Group 

February 2002 
Please cite as: 

Hatchery Scientific Review Group (HSRG)–Lars Mobrand (chair), John Barr, Lee Blankenship, 

Don Campton, Trevor Evelyn, Conrad Mahnken, Robert Piper, Lisa Seeb and Bill Smoker. 

February 2002. Hatchery Reform Recommendations for the Puget Sound and Coastal 

Washington Hatchery Reform Project. Long Live the Kings, 1305 Fourth Avenue, Suite 810, 

Seattle, WA 98101 (available from www.hatcheryreform.org). Cite in text as HSRG 

Recommendations 2002. 

All Hatchery Reform Project publications are available from the project’s web site 

(www.hatcheryreform.org) or by contacting Long Live the Kings at (206) 382-9555. 
Table of Contents 

Table of Contents Hatchery Reform Recommendations – February 2002 i 

 COMPONENTS OF THIS REPORT .................................................................................... 3

 EASTERN STRAIT OF JUAN DE FUCA ............................................................................ 7

Overview ..............................................................................................................................................................7

DUNGENESS ................................................................................................................................. 9 

Overview ..............................................................................................................................................................9

Dungeness Chinook............................................................................................................................................11

Dungeness Hatchery Coho.................................................................................................................................14

Dungeness Fall Pink ..........................................................................................................................................17

Dungeness Hatchery Winter Steelhead ..............................................................................................................19

ELWHA ...................................................................................................................................... 21 

Overview ............................................................................................................................................................21

Elwha Chinook...................................................................................................................................................23

Elwha Coho........................................................................................................................................................26

Elwha Chum.......................................................................................................................................................28

Elwha Hatchery Winter Steelhead .....................................................................................................................31

SMALLER WATERSHEDS ............................................................................................................ 33 

Overview ............................................................................................................................................................33

Smaller Watersheds Summer Chum ...................................................................................................................35

Smaller Watersheds Hatchery Winter Steelhead................................................................................................37

Snow Creek Coho...............................................................................................................................................39

Smaller Watersheds Other Hatchery Coho........................................................................................................41

 SOUTH PUGET SOUND ...................................................................................................... 43

Overview ............................................................................................................................................................43

CHAMBERS CREEK BASIN.......................................................................................................... 46 

Overview ............................................................................................................................................................46

Chambers Basin Hatchery Fall Chinook ...........................................................................................................48

Garrison Springs Chum .....................................................................................................................................51

NISQUALLY RIVER AND DELTA ................................................................................................. 53 

Overview ............................................................................................................................................................53

Nisqually River Fall Chinook.............................................................................................................................55

McAllister Creek Hatchery Fall Chinook ..........................................................................................................58

Nisqually River Coho.........................................................................................................................................60

DESCHUTES RIVER..................................................................................................................... 62 

Overview ............................................................................................................................................................62

Deschutes River Hatchery Fall Chinook............................................................................................................65

Deschutes River Hatchery Steelhead .................................................................................................................67

SQUAXIN/SOUTH SOUND NET PENS AND INDEPENDENT TRIBUTARIES ...................................... 69 

Overview ............................................................................................................................................................69

Squaxin/South Sound Net Pens Hatchery Coho.................................................................................................71

KEY PENINSULA ........................................................................................................................ 74 

Overview ............................................................................................................................................................74

White River Spring Chinook (Hupp Springs).....................................................................................................77

Minter Creek Hatchery Fall Chinook ................................................................................................................79

Coulter Creek Hatchery Fall Chinook...............................................................................................................81

Fox Island Net Pens Hatchery Fall Chinook .....................................................................................................83

Minter Creek Coho.............................................................................................................................................85
Table of Contents 

ii Hatchery Reform Recommendations – February 2002 Table of Contents 

Fox Island Net Pens Hatchery Coho..................................................................................................................87

Minter Creek Chum............................................................................................................................................89

Minter Creek Pink..............................................................................................................................................91

 STILLAGUAMISH/SNOHOMISH ..................................................................................... 93

Overview ............................................................................................................................................................93

STILLAGUAMISH ........................................................................................................................ 97 

Overview ............................................................................................................................................................97

North Fork Stillaguamish Summer Chinook ......................................................................................................99

North Fork Stillaguamish Chum ......................................................................................................................102

South Fork Stillaguamish Chum ......................................................................................................................105

Stillaguamish Coho..........................................................................................................................................107

North Fork Stillaguamish Hatchery Summer Steelhead ..................................................................................109

South Fork Stillaguamish Hatchery Summer Steelhead...................................................................................111

Stillaguamish Hatchery Winter Steelhead........................................................................................................114

SNOHOMISH ............................................................................................................................. 117 

Overview ..........................................................................................................................................................117

Snohomish/Skykomish Summer Chinook..........................................................................................................120

Snohomish/Skykomish Hatchery Coho.............................................................................................................123

Snohomish Hatchery Winter Steelhead ............................................................................................................125

Snohomish Hatchery Summer Steelhead..........................................................................................................128

TULALIP BAY AND INDEPENDENT TRIBUTARIES ...................................................................... 131 

Overview ..........................................................................................................................................................131

Tulalip Bay Hatchery Spring Chinook.............................................................................................................132

Tulalip Bay Hatchery Summer Chinook...........................................................................................................134

Tulalip Bay Hatchery Fall Chinook.................................................................................................................136

Tulalip Bay Hatchery Coho .............................................................................................................................138

Tulalip Bay Hatchery Chum.............................................................................................................................140

Other Hatchery Coho.......................................................................................................................................142

 APPENDICES ...................................................................................................................... 145

Appendix A: Jamestown S’Klallam Tribe Full Comments...............................................................................145

Appendix B: Nisqually Tribe Full Comments...................................................................................................150

Appendix C: Squaxin Island Tribe Full Comments..........................................................................................152

Appendix D: Stillaguamish Tribe Full Comments............................................................................................156

Appendix E: Tulalip Tribes Full Comments.....................................................................................................161
Components Hatchery Reform Recommendations – February 2002 3 

Components of This Report 

This report provides the recommendations developed by the Hatchery Scientific Review Group 

(HSRG) upon reviewing three regions during 2001—the Eastern Strait of Juan de Fuca, South Puget 

Sound, and the Stillaguamish and Snohomish rivers. It includes a chapter for each of the regions 

reviewed. Each of these chapters begins with a general overview of the region and/or its identified 

sub-regions, a table containing ratings for all salmonid stocks in that region (as provided by the 

managers), then reviews and recommendations for each salmonid stock that has an associated 

hatchery program. 

This report focuses primarily on issues that need to be addressed and recommends changes that need 

to be made. It should not be read as a complete review listing every positive attribute alongside those 

that need to be changed. The HSRG has, overall, been very impressed by the diligence—and 

frequently the ingenuity—with which the state and tribal staffs carry out their programs; and with 

their dedication to the resource. 

It is important to note that the recommendations contained in this document are based upon the goals 

stated and best scientific information available at the time the reviews were conducted. This 

document has not been updated since 2002 to take into account actions to implement these 

recommendations, nor to reflect refinements in the HSRG’s terminology and/or approach as the 

regional review process went along. In keeping with the tenets of adaptive management, 1 it will be 

necessary to review and adapt these recommendations as new scientific information arises and/or 

goals change. This and all other Hatchery Reform Project-related publications are available from the 

project’s web site (www.hatcheryreform.org) or by contacting Long Live the Kings at (206) 382-

9555. 

Program Recommendations 

Each individual salmonid stock program review and recommendations section begins with a listing of 

the managing agency(s) and/or tribe and a table that provides the current, short-term (10–12 year) and 

long-term (50 year) stock goals and associated hatchery program purpose and type, as they were 

expressed to the Scientific Group by the managers during the regional review process (see example 

below). Following the example table are definitions of each rating included in the table. 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability Critical Critical At Risk 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity None None Occasional 

Hatchery Program:

Purpose Conservation 

Type Integrated 

 

1 See HSRG Report, chapter on Emerging Issues in Hatchery Management, for a discussion on adaptive management.
4 Hatchery Reform Recommendations – February 2002 Components 

Biological significance is determined by considering a number of specific factors relating to stock 

origin, biological attributes and population subdivisions (see HSRG Scientific Framework and 

Hatchery Review Program for more detail), with the stock defined as being of either low, 

intermediate or high significance. 

Population viability is also determined by considering a number of specific factors such as age class 

structure, spawner escapement and proportion of hatchery-origin fish in natural spawning (see HSRG 

Scientific Framework and Hatchery Review Program for more detail), with the stock’s viability 

defined as being either critical, at risk or healthy. This rating refers to the stock’s ability to sustain 

itself in the natural environment (except in the case of a segregated harvest program, in which case 

the ratings are low, medium and high and refer to the stock’s ability to sustain itself in the culture 

environment). 

The stock’s spawning, freshwater, migration and estuarine habitat is rated as either inadequate

(target stock is unproductive and the population will go extinct, even without terminal harvest), 

limiting (target stock is productive enough for the population to sustain itself at a low level terminal 

harvest) or healthy (productivity of the stock is high and the population is capable of growth and 

supporting significant terminal harvest). 

Harvest opportunity is rated according to whether the goal is to provide no directed harvest 

opportunity, occasional opportunity, opportunity most years, or opportunity each year. 

The purpose of the hatchery program is defined as either conservation, harvest, both and/or another 

purpose (such as education, research or cultural/ceremonial). 

The type of program is also included. Hatchery programs are classified as integrated if the goal is to 

minimize potential genetic divergence between the hatchery broodstock and the naturally-spawning 

population in the watershed where fish are released and returning adults trapped for broodstock. 

Segregated programs are classified as those in which the goal is to maintain the hatchery population 

as a distinct, or genetically segregated, population.2

Following this table, each stock review and recommendations section includes: 1) the Program 

Description as provided by the managers, including Genetic Diversity Unit (GDU) information,3

 2) 

 

2 See HSRG System-Wide Recommendation on operating integrated and segregated hatchery programs.

3 A genetic diversity unit (GDU) is a group of genetically similar stocks that is genetically distinct from other such groups. The 

stocks typically exhibit similar life histories and occupy ecologically, geographically, and geologically similar habitats. Information 

about GDUs and broodstock origin included in these program descriptions provided by Washington State Department of Fish and 

Wildlife staff; GDU information is based on Busack, C. and J. B. Shaklee. 1995. Genetic Diversity Units and Major Ancestral 
Components Hatchery Reform Recommendations – February 2002 5 

Operational Considerations (elements recognized by the Scientific Group in considering the way the 

program is currently being operated), 3) the Benefits and Risks being conferred by the program on the 

target stock and other regional stocks,4

 4) the Recommendations from considering benefits and risks, 

5) a section for other Comments on the program from the Scientific Group, and 6) a section for a 

Response to the review and recommendations from the relevant management agency(s) and/or tribes. 

 Lineages of Salmonid Fishes in Washington. Washington State Department of Fish and Wildlife, Technical Report #RAD 95-02. A 

table listing all Puget Sound and Coastal Washington GDUs is included as an appendix to this report. 4 The HSRG understands that the terms "risk" and "benefit" are sometimes used to convey a specific legal or policy status, 

condition or decision about the results of a particular action, policy or program. For the purposes of the HSRG's review and 

recommendations, these terms are not being used in this manner, but rather in the general sense of whether a hatchery program, 

or some aspect of that program, is likely to be affecting one or more regional salmonid stocks in a positive and/or negative way. 

The intent is to provide policy makers with a sense of the trade-offs involved in different options or courses of action.

Eastern Straits Hatchery Reform Recommendations – February 2002 7 

Eastern Strait of Juan de Fuca 

Overview 

This region includes the eastern portion of the Strait of Juan de Fuca, from Point Wilson to the Hoko 

River. For the purposes of this review, the Scientific Group and the regional managers divided the 

region into three sub-regions and reviewed the hatchery programs involving each identified subregional salmonid stock (for example, Dungeness chinook). The review included a consideration of 

the program’s effects on all other hatchery and naturally spawning sub-regional salmonid stocks (see 

table in sub-regional overviews). The sub-regions identified for this region include: 

1. Dungeness River Watershed 

2. Elwha River Watershed 

3. Smaller Watersheds 

This chapter provides a general overview of the Eastern Straits and each sub-region, followed by 

reviews and recommendations for each salmonid stock that has an associated hatchery program. 

Habitat in the Eastern Straits is expected to be worse or the same in the short-term, but better in the 

medium- and, especially, long-term. There are ongoing efforts to modify the Dungeness River dikes 

to return the river to its meander channels. The upper Elwha River is scheduled to be available as 

salmon habitat, with the removal of two major dams. The Dungeness River Management Team, the 

Forest and Fish Initiative, the Critical Areas Ordinance of the Clallam County Growth Management 

Act, as well as more critical review of projects via the Shorelines Management Act and State 

Environmental Policy Act, should all combine to slow or reverse the habitat losses of the past. In 

addition, Jimmycomelately Creek has a lower stream channel and estuary restoration project that will 

significantly improve conditions for summer chum. Although all these sub-regions currently have 

much poor quality habitat, they are still producing coho, cutthroat and steelhead, at some level, over a 

large portion of each sub-region.5

 

5 Chris Byrnes, Washington State Department of Fish and Wildlife, May 1, 2001
8 Hatchery Reform Recommendations – February 2002 Eastern Straits 
Eastern Straits Hatchery Reform Recommendations – February 2002 9 

DUNGENESS 

Overview 

STOCK STATUS6

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Dungeness Chinook Y H H H M M H M M H 0 L M

Dungeness Hatchery Coho Y M M M M M M M M M H H H

Dungeness Fall Pink Y H H H L LML LM00 L

Dungeness Summer Pink N H H H M M H M M M 0 0 L

Dungeness Chum N ? ? ? L L ? L L M 0 0 0

Dungeness Hatchery Winter Steelhead Y M M H L L M M M H L L M

Dungeness Summer Steelhead N ? ? ? L L ? M M H 0 0 ?

Goals

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Hatchery Program?

Now Now Now Now

Goals Goals Goals

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Stocks

HABITAT

Salmonid habitat condition in the mainstem Dungeness River is currently fair to poor. Major habitat 

concerns include the diversion of instream flow for irrigation, loss of functional floodplain and 

estuary in the lower watershed, lack of habitat complexity, substrate instability, and poor riparian 

condition. Habitat conditions on lower watershed tributaries are also currently impaired. On 

McDonald, Seibert and Bagley Creeks, habitat concerns include fish access, substrate quality, use of 

stream for irrigation conveyance, and effects on some tributaries. The mouth of each of these streams 

is isolated from saltwater during summer months by formation of a natural sandbar across the mouth. 

This likely effectively limits access and production from these streams. 

Upper watershed tributaries in Olympic National Park remain in good condition. There are significant 

habitat restoration efforts underway in the watershed. Improvements in instream flow have been made 

in recent years. An evaluation of feasibility of floodplain and estuary restoration in the lower river is 

currently underway. There have been significant efforts to improve substrate stability and quality. 

Several projects are reintroducing habitat complexity. Currently impaired habitat conditions in US 

Forest Service-managed areas in the upper watershed are expected to significantly improve with 

implementation of the Forest Plan. There are mainstem and tributary “islands” of high-quality habitat 

that warrant protection or have high restoration potential. With anticipated habitat restoration actions, 

future watershed potential to produce naturally spawning salmonids is considered to be good7

. 

 

6 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction. 

7 Donald Haring, Washington Conservation Commission, March 19, 2001. 
10 Hatchery Reform Recommendations – February 2002 Eastern Straits 

HATCHERIES

Dungeness Hatchery 

Dungeness Hatchery is located six miles southwest of Sequim on the Dungeness River. The total 

hatching capacity is approximately 7.5 million fry. Release capacity for the station is approximately 

two million fish, depending upon the size of the fish. 

Hurd Creek Hatchery 

Hurd Creek Hatchery is located approximately four miles north of Sequim on Hurd Creek, a 

Dungeness River tributary. It is operated as a satellite to the Dungeness Hatchery. It was originally 

built to support the Dungeness and Elwha hatcheries. In recent years, considerable capital investment 

has been made at Hurd Creek Hatchery specifically aimed at providing optimum stock recovery 

capacity. The 1997 brood year was the last year that naturally spawning-origin Dungeness chinook 

were brought into the facility. It is anticipated that by 2003, all but a small group of captive brood fish 

will have matured. 8

 

8 Washington State Department of Fish and Wildlife Dungeness/Hurd Creek hatcheries staff. 
Eastern Straits Hatchery Reform Recommendations – February 2002 11 

Dungeness Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability At Risk At Risk Healthy 

Habitat Limiting Limiting Healthy 

Harvest Opportunity None Occasional Most Years 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Dungeness chinook stock was derived from pumping wild fish redds and seining of juveniles in 

the Dungeness River from 1992–97. This stock is maintained through a captive brood program at 

Hurd Creek Hatchery. Dungeness chinook salmon are one of two stocks in the Eastern Strait Chinook 

GDU. The purpose of this program is to conserve this biologically significant population of ESAlisted chinook. The resulting offspring are maintained in captivity to adulthood at the Hurd Creek 

Hatchery. Offspring from the captive-bred fish are incubated at Hurd Creek Hatchery and transferred 

to the Dungeness Hatchery until release as sub-yearling juvenile salmon. This program is being 

phased out. The current and future program size is limited to the 1,028 remaining captive broodstock 

(of 1995–97 brood year classes) currently on hand. 

The present program includes releases into the Dungeness River of 200,000 sub-yearlings at 450 fish 

per pound (fpp) in May, 400,000 at 200 fpp in July and 775,000 at 80 fpp in August. Approximately 

200,000–400,000 fish at 250 fpp and 80 fpp are released from an acclimation pond on the Gray Wolf 

River (upper Dungeness watershed). Additionally, 200,000 sub-yearlings at 450 fpp are released in 

May at various locations along the Gray Wolf River. 

OPERATIONAL CONSIDERATIONS

• The annual average chinook spawner escapement estimate from 1986–99 is 147 adults, ranging 

from 45–335. Dungeness River chinook recruit-to-spawner ratio has been less than 1:1 in five 

years, greater than 1:1 in five other years, and 1:1 in one year. 

• Release of Dungeness chinook as sub-yearlings presupposes that the predominant juvenile life 

history pattern of natural fish is less than one year of freshwater residence, and that out migration 

is as zero-age fish. Owing to low water temperatures at the Dungeness Hatchery, chinook do not 

attain the preferred release size of seven to ten grams until after the optimum release time in June, 

and are not released until late July or August. 

• Natural sub-yearlings migrate seaward and reside in the lower river, and/or adjacent estuary, for 

an unknown period before leaving the Dungeness Delta area. 
12 Hatchery Reform Recommendations – February 2002 Eastern Straits 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The short-term goals of maintaining the Dungeness chinook in protective custody, while maintaining 

genetic characteristics of the stock, in order to protect the stock from extinction, are likely being met. 

However, the program has not been successful to date in rebuilding runs and the stated goals for 

short- and long-term viability of naturally produced chinook in the system are a cause for concern. 

The offspring of the captive-bred Dungeness chinook, released as fry or small sub-yearling fish, will 

probably not exhibit survivals sufficient to attain conservation goals. The carrying capacity of the 

river and near-shore estuary appears to be unknown. This is of concern, considering the number and 

biomass of released sub-yearlings originating from the captive broodstock program and released from 

the Dungeness Hatchery. 

B. Likelihood of attaining goals? 

Chinook habitat in the mainstem Dungeness River is degraded due to diversion of instream flow for 

irrigation, loss of functional floodplain and estuary in the lower watershed, lack of habitat 

complexity, substrate instability, and poor riparian condition. This fair to poor habitat condition and 

the poor short-term outlook for improvement decreases the chances for recovery. 

C. Consistent with goals for other stocks? 

The program to conserve and enhance this stock appears to be consistent with the goals for other 

salmonid stocks in the Dungeness River Basin. 

RECOMMENDATIONS

• Initiate a field study to describe the life history patterns of Dungeness chinook, including a 

description of juvenile and adult life history phases, and their distribution, abundance and 

migratory movements into, within and out of the river and estuary. A careful study in relation to 

habitat quality and type will be invaluable in determining the carrying capacity for chinook 

juveniles in the Dungeness River and for designing future hatchery-based recovery programs. 

• Continue the restorative captive broodstock program with broodstock on hand. Size the hatchery 

program (adults used, smolts released) to match riverine carrying capacity. Discontinue zero age 

releases in July and August. Provide the capability to produce a mix of zero-age and yearling 

chinook. 

• Develop an alternate recovery plan. Consider phase-in of a new hatchery program that does not 

involve captive broodstock, but continues the goal of maintaining genetic resources and reduces 

the risk of extinction. 

• Seek new water source(s) to provide warmer rearing water than presently exists at the Dungeness 

Hatchery. 

• Remove the intake barrier at Canyon Creek to allow passage of adult and juvenile chinook to 

historic spawning/rearing habitat. Open the side channel above and across the river from Canyon 

Creek and near the current Dungeness River intake at the Dungeness Hatchery, to provide 

important off-channel rearing habitat for chinook juveniles. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 
Eastern Straits Hatchery Reform Recommendations – February 2002 13 

COMMENTS

• Evidence for the existence of an alternate life history pattern was seen in studies conducted in 

1996–97 (Jamestown S'Klallam Life History Study). Sampling of wild and captive broodstock 

offspring in this study began in June and was completed in October of 1996 and September of 

1997. The authors concluded that the dominant life history pattern of out-migration was in the 

form of sub-yearling migrants that left the system or migrated to the lower river in the spring of 

their first year. Few yearling individuals were observed. However, yearlings do not typically outmigrate that late in the year and, if present, would have likely left the Dungeness system prior to 

commencement of the sampling program. Recent evidence gathered during snorkel surveys in the 

lower Elwha River indicate the presence of large, yearling chinook salmon residing in that river 

system as well. Yearling chinook smoltification and out-migration may not be a numerically 

important life history form in these two river systems, but may nevertheless constitute an 

important alternate life history form important to survival, and should be included in future fish 

culture programs. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG and has taken the following actions: 

• Rearing strategy now targets the release of age-zero chinook prior to July. 

• Test wells are being drilled to evaluate the opportunities to obtain warmer water and facilitate the 

removal of the intake barrier at Canyon Creek. 

• Additional funding will be required to conduct studies to characterize the life history of this stock 

and identify habitat factors limiting stock productivity. 

The Jamestown S’Klallam Tribe generally supports the recommendations of the HSRG (the Tribe’s 

full comments are appended to this document). Many of the recommendations are consistent with 

those the co-managers have discussed for years. 

• The study of freshwater life history patterns can be implemented in both the freshwater and 

marine environments, but we note that additional funding will be necessary to accomplish this 

task. 

• Hatchery release strategies must be evaluated through analysis of coded wire tag recoveries. 

Evaluation of yearling release strategies will begin this year. 

• Efforts to develop a recovery plan that moves the managers beyond the captive broodstock 

program will begin this year. 

• Plans to develop well water sources for Dungeness hatchery are underway. 

• Restoration of Canyon Creek can begin immediately if an alternate ground supply is secured by 

WDFW. 

• Opening of the Dungeness side channel will be evaluated by experts in river hydrology. 
14 Hatchery Reform Recommendations – February 2002 Eastern Straits 

Dungeness Hatchery Coho 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate Intermediate 

Population Viability9 Medium Medium Medium 

Habitat Limiting Limiting Limiting 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Dungeness Hatchery coho stock originated primarily from wild spawners in the Dungeness 

River, with a few introductions from the Elwha River. This stock has been maintained primarily from 

returnees to the Dungeness Hatchery since 1902. The goal of this program is to provide for harvest. 

Natural stock conservation is not currently a goal of the program. To this end, 500,000 coho yearlings 

are released from the Dungeness Hatchery each year. Eggs are collected and incubated on-station. 

Fish are reared and released on-station. 

OPERATIONAL CONSIDERATIONS

• The operations of this program are consistent with guidelines for a segregated harvest program, 

particularly since conservation goals for the natural coho stock are considered secondary to 

meeting harvest goals in this watershed. 

• The program has also taken reasonable steps to reduce potential ecological interactions with pink 

salmon by delaying release of hatchery coho during pink years. 

• The program has recently reduced production from 800,000 yearlings to the current level of 

500,000 yearlings, primarily because of concern about negative ecological interactions with 

depressed natural stocks in the basin. 

• Because conservation goals are currently secondary to harvest goals, there is currently little or no 

monitoring of the natural coho populations in the Dungeness River. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is meeting regional harvest goals by providing a high level of terminal area fishing and 

contributing to pre-terminal harvest. The fishery supported by this program’s production is currently 

 

9 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in the 

culture environment. 
Eastern Straits Hatchery Reform Recommendations – February 2002 15 

the only significant fishery in Dungeness Bay and the Dungeness River. However, the goals stated for 

short- and long-term biological significance and viability of naturally produced coho in this system 

indicate that there is reason to be concerned about the effects of this program on the natural stock, 

including straying and ecological risks.

B. Likelihood of attaining goals? 

If the goal is to maintain the natural population as a segregated population (that is, with the natural 

escapement goal of 500 fish being primarily natural origin recruits), strays from the hatchery program 

are likely to be inconsistent with that goal and in the long-term may result in a reduction in biological 

significance and population diversity. 

C. Consistent with goals for other stocks? 

Risks to other populations include predation risks to Dungeness chinook, summer and fall pink 

salmon, and risks from competition and genetic interactions with naturally produced coho stocks in 

the region. There are also potential risks from harvest activities directed at this stock on naturally 

produced coho originating from other independent Eastern Straits tributaries. Naturally spawning, 

hatchery origin coho may be posing significant risks to chinook and pink redds in the Dungeness 

River.

RECOMMENDATIONS

• Determine the status and define goals for the natural coho stock in the Dungeness River. 

• Do not increase the size of the program above its current level because of the concern for 

negative ecological interactions with other important stocks within the basin. 

• Evaluate whether the program could be modified into an integrated harvest program, 

incorporating natural origin recruits into the hatchery broodstock, to reduce the genetic risk from 

hatchery straying. 

• Evaluate the effects of naturally spawning, hatchery-origin coho on the stability of chinook and 

pink salmon redds in the Dungeness River and modify the program to address this concern. 

COMMENTS

None. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG, but notes that additional funding will be 

required to evaluate the status of the natural coho stock and the effects of naturally spawning, 

hatchery-origin coho on chinook and pink redds. 

The Jamestown S’Klallam Tribe generally supports the recommendations and comments of the 

HSRG (the Tribe’s full comments are appended to this document). Of particular importance is the 

recognition of the contribution of this program to the culture and economy of the Tribe. 

• Evaluation of the status of the natural coho run and the interaction of smolt releases with natural 

stocks can be implemented in conjunction with the evaluation of life history strategies of 

Dungeness chinook. Additional funding will be necessary to accomplish this task. 

• Efforts to assess the origin and distribution of coho spawners, and potential interactions with 

chinook and pink salmon spawning have begun. 
16 Hatchery Reform Recommendations – February 2002 Eastern Straits 

• A better understanding of the current size and productivity of the natural coho stock as suggested 

in the HSRG’s first recommendation is necessary to evaluate the possibility of successful 

incorporation of natural spawners into the hatchery broodstock. 
Eastern Straits Hatchery Reform Recommendations – February 2002 17 

Dungeness Fall Pink 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability Critical Critical At Risk 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity None None Occasional 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Dungeness fall pink stock derives from, and is maintained by, wild adults trapped and genetically 

identified as fall (versus summer) in the Dungeness River. This program began in 1995. Dungeness 

fall pink salmon return in odd years and are the only stock within the Lower Dungeness GDU. The 

objective of this program is to conserve the fall pink stock (which has experienced significant 

declines) and to achieve this without genetic introgression from summer pinks (which use different 

sections of the river, but overlap somewhat in spawn timing). To this end, up to 1,200 adults are 

captured for spawning. Eggs are incubated at Hurd Creek and fry are released off-station.

OPERATIONAL CONSIDERATIONS

• Fall-run adults are collected via a weir or trap in the lower reach and transported to Hurd Creek 

Hatchery. 

• All individuals are typed by DNA to ensure only fall run individuals are included. Individuals 

identified as summer run, or those with indistinguishable genotypes, are excluded. 

• Incubation and rearing occurs in pathogen-free well water. 

• Development and ponding times are manipulated to achieve the characteristics of the natural run. 

• Individuals are transported to river mile 2.2 and released in May. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

Habitat in the Lower Dungeness River is currently poor, due to diversion of instream flow and loss of 

floodplain. This is not expected to change in the short-term. The fall-run pink salmon population is 

highly significant, representing the only stock in the GDU. Its viability is at a critical level. Given the 

condition of the habitat, the program is consistent with the stated goals.

B. Likelihood of attaining goals? 

Program risks to the fall-run pink salmon population include potential genetic divergence of the 

hatchery population from the naturally spawning population, decrease in effective population number, 
18 Hatchery Reform Recommendations – February 2002 Eastern Straits 

and incorporation of summer-run genes into the fall-run gene pool. Procedures are available to 

minimize these risks (see Recommendations).

C. Consistent with goals for other stocks? 

Potential risks to other stocks in the watershed include trapping mortality and handling stress to 

Dungeness chinook and summer-run pink salmon. Summer-run pink salmon may also experience 

delayed migration as a result of DNA testing. 

RECOMMENDATIONS

• Conduct a risk assessment analysis of the hatchery operations to evaluate the demographic and 

genetic benefits and risks. 

• Increase the probability of separating fall-run from summer-run individuals through improved 

genetic identification or other marking techniques. 

• Minimize potential genetic divergence between the hatchery and naturally spawning population. 

• Follow mating protocols that maximize effective population size. 

• Consider acclimation procedures to improve imprinting and survival. 

• Review procedures to ensure the security of the stock. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• DNA identification can correctly discriminate approximately 75% of individuals belong to the 

fall run. Therefore, the program will tend to amplify those genotypes that are the most divergent 

from the summer run, a form of directional selection. An increase in the number of markers to 

reduce the proportion of unidentifiable genotypes could improve the classification ability. 

Alternative types of external marks with improved coverage should also be investigated. 

• Current program operations collect a large proportion of the total individuals belonging to the 

Lower Dungeness GDU. This places the unique gene pool at risk, should a catastrophic failure 

occur. Protocols and facilities should be reviewed to ensure sufficient redundancy and security. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. 

The Jamestown S’Klallam Tribe generally supports the recommendations and comments of the 

HSRG (the Tribe’s full comments are appended to this document). 

• A risk assessment analysis of the demographic and genetics risks and benefits of the hatchery 

program, including an assessment of the current habitat’s ability to support this population, is 

appropriate. 

• In 2001, analytical tools used for stock separation improved measurably. Different marking and 

tagging methods for cultured fish are currently being considered. 
Eastern Straits Hatchery Reform Recommendations – February 2002 19 

Dungeness Hatchery Winter Steelhead 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate High 

Population Viability10 Low Low Medium 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Occasional Occasional Most Years 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Dungeness hatchery winter steelhead stock derives from Bogachiel Hatchery Chambers Creek 

(Puget Sound) stock. The program began in 1994. It is maintained through fish returning to the 

Dungeness Hatchery and through annual supplementation of fish or eggs from Bogachiel Hatchery. 

The objective of this program is to provide for harvest without impacting other stocks, including 

naturally spawning steelhead (if they exist), in the watershed. To this end, 10,000 winter steelhead 

juveniles returning to the Dungeness Hatchery are reared at Hurd Creek Hatchery and released from 

Dungeness Hatchery. 

OPERATIONAL CONSIDERATIONS

• Low water temperatures at the Dungeness Hatchery inhibit the ability to culture steelhead to the 

desired size for release at the appropriate time. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

Program is consistent with the short-term goal of occasional harvest opportunity. 

B. Likelihood of attaining goals? 

Short-term harvest goals seem achievable; achieving long-term goals will depend upon 

implementation of the wild steelhead management zones plan described below. 

C. Consistent with goals for other stocks? 

Low release numbers pose negligible risk to other stocks. The HSRG has concerns about potential 

genetic interactions (outbreeding depression), predation and competition with other steelhead stocks, 

particularly naturally spawning stocks. 

 

10 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
20 Hatchery Reform Recommendations – February 2002 Eastern Straits 

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of wild 

steelhead management zones, where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Release hatchery yearling steelhead smolts between May 1 and May 15, at a target size of six to 

the pound, and at a condition factor of less than 1.0.

• Remove intake barrier at Canyon Creek. 

• Switch to well water, if possible, to address water temperature problems. 

COMMENTS

None. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG, but notes the following: 

• Implementing a regional system of wild steelhead management zones has a number of 

implications that will require discussion with the affected tribes and the Fish and Wildlife 

Commission. 

• Test wells are being drilled to evaluate the opportunities to obtain warmer water and facilitate the 

removal of the intake barrier at Canyon Creek. Achieving the target release size and date for 

yearling steelhead smolts will be difficult until that water supply is available. 

The Jamestown S’Klallam Tribe generally supports the recommendations and comments of the 

HSRG (the Tribe’s full comments are appended to this document), but notes the following: 

• Implementation of region-wide, wild steelhead management zones must be carefully evaluated 

based on biological factors and contribution to sustainable tribal fisheries. 

• Regional differences in appropriate release sizes and times may exist that warrant analysis of 

available size and time release data. 

• Dam removal and additional restoration of Canyon Creek likely represent some of the best 

tributary spawning habitat for steelhead, cutthroat, and coho. 

• Plans to develop well water sources for Dungeness hatchery are underway. If this source of water 

becomes available, all aspects of incubation and initial rearing should be improved. 
Eastern Straits Hatchery Reform Recommendations – February 2002 21 

ELWHA 

Overview 

STOCK STATUS11

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Elwha Chinook Y H H H M M H L M H 0 0 M

Elwha Coho Y M M H M M H L M H H L H

Elwha Pink N M M H L M H L M H 0 0 M

Elwha Chum Y M M H L M H L M H 0 0 M

Elwha Hatchery Winter Steelhead Y M M H M M H L M H H M H

Elwha Summer Steelhead N L ? ? L ? ? L M H L L ?

Now

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals Goals Goals

Now

Stocks Goals Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Now

HABITAT

Salmonid production in the Elwha River watershed is currently severely impaired due to the presence 

of the Elwha and Glines Canyon dams. Although habitat in the upper watershed is within the 

Olympic National Park and remains pristine, fish access is limited to only the lower 4.9 miles of what 

was historically a 77-mile range. Removal of the dam(s) has been authorized by Congress. Habitat 

condition downstream of Elwha Dam is poor (severely impaired) due to loss of suitable spawning 

substrate and loss of channel complexity. Some remaining floodplain side channels in the lower 

watershed have high-quality habitat. Potential to produce naturally spawning salmonids in the future 

is high, once the dams are removed and the associated habitat restoration matures. However, hatchery 

operations to maintain genetic integrity are imperative until habitat productivity is restored.12

HATCHERIES

Lower Elwha Hatchery 

The coho program at the Lower Elwha Fish Hatchery began in 1978 using Elwha River broodstock. 

Facility water is a mix of surface and ground water. Water quality of the facility is similar to that 

found in the Elwha River. Groundwater is collected using two wells located on the facility. Fish enter 

the facility by means of an outfall creek constructed for the hatchery. Holding facilities consist of a 

three-quarter acre earthen pond divided into three sections: the trap, a section for females, and a 

section for males. Spawning facilities consist of two sheds. The program uses an incubation facility 

located on the hatchery grounds with a maximum instantaneous incubational capacity of 6.7 million 

 

11 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.

12 Donald Haring, Washington Conservation Commission, March 19, 2001.
22 Hatchery Reform Recommendations – February 2002 Eastern Straits 

eggs. The hatchery’s rearing facility consists of 24 concrete raceways, eight fiberglass circular tanks, 

four asphalted rearing ponds and an earthen rearing pond. Fish are released directly from rearing 

ponds.13

Elwha Rearing Channel 

The Elwha Rearing Channel was built in 1974 to maintain and enhance the run of fall chinook salmon 

indigenous to the Elwha River system. Since its inception, this facility has attained the goal of 

maintaining this stock and forestalling further decline in numbers. However, some factors limit the 

success of this facility. These include poor and limited natural habitat, pre-spawning adult mortality 

caused by the protozoan Dermocystidium (sp.), hatchery juvenile mortality as result of air bladder 

fungus (Phoma), and an inability to secure enough broodstock from the river (via trapping, netting 

and/or gaffing). In recent years, winter steelhead or coho salmon rearing has also taken place. 

The Channel is located on the Elwha River, approximately seven miles west of Port Angeles, at river 

mile 2.9. The unscreened river intake is owned and operated by the city of Port Angeles. The Channel 

itself is 1400' x 50' and is divided into two sections by means of screens and stop logs. It was 

originally built as a spawning channel, but was never effective in that capacity, so it was modified 

into a rearing channel. A 125' x 50' adult trapping/holding area is located directly below the Channel 

outfall and is equipped with a 20' x 15' spawning shed. A 161⁄2 stack incubation system covered by 28' 

x 21' canvas Quonset hut is available for incubation of eggs that cannot be transferred off-station.14

(Note: See descriptions of Dungeness and Hurd Creek hatcheries, which are involved in Elwha subregional programs, in the Dungeness Overview) 

 

13 Larry Ward, Elwha Klallam Tribal staff, May 2001.

14 Greg Travers, WDFW Hatchery Specialist, with edits by Darrell Mills, WDFW, April 27, 2001.
Eastern Straits Hatchery Reform Recommendations – February 2002 23 

Elwha Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability At Risk At Risk Healthy 

Habitat Inadequate Limiting Healthy 

Harvest Opportunity None None Most Years 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Elwha chinook salmon stock derives from fish captured in the Elwha River during the 1920s, and 

has been supplemented with primarily Dungeness and Satsop (Chehalis basin) hatchery stocks. This 

stock is maintained through adults returning to the hatchery trap and through netting or gaffing adults 

on the spawning grounds. Elwha chinook salmon are one of two stocks in the Eastern Strait Chinook 

GDU. The primary purpose of this program is to maintain existing genetic resources in support of 

natural production in the basin, including the re-colonization of the upper watershed following dam 

removals. To this end, the program calls for the take of 4.3 million eggs (some adults are trapped at 

the Elwha Rearing Channel; most are collected in the Elwha River). Gametes are taken to the Hurd 

Creek Hatchery where they are eyed and then transferred to Soleduck Hatchery for hatching and early 

rearing. Final rearing occurs at the Elwha Rearing Channel. About 3.8 million sub-yearling smolts are 

released into the Elwha River. 

OPERATIONAL CONSIDERATIONS

• Brood stock management (collection and holding) is particularly challenging in this basin. 

• Current facilities require transfer of eggs and juveniles out of basin. 

• Rearing conditions and protocols do not simulate those in the naturally spawning environment 

with respect to temperature, growth pattern, release size and age. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The use of a single, large-scale rearing and release strategy puts the short- and long-term conservation 

goals at some risk, especially in light of the poor smolt-to-adult survival. Transfers of eggs and 

juveniles are potentially costly to the health and fitness of the population.
24 Hatchery Reform Recommendations – February 2002 Eastern Straits 

B. Likelihood of attaining goals? 

Recruits per spawner hovers around one, with no recent surplus for harvest. The likelihood of meeting 

short- and long-term goals would increase if the program were better tailored to the gene conservation 

and re-colonization objectives, with greater emphasis on quality and diversity.

C. Consistent with goals for other stocks? 

The program is consistent with goals for other Elwha River stocks, as significant adverse effects on 

these stocks appear unlikely. Ecological interaction among stocks should be a consideration in the 

development of the Elwha Restoration Plan. 

RECOMMENDATIONS

• Review the current program. A revised program may be more consistent with the conservation 

and re-colonization goals for the chinook stock. Maintain program size to provide an effective 

number of breeders of at least 500–1,000 adults per year. The program’s primary focus should be 

on improved quality and diversity of smolts. Success should not be equated with the number of 

juveniles reared and released, but rather on achieving the necessary effective number of adult 

broodstock (the HSRG has drafted a white paper on the subject of smolt quality). 

• Reduce or eliminate the need for transport of eggs and fry outside the watershed. This will require 

new or expanded facilities for incubation and early rearing. 

• Mimic natural life history patterns of the stock using a combination of release strategies, 

including yearling releases, growth modulation and natural rearing. 

• Ensure security of the stock through diverse rearing and release strategies and redundancy of 

facilities and systems. 

• Develop an explicit schedule that takes into account both genetic and demographic risks as a 

function of spawner abundance, composition and population trends. This will benefit broodstock 

management. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• This program has succeeded in preserving the Elwha chinook stock over a long period of time, 

under challenging conditions. 

• The review above is based on the current program. The HSRG is aware of current efforts to 

develop a plan for the recovery of chinook and other salmonids following the removal of two 

dams. The HSRG has provided informal comments on preliminary drafts of this plan. 

Specifically, the HSRG has suggested that this plan include contingencies for custody of the 

genetic resource under different environmental scenarios, including a schedule for disposition of 

returning adults as a function of run size. The HSRG has also urged the managers to consider the 

out-planting of adults into the upper watershed as a part of the recovery strategy. The plan should 

also emphasize the critical importance of monitoring and evaluation as a key component of a 

strategy for success. Additional consultation between the Elwha Recovery Team and the HSRG 

would likely be beneficial for development and refinement of the restoration and recovery plan. 
Eastern Straits Hatchery Reform Recommendations – February 2002 25 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG and notes the following: 

• The Elwha Fish Restoration Team is evaluating options to ensure the security of the stock during 

removal of the dams and reintroduction of the stock into the upper watershed. 

• Additional funding will be required to provide the facilities necessary to implement the 

recommendations. 

The Elwha Tribe generally supports the recommendations of the HSRG and notes the following: 

• The program will maintain a program size to provide greater than the recommended effective 

number of breeders of 500–1,000 adults per year. This approach will ensure stock maintenance 

and survival during dam removal. 

• Recommendations to focus on smolt quality are consistent with our current effort to evaluate 

enhanced rearing environments for possible incorporation into restoration efforts. 
26 Hatchery Reform Recommendations – February 2002 Eastern Straits 

Elwha Coho 

Lower Elwha Klallam Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate High 

Population Viability At Risk At Risk Healthy 

Habitat Inadequate Limiting Healthy 

Harvest Opportunity Each Year Occasional Each Year 

Hatchery Program:

Purpose Harvest and Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Elwha coho stock originated from wild stock in the Elwha River and has been supplemented with 

one-time introductions from the Satsop and Dungeness rivers. This stock is maintained through 

natural- and hatchery-origin fish that volunteer into the Lower Elwha Hatchery. Elwha coho belong to 

the Puget Sound/Strait of Georgia ESU. The goal of this program is the provision of harvest and 

simultaneous conservation of the stock for restoration of naturally spawning coho in the Elwha River 

after the dams are removed and habitat is restored. To this end, the program calls for the take of 1.2 

million eggs from 1,250 returning adults and 250 wild spawners. All incubation and rearing occurs 

onsite at the Lower Elwha Hatchery. 750,000 smolts are released from the Lower Elwha Hatchery. 

OPERATIONAL CONSIDERATIONS

• The program takes eggs from all parts of the run and culls down to an appropriate size. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program has been self-sustaining, importing eggs only once in the past three decades. 

Performance has been consistent with the goal of annual harvest. 

B. Likelihood of attaining goals? 

The program is likely to succeed in maintaining a viable population of coho in the lower river and 

some annual harvest. 

C. Consistent with goals for other stocks? 

There is the potential for coho to prey on chum fry, but there are no data suggesting that this is 

occurring here. The program is otherwise consistent with goals for other Elwha River stocks, as 

significant adverse effects on other stocks appear unlikely. Ecological interaction among stocks 

should be a consideration in the development of the Elwha Restoration Plan. 
Eastern Straits Hatchery Reform Recommendations – February 2002 27 

RECOMMENDATIONS

• Continue and strengthen the use of natural rearing. 

• Incorporate marking and tagging as a necessary tool for evaluation of program practices. 

• Control and retard domestication in broodstock by purposeful incorporation of natural-origin 

returns in each generation. 

• Estimate the proportion of hatchery-origin fish among the natural spawners. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• This is a good example of a natural rearing hatchery program. 

• The review above is based on the current program. The HSRG is aware of current efforts to 

develop a plan for the recovery of salmonids following the removal of two dams. The HSRG has 

provided informal comments on preliminary drafts of this plan. Specifically, the HSRG has 

suggested that this plan include contingencies for custody of the genetic resource under different 

environmental scenarios, including a schedule for disposition of returning adults as a function of 

run size. The HSRG has also urged the managers to consider the out-planting of adults into the 

upper watershed as a part of the recovery strategy. The plan should also emphasize the critical 

importance of monitoring and evaluation as a key component of a strategy for success. Additional 

consultation between the Elwha Recovery Team and the HSRG would likely be beneficial for 

development and refinement of the restoration and recovery plan. 

MANAGERS RESPONSE

The Elwha Tribe supports the recommendations of the HSRG to continue the use of natural rearing, 

incorporation of marking/tagging for program evaluation, incorporation of natural origin recruits into 

the hatchery broodstock, and monitoring the origin of natural spawners. 

WDFW supports the recommendations of the HSRG. 
28 Hatchery Reform Recommendations – February 2002 Eastern Straits 

Elwha Chum 

Lower Elwha Klallam Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate High 

Population Viability Critical At Risk Healthy 

Habitat Inadequate Limiting Healthy 

Harvest Opportunity No Harvest No Harvest Most Years 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The original Lower Elwha chum salmon program began in 1976 and continued through 1985, using 

broodstock from Walcott Slough in Hood Canal, Enetai Creek, Lyre River, and the Elwha River. 

Only eggs from the Elwha River were used after 1981. Based on genetic information, the early 

portion of the run appears to be closest to the native gene pool. The current program began in 1995 

and is maintained by annually capturing wild fish from the Elwha River spawning grounds. Elwha 

River chum salmon belong to the Strait of Juan de Fuca fall-run GDU. There are five additional 

stocks in this GDU. The objective of the program is to conserve the existing Elwha River chum stock, 

which has been on the decline for years and is now chronically depressed. To this end, 75,000 eyed 

eggs are out-planted annually. The eggs are incubated to the eyed stage at the Lower Elwha Hatchery. 

OPERATIONAL CONSIDERATIONS

• Though the early timed portion of the run is native, there is a history of introduced broodstock not 

native to the Elwha River. 

• The use of Hood Canal stocks resulted in chum with a later run timing than that of native Elwha 

River chum. 

• The program is experiencing difficulties in obtaining the needed number of adults. 

• Outplants are not tagged or marked. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is consistent with the short- and long-term goals for the stock. However, a small 

effective population size constitutes a potential genetic risk. 

B. Likelihood of attaining goals?
Eastern Straits Hatchery Reform Recommendations – February 2002 29 

There is a reasonable likelihood of attaining the program’s goals, particularly if harvest is held to zero 

currently and in the near-term (as planned), and if habitat improves to “healthy” in the long-term (as 

anticipated). 

C. Consistent with goals for other stocks? 

The program is consistent with goals for other Elwha River stocks, as significant adverse effects on 

other stocks appear unlikely. 

RECOMMENDATIONS

• Develop and implement a plan to increase effective broodstock size. 

• Focus broodstock collections on the early part of the run, to produce a run timing more akin to 

that of the original Elwha stock. If necessary, use another Strait of Juan de Fuca chum source, 

should the present early Elwha chum run prove unable to meet program needs. 

• Outplant not only eyed eggs, but also fry that have been hatchery-reared to about one gram in 

size. 

• Time fry outplants to avoid predation from coho, chinook and steelhead in the Elwha River. 

• Use some form of marking, so that success of the program and its release strategies can be 

evaluated. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• Fry releases are likely to increase the program’s chances of success. 

• Take precautions to minimize the likelihood of introducing exotic pathogens with any chum stock 

used for satisfying the second recommendation, above. 

• The review above is based on the current program. The HSRG is aware of current efforts to 

develop a plan for the recovery of salmonids following the removal of two dams. The HSRG has 

provided informal comments on preliminary drafts of this plan. Specifically, the HSRG has 

suggested that this plan include contingencies for custody of the genetic resource under different 

environmental scenarios, including a schedule for disposition of returning adults as a function of 

run size. The HSRG has also urged the managers to consider the out-planting of adults into the 

upper watershed as a part of the recovery strategy. The plan should also emphasize the critical 

importance of monitoring and evaluation as a key component of a strategy for success. Additional 

consultation between the Elwha Recovery Team and the HSRG would likely be beneficial for 

development and refinement of the restoration and recovery plan. 

MANAGERS RESPONSE

The Elwha Tribe generally agrees with the recommendations of the HSRG and notes the following: 

• Broodstock collection currently targets the early portion of the return timing as recommended by 

the HSRG. 

• The Elwha Fish Restoration Team will evaluate the use of fry outplants in addition to the current 

eyed egg plants. 

• Marking will be incorporated into the evaluation of the chum program if resources are available 

for implementation. 
30 Hatchery Reform Recommendations – February 2002 Eastern Straits 

WDFW supports the recommendations of the HSRG. 
Eastern Straits Hatchery Reform Recommendations – February 2002 31 

Elwha Hatchery Winter Steelhead 

Lower Elwha Klallam Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate High 

Population Viability15 Medium Medium High 

Habitat Inadequate Limiting Healthy 

Harvest Opportunity Each Year Most Years Each Year 

Hatchery Program:

Purpose Harvest and Conservation 

Type Segregated 

PROGRAM DESCRIPTION

The Elwha hatchery winter steelhead stock derives from a variety of sources, with the primary stocks 

being Chambers and Bogachiel (Puget Sound derivatives). This program has been maintained with 

adult returns to the Lower Elwha Hatchery since 1977. The objective of the program is to provide for 

harvest, while conserving winter steelhead in the Elwha River. To this end, 120,000 smolts are reared 

annually for release into the Elwha River. 

OPERATIONAL CONSIDERATIONS

None. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This segregated program is consistent with short- and long-term harvest goals. Use of this early 

running, non-native broodstock is not consistent with the long-term conservation goals. 

B. Likelihood of attaining goals? 

The current program is likely to attain harvest goals but not conservation goals. 

C. Consistent with goals for other stocks? 

The relatively large number of smolt releases of a segregated hatchery stock will pose significant risk 

to a native population that may be residualized above dams and used as a possible core for 

recolonization. Large out-plants of smolts are likely to pose a risk of predation on other salmonids in 

the watershed. 

 

15 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
32 Hatchery Reform Recommendations – February 2002 Eastern Straits 

RECOMMENDATIONS

• Implement System-wide Recommendations for establishing a regional system of “wild steelhead 

management zones,” consistent with the Elwha Restoration Plan, where streams are not planted 

with hatchery fish and are instead managed for native stocks. Fishing for steelhead in these zones 

would not be incompatible with this approach, but no hatchery-produced steelhead should be 

introduced. Such zones would reduce the risk of naturally spawning fish interbreeding with 

hatchery fish, and provide native stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• If a conservation program is desired, it will need to be considered separately, using a more 

appropriate broodstock. 

• Release hatchery yearling steelhead smolts between May 1 and May 15, at a target size of six to 

the pound, and at a condition factor of less than 1.0.

COMMENTS

• The HSRG believes this is an inappropriate stock for recolonization of the upper watershed. 

• The review above is based on the current program. The HSRG is aware of current efforts to 

develop a plan for the recovery of salmonids following the removal of two dams. The HSRG has 

provided informal comments on preliminary drafts of this plan. Specifically, the HSRG has 

suggested that this plan include contingencies for custody of the genetic resource under different 

environmental scenarios, including a schedule for disposition of returning adults as a function of 

run size. The HSRG has also urged the managers to consider the out-planting of adults into the 

upper watershed as a part of the recovery strategy. The plan should also emphasize the critical 

importance of monitoring and evaluation as a key component of a strategy for success. Additional 

consultation between the Elwha Recovery Team and the HSRG would likely be beneficial for 

development and refinement of the restoration and recovery plan. 

MANAGERS RESPONSE

The Elwha Tribe generally agrees with the recommendations of the HSRG and notes the following: 

• The Wild Steelhead Management zones are a good concept. This is currently implemented to 

some degree in the Strait region. 

• Alternate broodstock sources are being considered for use in the Elwha Restoration Plan. 

• Additional consultation has occurred between the Elwha Fisheries Technical Group and the 

HSRG. Further consultation would be beneficial to the planning process. 

WDFW supports the recommendations of the HSRG. 
Eastern Straits Hatchery Reform Recommendations – February 2002 33 

SMALLER WATERSHEDS

Overview 

STOCK STATUS16

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Smaller Watersheds Summer Chum Y H H H L L M L L M 0 0 L

Smaller Watersheds Win. Steelhead Y M M M L L M M M M M M M

Snow Creek Coho Y M M M L L M L L M 0 0 L

Smaller Watersheds Other Coho Y L L L L L L M M M 0 0 0

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Stocks

HABITAT

The major tributaries to Discovery Bay are Snow and Salmon Creeks. Minor tributaries include 

Contractors Creek and Eagle Creek. Minor tributaries to Sequim Bay include Jimmycomelately 

Creek, Johnson Creek, and Chicken Coop Creek. Habitat in the largest of these tributaries, 

Jimmycomelately Creek as currently poor, with severe channel confinement, lack of floodplain 

connectivity, and loss of estuarine function. Habitat conditions in the Morse Creek watershed are 

currently poor. Morse Creek has a small population of summer chum. Chinook are likely extirpated in 

the creek. Ennis Creek is the smallest of the snow-fed streams on the north Olympic Peninsula. 

Although considered to be the healthiest of the Port Angeles urban streams, overall habitat condition 

would probably be considered to be only fair. Bell Creek drains a rapidly urbanizing area in Sequim. 

Habitat conditions are generally poor, except where habitat has been restored. Gierin Creek habitat 

conditions are generally fair to good, due in large part to the management of a large wetland area in 

the lower watershed (Graysmarsh) for the benefit of fish and wildlife. Casselery and Cooper Creeks 

offer limited salmonid production potential. Each of the creek systems has a significant wetland 

upstream of the mouth, although these wetland areas may have been naturally isolated from saltwater 

by presence of a natural sandbar. 

Habitat conditions are generally poor in Port Angeles urban streams (Lees Creek, Peabody Creek, 

Valley Creek, Tumwater Creek, Dry Creek). The larger watersheds that drain into the Strait of Juan 

de Fuca, bounded by Colville Creek to the east and the mouth of the Strait of Juan de Fuca to the 

west, include the Hoko, Seiku, Pysht, Clallam, and Lyre Rivers. Fall chinook salmon were 

historically abundant throughout many of the larger watersheds, but currently, the only large 

population spawns in the Hoko River, and that stock is considered to be “depressed.” Small numbers 

are sometimes recorded in the Lyre River, Seiku River, and the Pysht River. Historically, chinook 

 

16 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.
34 Hatchery Reform Recommendations – February 2002 Eastern Straits 

were also noted in the Clallam River, Salt Creek, Bullman Creek, Sail River, and Deep Creek, but this 

species has not been documented in these streams for several years. Chum salmon have been 

documented in the Sail River, Bullman Creek, Seiku River, Hoko River, Clallam River, Pysht River, 

Deep Creek, Twin Rivers, Lyre River, and Salt Creek. However in recent years, chum salmon have 

not been noted in Salt Creek, and the levels in Deep Creek have sharply declined. Coho salmon and 

winter steelhead trout are distributed throughout all of the drainages discussed below, with steep 

declines for both species in Deep Creek. Small numbers of pink salmon have been seen in the Lyre 

River.17

HATCHERIES

No hatchery facilities are located within this sub-region. 

 

17 Donald Haring, Washington Conservation Commission, March 19, 2001. 
Eastern Straits Hatchery Reform Recommendations – February 2002 35 

Smaller Watersheds Summer Chum 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability Critical Critical At Risk 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity None None Occasional 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Smaller Watersheds summer chum stock derives from Salmon and Jimmycomelately creeks and 

is maintained through yearly collection of green eggs from these creeks. The eggs are placed in 

remote site incubators (RSI). Salmon and Jimmycomelately are the only stocks in the Strait of Juan 

de Fuca Summer Chum GDU. The purpose of this program is summer chum salmon restoration. To 

this end, 200,000 green eggs are taken at Salmon Creek and eyed at Dungeness Hatchery. The 

planting goal is 80,000 fish between 350–650 fish per pound released into Chimicum Creek and 

91,000 fish between 350-650 fish per pound into Discovery Bay. 90,000 green eggs are taken at 

Jimmycomelately Creek, incubated and ponded at Hurd Creek Hatchery and at Jimmycomelately. 

The planting goal is 86,000 fish at 450 fish per pound into Jimmycomelately Creek. 

OPERATIONAL CONSIDERATIONS

• The summer chum salmon restoration programs include Salmon, Jimmycomelately, and 

Chimacum Creeks in the regional management goals. The program follows the guidelines of the 

Summer Chum Conservation Initiative18, the goal of which is to restore healthy, natural selfsustaining, summer chum salmon populations. 

• Conservation goals either maintain genetic characteristics of native stocks (i.e., Salmon, 

Jimmycomelately creeks), or will develop locally adapted broodstocks (initially using brood 

stock from the Salmon Creek project for Chimacum Creek). 

• All programs recognize future options, with up to 12 years of an “integrated recovery” 

supplementation program. Directed harvests may occur after full recovery. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is consistent with short- and long-term goals. 

 

18 Summer Chum Conservation Initiative, Washington State Department of Fish and Wildlife and Point No Point Treaty Tribes, April 2000.
36 Hatchery Reform Recommendations – February 2002 Eastern Straits 

B. Likelihood of attaining goals? 

The program, if executed correctly, is likely to achieve its goals. 

C. Consistent with goals for other stocks? 

Restoring chum would be consistent with goals for other stocks. 

RECOMMENDATIONS

• Continue to conduct this program consistent with the Summer Chum Conservation Initiative. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• The conservation goals, harvest objectives, and social and cultural objectives are realistic and 

well thought out. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. The summer chum restoration programs are an 

example of the carefully designed and successfully implemented programs that WDFW believes can 

play an important role in the restoration of salmonid populations. Funding to undertake this program 

was provided under a special appropriation from the Washington Legislature. 
Eastern Straits Hatchery Reform Recommendations – February 2002 37 

Smaller Watersheds Hatchery Winter Steelhead 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate Intermediate 

Population Viability19 Low Low Medium 

Habitat Limiting Limiting Limiting 

Harvest Opportunity Most Years Most Years Most Years 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Smaller Watersheds hatchery winter steelhead program relies on annual outplants from 

Bogachiel Hatchery. The stock originates from Chamber Creek. The purpose of the program is to 

provide for harvest, while avoiding adverse interactions with naturally spawning stocks. To this end, 

smolts are planted into the Lyre River (25,000), Pysht River (10,000) and Morse Creek (5,000). 

OPERATIONAL CONSIDERATIONS

• Fish are incubated and reared at Bogachiel (a hatchery in a region not yet reviewed by the 

HSRG), so operations have not yet been evaluated. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is consistent with the short-term goal of occasional harvest opportunity. 

B. Likelihood of attaining goals? 

Short-term harvest goals seem achievable; achieving long-term goals will depend upon 

implementation of the wild steelhead management zones plan described below. 

C. Consistent with goals for other stocks? 

Low levels of spawning overlap between a segregated, early winter steelhead hatchery stock and late 

winter native stock may pose increasing risk over the long-term that could compromise the native 

stock. There may also be some predation risk to naturally produced chum. 

 

19 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
38 Hatchery Reform Recommendations – February 2002 Eastern Straits 

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of “wild 

steelhead management zones” where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Release hatchery yearling steelhead smolts between May 1 and May 15, at a target size of six to 

the pound, and at a condition factor of less than 1.0. 

COMMENTS

None. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG, but notes that implementing a regional system 

of wild steelhead management zones has a number of implications that will require discussion with 

the affected tribes and the Fish and Wildlife Commission. 
Eastern Straits Hatchery Reform Recommendations – February 2002 39 

Snow Creek Coho 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate Intermediate 

Population Viability Critical Critical At Risk 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity None None Occasional 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Snow Creek coho stock program at Hurd Creek Hatchery derives from and is maintained through 

returns to Snow Creek. This stock belongs to the Puget Sound/Strait of Georgia ESU. The objective 

of the program is to restore a healthy, natural, self-sustaining coho salmon population in Snow Creek. 

To this end, eggs from coho adults returning to Snow Creek are collected and outplanted in the 

watershed in remote satellite incubators, or are hatched and the resulting progeny hatchery-reared for 

release into the watershed at two different ages. 

OPERATIONAL CONSIDERATIONS

• The program will be comprised of supplemented and naturally spawning fish, using Snow Creek 

natural-origin brood stock. 

• The Snow Creek program also supports public education on salmon, and ceremonial and 

subsistence harvest in Discovery Bay. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

B. Likelihood of attaining goals? 

C. Consistent with goals for other stocks? 

The program is consistent with short- and long-term goals and is likely to achieve these goals. There 

is some risk of predation on natural stocks, including chum. 

RECOMMENDATIONS

• Continue conducting the program as designed. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 
40 Hatchery Reform Recommendations – February 2002 Eastern Straits 

COMMENTS

• The conservation goals, harvest considerations, and educational objectives are realistic and well 

thought out. It is apparent that much productive effort has been put into program design, and 

collecting and analyzing data. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. The Snow Creek coho project is an example of 

the carefully designed and successfully implemented programs that WDFW believes can play an 

important role in the restoration of salmonid populations. While the project is an important tool for 

restoring coho salmon in Snow Creek, it could potentially play an even more important role in 

developing improved strategies for restoring depressed populations of coho salmon throughout the 

state. However, it is critically important that the HSRG maintain funding for this project, to assure 

that these goals are achieved. 
Eastern Straits Hatchery Reform Recommendations – February 2002 41 

Smaller Watersheds Other Hatchery Coho 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability Low Low Low 

Habitat Limiting Limiting Limiting 

Harvest Opportunity None None None 

Hatchery Program:

Purpose Education 

Type Segregated 

PROGRAM DESCRIPTION

The Smaller Watersheds other hatchery coho program is used for an education project (eggs in the 

classroom) and rehabilitation for a local creek (Cooper Creek). This program relies on annual 

outplants from Hurd Creek Hatchery. The stock originates from the Dungeness River. The purpose of 

this program is education. To this end, 6,750 Dungeness River fry are provided from Hurd Creek 

Hatchery, reared in ten elementary and high school classroom aquaria, and released into Bell, Ennis, 

Matriotti, Tumwater and Valley creeks. 

OPERATIONAL CONSIDERATIONS

None. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

B. Likelihood of attaining goals? 

C. Consistent with goals for other stocks? 

This program provides a valuable educational benefit. It is too small to produce significant risks. 

RECOMMENDATIONS

• Continue these education programs. 

COMMENTS

• These programs are using appropriate fish stocks. 
42 Hatchery Reform Recommendations – February 2002 Eastern Straits 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG to continue education programs. These 

programs are an essential component of our efforts to spark public interest, education, and 

participation in salmon recovery. 
South Puget Sound Hatchery Reform Recommendations – February 2002 43 

South Puget Sound 

Overview 

This region includes the portion of Puget Sound south of the Tacoma Narrows. For the purposes of 

this review, the Scientific Group and the regional managers divided the region into five sub-regions 

and then reviewed the hatchery programs involving each identified sub-regional salmonid stock (for 

example, Chambers Basin fall chinook). The review included a consideration of the program’s effects 

on all other hatchery and naturally spawning sub-regional salmonid stocks (see table in sub-regional 

overviews). The sub-regions identified for this region include: 

1. Chambers Creek Basin (Fort Lewis and north) 

2. Nisqually River and Delta 

3. Deschutes River 

4. Squaxin/South Sound Net Pens and Independent Tributaries 

5. Key Peninsula (including Fox Island Net Pens) 

This chapter provides region-wide recommendations for the South Sound, a general overview of each 

sub-region, followed by reviews and recommendations for each salmonid stock that has an associated 

hatchery program. 

FISHERIES

Since 1977, South Sound salmon management has been directed by the Puget Sound Salmon 

Management Plan. Under that plan, South Sound chinook and coho stocks have been harvested at 

rates appropriate for hatchery stocks, with natural escapements being a secondary consideration. 

Unless there were specific accommodations made to protect natural stocks (e.g. Deschutes coho), 

natural escapements have been the result of whatever natural fish escaped fisheries designed to fully 

harvest the available hatchery stocks.20

CONSERVATION

Effort levels devoted to stock assessment of South Sound salmon stocks have been prioritized by the 

harvest management strategy outlined for this region by the Puget Sound Salmon Management Plan 

and other efforts pursued by the co-managers to increase understanding of salmon in the region. 

Emphasis has been given to species and stocks that have been managed for natural escapement goals 

(winter chum, fall chum, summer chum, pinks and winter steelhead). Conversely, natural stocks of 

species managed at a hatchery harvest rate in this region (coho and chinook) have been generally 

sampled at a lower rate than stocks of the same species in a region that managed them for natural 

escapement. The Comprehensive Coho planning process is providing a forum for discussion by the 

co-managers regarding means by which protection can be afforded South Sound coho natural stocks 

throughout the gauntlet of terminal and pre-terminal fisheries.21

 

20 Chuck Baranski, Washington State Department of Fish and Wildlife July 2001. 

21 Ibid 
44 Hatchery Reform Recommendations – February 2002 South Puget Sound 

HABITAT

South Puget Sound future fish habitat expectations are directly correlated to the effects of human 

population growth and development, and aquatic and land use regulations intended to mitigate their 

adverse effects. Growth-planning projections indicate continued growth expansion in the South 

Sound region. Major employers, state government and federal military, are relatively stable. Other 

businesses and industries are diversified. The Growth Management Act (GMA) and Shoreline 

Management Act (SMA) have required local governments to provide improved aquatic area 

protection, including increased aquatic buffers. Instream flows are expected to be minimally affected 

by development water use and only in selected sub-watersheds, because of generally good watershed 

hydrographs. Storm water, development sedimentation, and beach and stream bank channelization 

impacts are expected to still be significant in the future, although improved local regulations, facility 

upgrades, and Best Management Practices (BMPs) should lessen, but not prevent, such impacts. The 

cumulative consequences of the projected population and development expansion are expected to 

have some degree of negative effect on aquatic fish habitats. Nonetheless, the long-term goal for 

South Sound is for healthy, protected habitat for fish and wildlife. 

The most notable South Sound watershed-scale restoration effort is on the Nisqually River main stem, 

where the Nisqually Tribe and the Nisqually Land Trust are purchasing sensitive floodplain and 

estuarine land and using conservation easements to retain estuarine and riparian habitat. Other stream 

restoration efforts exist for South Puget Sound watersheds, although most are only selected reachscale restoration efforts, such as the Goldsborough Dam Removal and Stream Restoration Project, 

Kennedy Creek watershed planning, Woodland Creek watershed planning, and the Capitol Lake and 

Dam Fish Passage and Estuary Review. Numerous small projects (primarily fish passage corrections) 

are being conducted by a variety of local governments, county conservation districts, and regional 

fish enhancement groups with technical assistance from WDFW. These projects are not long-term, 

with dedicated funds. Most are supported by the Salmon Recovery Funding Board (SRFB).22

 

22 Jim Frasier, Washington State Department of Fish and Wildlife, July 2001. 
South Puget Sound Hatchery Reform Recommendations – February 2002 45 
46 Hatchery Reform Recommendations – February 2002 South Puget Sound 

CHAMBERS CREEK BASIN

Overview 

STOCK STATUS23

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Chambers Basin Hatchery Fall Chinook Y L L L L L L L L L H H H

Chambers Basin Coho N L M M L L M L M M L L M

Garrison Springs Chum Y H H H M M H L L M 0 0 L

Chambers Basin Steelhead N L L L/M L L M L M M 0 0 0

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Stocks

HABITAT

Although Chambers Creek still has some good habitat in the lower end, it suffers from water quality 

problems, including high copper levels resulting from ongoing algae control efforts in Steilacoom 

Lake. Some excellent spawning and rearing habitat exists in the upper end but passage problems 

preclude access to it by anadromous fish in most years. Some of the blockages are scheduled to be 

modified to allow passage. WDFW transports several hundred adult coho salmon above the blockages 

each fall. 24

This watershed currently supports runs of winter chum, coho, coastal cutthroat and winter steelhead 

trout. Salmonid habitat conditions in the mainstem Chambers and Clover Creeks can be described as 

fair to poor in the lower reaches and as fair with increasing pressure from urbanization in the upper 

reaches. 

The major habitat concerns associated with the mainstem Chambers-Clover Creek and tributaries 

include: 1) the tidal headwater dam where historically all migrating anadromous adults were handled 

prior to either being incorporated into a hatchery broodstock or released upstream; 2) the loss of 

functional floodplain due to extensive channel relocations, channelization, and tight-lining (pipes); 3) 

the alteration to stream hydrology due to high levels of impervious surfaces; 4) a lack of properly 

functioning riparian habitats; 5) impacts to smoltification through the application of pesticides and in 

particular the herbicides used to treat algae in Steilacoom Lake; and 6) the loss of portions of estuary 

habitats caused by the dam at the head of Chambers Bay.25

 

23 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.

24 Conservation Priorities: An Assessment of Freshwater Habitat For Puget Sound Salmon, The Trust For Public Land, Seattle, WA, November 2000.

25 John Kerwin, Washington Conservation Commission, July 2001.
South Puget Sound Hatchery Reform Recommendations – February 2002 47 

HATCHERIES

Lakewood Hatchery 

The Lakewood Hatchery (formerly the South Tacoma Hatchery) is located on Chambers Creek in 

South Puget Sound, adjacent to the South Puget Sound Wildlife Area approximately 500 yards from 

Chambers Creek at river mile 3.3. The Lakewood Hatchery is part of the South Sound Hatchery 

Complex which includes Garrison Springs Hatchery, Chambers Creek Hatchery, and the Chambers 

Creek Adult Trap; all in the Chambers Creek Basin. Until 1997, Lakewood Hatchery (and the other 

facilities in this complex) provided significant support for winter-run and summer-run steelhead and 

catchable rainbow trout programs throughout western Washington. In 1997, fish management 

decisions to develop locally-adapted steelhead broodstocks and to substantially cut catchable trout 

production reduced the need for support from these facilities. Today, Lakewood Hatchery produces 

200,000 yearling fall chinook, maintains a small rainbow trout broodstock population, and provides 

support for other trout programs in the region. 

Chambers Creek Hatchery 

The Chambers Hatchery is located on Chambers Creek in South Puget Sound. The primary goal of 

the current hatchery program is to provide chinook salmon for recreational harvest in the Puget Sound 

(released as yearlings). Today, Chambers produces 100,000 yearling fall chinook, 200,000 cutthroat 

fry and more than 400,000 kokanee. The hatchery was originally a private trout hatchery. It was 

purchased by the Game Department in the late 1960s and was rebuilt in the late 1970s. It was opened 

as a Game Department facility in 1976. 

Garrison Springs Hatchery 

Garrison Springs Hatchery is located in a canyon between Western State Hospital and the Abitibi 

Paper Mill. There is no migratory outlet from the hatchery, as the water passes several man-made 

cascades and a portion enters the paper mill. Garrison Creek enters the tidewater in Chambers Bay 

approximately one quarter mile below the Chambers Creek Trap. All fish reared at Garrison Springs 

Hatchery are shipped out on planting trucks. Garrison Springs Hatchery is currently programmed to 

release 850,000 sub-yearling chinook at 50 fish per pound into Chambers Creek. This program has 

been in existence for about 20 years. Garrison Springs Hatchery also supports other facilities by 

incubating eggs and rearing fish during the summer. 

The Chambers Creek trap is at river mile 0.4 on Chambers Creek and is at the terminal limit of tidal 

influence, the Chambers Creek Dam. A satellite to Garrison Creek Hatchery, the Chambers Trap is 

located at tidewater near the Abitibi Paper Mill and the Pierce County Waste Treatment Facility. This 

facility provides the backbone for hatchery chinook production in Chambers Creek. The main uses of 

the Chambers Trap are to collect broodstock for salmon programs in the basin, enumerate and pass 

other species of naturally spawning salmon and trout upstream, and to acclimate chinook fingerlings 

prior to release into Chambers Creek.26

 

26 Rich Eltrich, Washington State Department of Fish and Wildlife, July 2001.
48 Hatchery Reform Recommendations – February 2002 South Puget Sound 

Chambers Basin Hatchery Fall Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability27 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Chambers Creek Basin hatchery fall chinook program began in the 1980s with fish of Green 

River origin from Deschutes, Soos and Puyallup hatcheries. This stock is maintained through adult 

returns to the Chambers Creek trap, but can be supplemented with Minter Creek and Deschutes stock. 

The purpose of this program is to provide for harvest. To this end, 300,000 yearlings (200,000 at 

Lakewood Hatchery, 100,000 at Chambers Creek Hatchery) and 850,000 fingerlings (600,000 at 

Chambers Creek trap, 250,000 at Steilacoom Lake) are released into the Chambers Creek drainage. 

Yearling production is eyed and hatched at Chambers Creek Hatchery and reared at both Chambers 

Creek and Lakewood hatcheries. Fingerling production is eyed, hatched and reared at Garrison 

Springs Hatchery. 

OPERATIONAL CONSIDERATIONS

• The operations of this program are generally consistent with guidelines for a segregated harvest 

program. 

• Evaluation of the contribution of the yearling program was not possible because the program is 

relatively new, with minimal tagging to date. 

• Use of circular ponds previously used in the trout program and seasonal water quality problems 

were identified as contributing to infections of furunculosis and parasites, both of which require 

regular drug treatments to control. 

• The size of the current yearling program is too large for the existing facilities, requiring excessive 

transfer between stations to maintain the program level. 

 

27 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
South Puget Sound Hatchery Reform Recommendations – February 2002 49 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program currently provides significant benefits to the terminal area treaty and recreational fishery 

from its fingerling component. This program is not only consistent, but necessary to attain, the shortterm and long-term harvest goals for the basin, since natural production potential for fall chinook in 

this basin is severely limited by habitat quantity and quality. Since the yearling component of this 

program is relatively new, it was not possible to evaluate its contribution to he harvest goals for this 

stock. 

B. Likelihood of attaining goals?

The likelihood of attaining the goals is dependent on improving rearing conditions at the facilities, 

evaluation of the release strategies employed, and implementation of the most successful strategy or 

strategies. 

C. Consistent with goals for other stocks? 

Risks to other populations include competition risks to other South Sound chinook stocks, including 

those in the Nisqually, Deschutes and Key Peninsula basins. A general concern exists across all 

species regarding the current South Sound carrying capacity. There are also potential predation risks 

to natural chum salmon stocks from the region, particularly from the yearling component of the 

program. 

RECOMMENDATIONS

• Evaluate the success of the different fall chinook release strategies (yearling and fingerling) in the 

basin. 

• Develop a local fall chinook broodstock for the basin. 

• Operate programs and facilities to allow for full volitional release of chinook. 

• Develop a facility in the lower basin to improve acclimation, rearing and release options for 

fingerlings and yearlings. WDFW has property and a water right in the lower basin near the 

Chambers Creek trap that can be used for this purpose. 

• Resize the program for current and planned facilities to minimize the need for periodic fish 

transfers between facilities. 

• Operate Chambers Creek Hatchery with Garrison Springs Hatchery for fall chinook fingerlings. 

• Transition the Lakewood facility from a chinook production facility to more appropriate species 

for this facility. 

• Enhance educational opportunities at Lakewood to take advantage of the open space at this 

facility, in the middle of an increasingly urban environment. 

COMMENTS

• The water supply and facilities used for the yearling program have a significant potential use for 

resident fish. 

• Rearing and release strategies need to consider potential interspecific effects. 
50 Hatchery Reform Recommendations – February 2002 South Puget Sound 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG and has initiated a scoping study (using funding 

from the Puget Sound Recreational Enhancement account) to evaluate options for developing a 

facility in the lower basin. Additional funding will be required to evaluate the success of different 

release strategies and modify the facilities as recommended. 
South Puget Sound Hatchery Reform Recommendations – February 2002 51 

Garrison Springs Chum 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability At Risk At Risk Healthy 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity None None Occasional 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Garrison Springs chum stock derives from wild chum collected in Chambers Creek from 1979 to 

the present. The stock is maintained through adult returns to Chambers Creek trap. Garrison Springs 

chum salmon belong to the Central/South Puget Sound Fall Chum GDU. Eight other stocks are in this 

GDU. The purpose of the program is to restore a chum stock that has recently shown steep declines in 

returning adults. To this end, 50,000 unfed chum fry are released into Flett Creek. Eggs are eyed at 

Garrison Springs Hatchery and smolts released from a remote site incubator (RSI). 

OPERATIONAL CONSIDERATIONS

• Even though this is a small program, because of recent low returns of chum salmon to this 

watershed, collection of even a small number of eggs could be considered “broodstock mining.” 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The benefit of this program to conservation is currently unknown. There is an educational benefit 

from this program that is linked to watershed protection. If the program is not successful, there is a 

risk to this population from removing natural spawners from an already depressed population 

B. Likelihood of attaining goals? 

The likelihood that this program will attain its goal is dependent on the fish released from the remote 

site incubator being representative of the natural stock and surviving to reproduce at a higher rate than 

naturally spawning chum. These factors are currently unknown. 

C. Consistent with goals for other stocks? 

The program is consistent with goals for other stocks.
52 Hatchery Reform Recommendations – February 2002 South Puget Sound 

RECOMMENDATIONS

• Evaluate the success of the RSI program in providing naturally spawning fish in the newly 

available habitat. 

• Use the results of the evaluation to determine if the program should be continued, eliminated or 

expanded to additional restoration efforts in the basin. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• Recent returns to the basin (1999 and 2000) have been only a few hundred fish, after averaging 

several thousand per year over the last 30 years. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG but notes that additional funding will be 

required to evaluate the success of the RSI program. 
South Puget Sound Hatchery Reform Recommendations – February 2002 53 

NISQUALLY RIVER AND DELTA

Overview 

STOCK STATUS28

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Nisqually River Fall Chinook Y L M H M M H M M H H H H

McAllister Creek Hatchery Fall Chinook Y L L L L L L L L L H H H

Nisqually River Late Coho N M M M M M M M M H 0 0 L

Nisqually River Coho Y L M M L M M L M M L L M

Nisqually River Late Chum N H H H H H H M/H H H H H H

McAllister Creek Chum N H H H H H H M M H H H H

Nisqually River Pink N H H H L M H M M H 0 L M

Nisqually River Steelhead N H H H L M H M M H 0 M H

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Stocks

HABITAT

The Nisqually River has the largest estuary in southern Puget Sound and the last major undeveloped 

delta in Puget Sound. The historic estuary area has been reduced about 30% percent by dikes. Much 

of the riparian area along the lower river is already in protected status. Of the 40 miles of mainstream 

accessible to anadromous fishes, 64% is in protected status. The mainstem Nisqually has three dams. 

The present upstream distribution limit of anadromous fish is river mile 41.4. 

The largest watersheds in the Nisqually River Basin are Muck Creek and the Mashel River. Ohop 

Creek and Tanwax Creek are medium-sized, with stream flows dominated by rainfall. There are a 

number of smaller, independent drainages. McAllister Creek is a medium-sized, spring water fed 

creek that flows into Puget Sound through the western edge of the Nisqually Delta. It provides some 

spawning and good rearing habitat primarily for chum.29

Nisqually River spawning sockeye salmon are observed annually, downstream of the Centralia 

Diversion Dam. The status of native char populations in the basin is unknown. Salmonid habitat 

condition in the mainstem Nisqually River is currently fair to good. The status of the pink salmon 

population is depressed at best. The major habitat concerns associated with the mainstem Nisqually 

River include a loss of functional floodplain due to remnant flood control dikes that reduce sidechannel habitats; the loss of portions of the estuary; and the possible loss of coarse sediment transport 

 

28 This table contains ratings for all the salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the 

Components of This Report section of the Introduction.

29 Conservation Priorities: An Assessment of Freshwater Habitat For Puget Sound Salmon, The Trust For Public Land, Seattle, WA, November 2000.
54 Hatchery Reform Recommendations – February 2002 South Puget Sound 

and large, woody debris recruitment out of the upper mainstem basin, past the Alder and LaGrande 

water storage and power dams, respectively. 

Habitat conditions in the McAllister Creek watershed are currently poor. Major habitat concerns 

include a significant loss of historic estuary, a reduction in floodplain connectivity, a lack of habitat 

complexity, and poor substrate condition. Red Salmon Creek is a small, independent tributary to the 

Nisqually Delta entering along the eastern edge of the delta. The creek is fed by surface water runoff 

and groundwater. It currently supports steelhead, coho, chum and coastal cutthroat. The overall 

habitat condition would probably be considered fair. Sequalitchew Creek is a medium-sized 

independent tributary to Puget Sound located northeast of the Nisqually Delta. The creek is fed by 

surface water runoff and groundwater and has several lakes, dominated by Lake Sequalitchew, and 

marsh complexes associated with its upper reaches. Habitat conditions are generally fair in the 

upstream reaches and generally good in the lower reaches.30

HATCHERIES

McAllister Hatchery 

McAllister Hatchery is located in South Puget Sound on McAllister Creek at river mile 4.0. 

McAllister Creek is an independent drainage in the Nisqually Valley, west of the Nisqually River. 

The hatchery was originally designed to rear large numbers of chum and smaller numbers of delayedrelease (yearling) chinook. Today, the primary goal of the programs at McAllister is to raise chinook 

salmon for recreational harvest in Puget Sound. The present program calls for the release of 300,000 

fall chinook yearlings in April at 6 FPP and 1,000,000 zero-age fall chinook in May at 50 FPP. 

McAllister also provides incubation support for the Tumwater Falls chinook program.31

Kalama and Clear Creek Hatcheries 

Fall chinook are reared at two tribal facilities on the Nisqually River. Kalama Creek Hatchery is 

located on a left bank tributary of the Nisqually at approximately river mile 9.2. Clear Creek Hatchery 

is located on a right bank tributary at approximately river mile 6.2. Kalama Creek Hatchery began 

releasing fall chinook in 1980 (brood year 1979) and Clear Creek Hatchery began releasing chinook 

in 1991 (brood year 1990). Both programs began with importation of various South Sound chinook 

stocks, but the current broodstock policy allows only the use of Nisqually River stocks at both 

facilities. Incubation and rearing takes place on-station with a release goal of 600,000 zero-age smolts 

at Kalama Creek Hatchery and 3,500,000 zero-age smolts at Clear Creek Hatchery. Both Kalama and 

Clear Creek hatcheries also produce coho salmon. Like fall chinook, both of these coho programs 

began with the importation of several Puget Sound stocks. The present program calls for the release 

of 350,000 coho smolts at Kalama Creek and 630,000 smolts at Clear Creek. Incubation and rearing 

take place on-station. The primary goal for both facilities is to produce fish for treaty-reserved fishing 

opportunity for the Nisqually Indian Tribe and recreational opportunity for Puget Sound recreational 

fishers.

32

 

30 John Kerwin, Washington Conservation Commission, July 2001.

31 Rich Eltrich, Washington State Department of Fish and Wildlife, July 2001.

32 John Barr, Nisqually Tribe, July 2001.
South Puget Sound Hatchery Reform Recommendations – February 2002 55 

Nisqually River Fall Chinook 

Nisqually Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Intermediate High 

Population Viability At Risk At Risk Healthy 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest and Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Nisqually River fall chinook at Kalama Creek and Clear Creek hatcheries derive from Green 

River origin stock from Soos Creek, Puyallup, Tumwater Falls, McAllister and George Adams 

hatcheries. Kalama Creek Hatchery began releases in 1980 with Soos Creek and Puyallup hatchery 

fish and has been self-sustaining since 1991. Clear Creek (using Kalama Creek Hatchery fish) began 

releases in 1991 and has been self-sustaining since 1996. Nisqually River fall chinook belong to the 

South Puget Sound, Hood Canal, and Snohomish Summer+Fall GDUs. This program’s current goal is 

to support treaty-reserved fisheries for the Nisqually Tribe and recreational fishing in the South 

Sound region. The long-term goal is to assist with restoration of naturally spawning populations of 

fall chinook salmon in the Nisqually River. To these ends, eggs are collected from adults returning to 

the Nisqually River to satisfy the following hatchery production targets: Kalama Creek Hatchery, 

630,000 smolts; Clear Creek Hatchery, 3.4 million smolts. 

OPERATIONAL CONSIDERATIONS

• Existing genetic data (allozyme data) unable to detect any significant allele frequency differences 

among the two hatchery stocks, natural-origin chinook in the Nisqually River, and the Green 

River Hatchery stock. However, sample sizes for naturally spawning fish from the Nisqually 

River were only 30 and 23 fish in 1998 and 1999, respectively. In contrast, sample sizes for the 

hatchery stocks ranges from 99 to 106 fish.

33

• Efforts are made to maintain an effective number of breeders of 1,500–2,500 adult fish per year. 

• Pre-spawning mortality of adults is less than one percent. 

• All released fish are marked to assess potential contribution of hatchery fish to naturally 

spawning populations, and to better assess the status of the natural populations themselves. 

• Recent changes in harvest management will allow greater escapement and natural spawning. 

There has been a strong attempt to match smolt releases to the carrying capacity of the Nisqually 

River and estuary via the Ecosystem Diagnosis and Treatment (EDT) model and analyses. 

 

33 Data provided by Anne Marshall and Craig Busack, Washington State Department of Fish and Wildlife.
56 Hatchery Reform Recommendations – February 2002 South Puget Sound 

• The program features a complete volitional release of sub-yearling smolts. A yearling program 

was terminated recently. 

• The program has generated significant numbers of precocious males. Procedures are now in place 

to address this problem. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

A high contribution of hatchery-origin fish to harvest indicates that the program is meeting harvest 

goals and is successful from that perspective. Recent changes in operations and proposed activities in 

the future are consistent with potentially restoring naturally spawning populations in the Nisqually 

River. 

B. Likelihood of attaining goals? 

A high likelihood exists of continuing to achieve harvest goals. Much uncertainty surrounds the 

ability of the current hatchery stock to establish a viable, self-sustaining, naturally spawning 

population that can be integrated genetically with the hatchery population. Nevertheless, given the 

current status of chinook salmon in the Nisqually River, activities to achieve restoration/conservation 

goals pose little risks, but can potentially yield high benefits. 

C. Consistent with goals for other stocks? 

The HSRG is concerned about possible impacts of chinook salmon releases on pink and chum salmon 

fry in the Nisqually River. The risk analysis performed by the Tribe assumes that pink and chum outmigration occurs prior to the release and out-migration of hatchery-origin chinook salmon smolts. If 

this assumption is wrong, then the hatchery program could potentially be posing risks to those other 

species. The HSRG is particularly concerned about the status of the pink salmon population, which is 

rated as being of “high” biological significance, but for which the total estimated escapement has 

been less than 600 adults in each of the past four brood years (1993, 1995, 1997, 1999). This low 

number of adults is becoming dangerously close to the level at which genetic concerns are an issue. 

Thus, risks posed by the hatchery program could be particularly significant. 

RECOMMENDATIONS

• Obtain a better understanding of the status of the naturally spawning population of chinook 

salmon in the Nisqually River. Marking all hatchery-origin smolts prior to release will potentially 

assist with obtaining this information. 

• Introduce an average of 10% naturally spawning fish into the hatchery broodstock each year for 

on-station releases. 

• Conduct additional genetic studies to better understand the genetic relationship between hatchery 

and naturally spawning populations in the Nisqually River and their relationship to the Green 

River Hatchery stock. Sample sizes for natural-origin fish from the Nisqually River in previous 

genetic studies are too small to test, with a desirable level of power, the null hypothesis of a 

single gene pool for hatchery and natural-origin fish. 

• Test and evaluate, via field studies, the assumption that pink and chum out-migration occurs prior 

to the release and out-migration of hatchery-origin chinook smolts. 

• Develop a protection strategy for pink salmon, including an assessment of the effects of the 

hatchery program at each of the key life history stages. Protection of the existing pink salmon 
South Puget Sound Hatchery Reform Recommendations – February 2002 57 

population in the Nisqually River, including if appropriate an enhancement program, is important 

because of its high biological significance at the southern end of the species’ range. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• Recent termination of the yearling program was a positive move towards reducing potential 

ecological risks. 

• The HSRG commends the Nisqually Tribe for initiating a plan to help restore and recover 

naturally-spawning populations of chinook salmon in the Nisqually River. To this end, the HSRG 

is reviewing two plans: an adaptive management plan and the stock management section of the 

Chinook Salmon Recovery Plan for the Nisqually River. 

• In response to the HSRG’s informal verbal review, a Nisqually Tribal biologist noted that 

Nisqually pink salmon may be heavily affected by the intensive harvests in Canada and those 

targeting fish returning to the Skagit River in north Puget Sound. The biologist noted that genetic 

studies to distinguish Nisqually, Skagit, and Canadian stocks of pink salmon might be useful to 

protect Nisqually River fish in pre-terminal, mixed fisheries. This latter study could be performed 

by the WDFW Genetics Unit. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG and has taken the following actions with the 

Nisqually Tribe: 

• All hatchery origin smolts have been marked to facilitate identification of the origin of returning 

adults. 

• A three-year study has been initiated to collect samples and analyze the genetic relationship 

between natural and hatchery spawning populations. 

The Nisqually Tribe supports the recommendations of the HSRG (the Tribe’s full comments are 

appended to this document) and has taken the following actions with WDFW: 

• All hatchery origin smolts have been marked to facilitate identification of the origin of returning 

adults. 

• A three-year study has been initiated to collect samples and analyze the genetic relationship 

between natural and hatchery spawning populations. 

• The Nisqually Tribe has obtained funds through the tribal hatchery reform efforts to better 

estimate the escapement contribution of both hatchery and natural origin fall chinook and to 

better characterize juvenile salmon utilization of the Nisqually River estuary. 

• Additional discussion and funding to develop an adequate broodstock collection facility will be 

required to properly incorporate natural origin recruits into the artificial production program. 
58 Hatchery Reform Recommendations – February 2002 South Puget Sound 

McAllister Creek Hatchery Fall Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability34 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The McAllister Creek Hatchery fall chinook stock derives from transplants primarily from the 

Deschutes Hatchery in 1984. This stock is Green River origin and has been self-sufficient since the 

late 1980s. The objective of the program is to support recreational and treaty harvest in Puget Sound. 

To this end, eggs are collected from adults returning to McAllister Creek Hatchery in sufficient 

numbers to satisfy the following hatchery production targets: one million sub-yearlings and 300,000 

yearlings released per year into McAllister Creek. 

OPERATIONAL CONSIDERATIONS

• McAllister Creek Hatchery is located at river mile 4.0 of McAllister Creek, an independent 

stream draining into the Nisqually River estuary. 

• The hatchery was originally built to rear chum salmon. 

• The hatchery has a number of significant problems including the following: 

o Presence of the parasite Nanophyetus salmincola. in the watershed severely limits the use 

of the facility to only six months of the year (December through May). 

o This requires the use of a variety of in- and out-of-basin facilities for rearing. 

o There is a very high organic loading of the watershed, due to the prevalence of livestock 

farms. 

o The hatchery is located too low in the watershed. McAllister Creek at this location is 

affected by tidal fluctuations and this causes effluent from the hatchery to be entrained 

with the hatchery intake water during high tides. 

o The hatchery depends exclusively on returning adults to voluntarily enter the hatchery, 

which has poor attraction water due to its low location within the watershed. As a result, 

only about two-thirds of the returning fish are trapped, which makes it difficult to meet 

 

34 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
South Puget Sound Hatchery Reform Recommendations – February 2002 59 

broodstock requirements. The other one-third of the returning fish remaining in 

McAllister Creek far exceeds natural spawning habitat capacity. Hatchery fish carcasses 

further contribute to the high organic nutrient load of the creek. 

o Fish exhibit questionable survival and require extensive transfers among different 

facilities to avoid water quality and disease problems. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is providing few benefits. This program and hatchery pose significant risks, because fish 

must be transferred out of the facility prior to release, due to parasite problems. Risks and biological 

problems with this hatchery outweigh the questionable benefits of the program. 

B. Likelihood of attaining goals? 

There is little likelihood that this program or hatchery could ever achieve desired goals, because of 

physical problems with the facility and parasite problems in the watershed. 

C. Consistent with goals for other stocks? 

There are potential predation problem from this program’s yearling component for Nisqually and 

McAllister late chum. Multiple transfers increase risk from pathogens. 

RECOMMENDATIONS

• Discontinue this program and use of this facility for salmonid culture. Resources devoted to this 

program and facility could be better used to achieve regional goals. 

COMMENTS

• The McAllister Hatchery was built at a very poor site and provides little hope of ever supporting 

a successful program. 

MANAGERS RESPONSE

WDFW supports the termination of the fall chinook program at McAllister Creek Hatchery and is 

currently proposing this action to the Washington State Legislature. If the program is terminated, 

alternative uses of the facility will be considered. The Fish and Wildlife Commission has the ultimate 

authority for determining the use of agency facilities. 
60 Hatchery Reform Recommendations – February 2002 South Puget Sound 

Nisqually River Coho 

Nisqually Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Medium Medium 

Population Viability Critical Critical At Risk 

Habitat Inadequate Limiting Limiting 

Harvest Opportunity Occasional Occasional Most Years 

Hatchery Program:

Purpose Harvest and Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Nisqually River coho program began in 1979 with pre-smolts from George Adams Hatchery on 

Hood Canal, changed to Skykomish Hatchery stock in 1989, and changed again to Minter Creek 

Hatchery fish in 1998. Skagit River stock was also used initially for this program. Currently, this 

program is maintained by annual egg transfers from Minter Creek Hatchery. The objective of this 

program has been to support treaty-reserved harvest for the Nisqually Tribe and recreational fisheries 

in the South Sound region. Minter Creek stock is now being used in an attempt to establish a selfsustaining, natural spawning coho population, while conducting an integrated hatchery program to 

also provide harvest. To these ends, eggs are collected, incubated, and hatched at Kalama Creek 

Hatchery (350,000 smolts) and Clear Creek Hatchery (630,000 smolts). The fish are reared and 

released onsite. 

OPERATIONAL CONSIDERATIONS

• This program was initially managed as a segregated harvest program using Skykomish River 

hatchery stock. With the change to the South Sound Minter Creek stock, the long-term goal of the 

program is now to manage coho salmon as an integrated hatchery program with both harvest and 

conservation goals. 

• To potentially achieve goals for an integrated hatchery program, 125,000 smolts are to be outplanted into Beaver Creek when fish are available. 

• Constant temperature ground water is used to rear coho salmon to the smolt stage at Clear Creek 

Hatchery. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program, with the Skykomish stock, was not meeting either harvest or conservation goals nor 

was it meeting broodstock needs. 
South Puget Sound Hatchery Reform Recommendations – February 2002 61 

B. Likelihood of attaining goals? 

Success will depend on the return rate and survival of Minter Creek stock back to the Nisqually River 

as part of the revised program. The program’s water source may present a risk to proper 

smoltification and subsequent life history responses of released fish, including survival. 

C. Consistent with goals for other stocks? 

Hatchery coho smolts may prey on pink salmon fry (see also discussion of Nisqually fall chinook 

program). 

RECOMMENDATIONS

• Reduce program to a size no larger than needed for evaluation of Minter Creek stock. 

• Introduce an average of 10% naturally spawning fish into the hatchery broodstock each year for 

on-station releases. The exact percentage will depend on the status of the natural population. This 

will require the establishment of a marked hatchery stock and a naturally spawning population. 

• Evaluate return rates and contributions to fisheries of new broodstock for three brood years (five 

to six calendar years), including results of recently-implemented rearing strategies. 

• Evaluate the contribution of hatchery fish to the natural spawning population. 

• Discontinue the hatchery program for coho salmon in the Nisqually River if survival and return 

rates do not increase significantly (that is, if the benefits of the program do not outweigh the risks 

and economic costs). 

• Evaluate the contribution to harvest and conservation of the Beaver Creek outplanting program. 

Continue program if goals are achieved. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• The Nisqually Tribe has taken important steps to rectify poor adult returns including: 1) 

replacement of the Skykomish stock with a South Sound stock (Minter Creek); and 2) 

development of alternative rearing strategies (volitional release of smolts, growth modulation via 

temperature and diet manipulations, and semi-natural rearing). 

MANAGERS RESPONSE

WDFW generally supports the recommendations of the HSRG but notes that: 

• Eliminating or reducing the size of the program has numerous implications that will require 

discussion with the Nisqually Tribe. 

• Identification of the number of natural-origin spawners incorporated in the hatchery broodstock is 

a complex topic that will require additional analysis and discussion. 

The Nisqually Tribe supports the recommendations of the HSRG (the Tribe’s full comments are 

appended to this document), and notes the following: 

• Additional discussion and funding to develop an adequate broodstock collection facility will be 

required to properly incorporate natural origin recruits into the artificial production program. 
62 Hatchery Reform Recommendations – February 2002 South Puget Sound 

DESCHUTES RIVER

Overview 

STOCK STATUS35

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Deschutes River Hatchery Fall Chinook Y L L L L ? ? M M H H H H

Deschutes River Coho N L/M M M L L M L L M 0 L M

Deschutes River Hatchery Steelhead Y L L L L L L M M M L M M

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Stocks

HABITAT

The Deschutes River, draining into Budd Inlet, is the largest of the southwest Puget Sound-area 

independent drainages, with a drainage area of about 166 square miles and a length of 52 miles.36

Included within the sub-region are one large watershed (Deschutes River/Percival Creek), several 

medium-sized watersheds (Woodland Creek, Woodard Creek, McLane Creek, Green Cove Creek) 

and a number of smaller independent streams. 

The Deschutes River is the second largest watershed south of the Tacoma Narrows. Anadromous 

salmon and steelhead runs in the Deschutes are artificially introduced, as there is an impassable falls 

at the upper end of Capitol Lake that was only recently laddered (in the mid-1900s). Chinook 

production has been managed strictly as a hatchery return, with sporadic releases of varying 

magnitude and composition released upstream of the hatchery; coho and steelhead are passed 

upstream of the hatchery facility to spawn naturally throughout the watershed. The lower part of the 

Deschutes flows through the cities of Olympia and Tumwater, with the majority of the watershed 

being suburban and agricultural in the lower/middle portions and commercial forest (Weyerhaeuser) 

in the upper watershed. Composite habitat condition for the Deschutes should probably be considered 

as fair. Natural salmonid productivity in the watershed is impaired by: 

• Lack of large, woody debris and pools, which reduces the habitat complexity, 

• Lack of off-channel rearing habitat in the lower watershed, 

• Debris flows and stream bank instability that results in high turbidity and high presence of fine 

sediments in the substrate, 

 

35 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.

36 Conservation Priorities: An Assessment of Freshwater Habitat For Puget Sound Salmon, The Trust For Public Land, Seattle, WA, November 2000.
South Puget Sound Hatchery Reform Recommendations – February 2002 63 

• Altered peak flows from heavily logged areas in the headwaters, agricultural runoff, and urban 

storm-water runoff, 

• Water quality (high water temperatures and low dissolved oxygen) in the lower river, Capitol 

Lake, and lower Budd Inlet, particularly in late summer, and 

• Adult and juvenile fish passage impacts associated with direct transition between Capitol Lake 

and Budd Inlet. 

Much of the coho production from the Deschutes originated from Huckleberry Creek, which is 

located on commercial forestland in the upper watershed. A large slide and debris flow eliminated 

much of the suitable spawning and rearing habitat in Huckleberry Creek. Percival Creek is a mediumsized watershed that also flows into Capitol Lake. Although Percival Creek flows through an urban 

area, with hydrology significantly impacted by urban storm water runoff, much of the watershed is 

within a deep ravine with good riparian buffers. 

Woodland Creek flows into the southern end of Henderson Inlet, with headwaters in the City of 

Lacey. It supports stocks of coho, chum, steelhead and cutthroat, plus a low number of chinook. 

Habitat condition should be generally considered as fair. Woodard Creek flows into the west side of 

Henderson Inlet, with headwaters in the City of Olympia, flowing through a rapidly urbanizing area 

northeast of Olympia. It supports stocks of coho, chum, steelhead, and cutthroat. Habitat condition 

should generally be considered as fair to poor. McLane Creek flows into the southern end of Eld Inlet, 

on the western edge of WRIA 13. Land use in the watershed is primarily rural residential and forest 

land. The creek supports stocks of coho, chum, steelhead, and cutthroat. Habitat condition should 

generally be considered as fair to good, providing good natural production of coho and chum. Green 

Cove Creek flows into the northwest shoreline of Eld Inlet. It supports stocks of coho, chum, 

steelhead, and cutthroat. Habitat condition should generally be considered as fair. There are a number 

of small, independent drainages throughout WRIA 13. These streams have potential to support coho, 

chum, steelhead, and cutthroat. Habitat conditions should generally be considered as fair to poor. 

There are approximately 90 miles of marine shoreline in WRIA 13 (estimate also includes the Eld 

Inlet shoreline within WRIA 14). Natural shoreline functions have been altered by extensive bulk 

heading. As of 1993, 31% of the entire marine shoreline was armored (bulk headed), with armoring 

being as high as 47% in Budd Inlet. Estuarine water quality is also impaired by high water 

temperature and low dissolved oxygen resulting from freshwater inflow, particularly in lower Budd 

Inlet.37

HATCHERIES

Tumwater Falls 

Tumwater Falls Trap/Acclimation Pond is located on the Deschutes River at river mile 2.0, inside the 

Tumwater Falls Park. The Percival Cove Net Pens facility is located at the mouth of Percival Creek. 

Percival Creek enters Capitol Lake at its midpoint, on the west shore. Capitol Lake is actually the 

mouth of the Deschutes River, which was dammed in the early 1950s. The current program calls for 

the release of 3.8 million chinook fingerings at two locations, Tumwater Falls Park (river mile 3.3) 

 

37 Donald Haring, Washington Conservation Commission, March 19, 2001. 
64 Hatchery Reform Recommendations – February 2002 South Puget Sound 

and Percival Cove (river mile 0.5). The goal of both of these programs is to provide for harvest 

opportunity in sport, commercial and tribal fisheries in Puget Sound and coastal areas.38

 

38 Rich Eltrich, Washington State Department of Fish and Wildlife, July 2001.
South Puget Sound Hatchery Reform Recommendations – February 2002 65 

Deschutes River Hatchery Fall Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability39 Low ? ? 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Deschutes River hatchery fall chinook stock was derived from Green River origin stock in the 

1950s. This stock has been maintained through adult fish returns to the Tumwater Falls Trap on the 

Deschutes River. The objective of the program is to provide for harvest while avoiding adverse 

impacts on other fish stocks in the basin. To this end, the program currently releases 3.8 million subyearlings as well as 250,000 yearlings (see below). Sub-yearling production is eyed at McAllister 

Hatchery and Minter Creek Hatchery. Fry are hatched and reared at Wallace River Hatchery (two 

million; Snohomish drainage) and Coulter Creek Hatchery (1.8 million) via Minter Creek. Yearling 

production is eyed at McAllister Hatchery and hatched and reared at McKernan Hatchery (Skykomish 

drainage). Sub-yearling releases include 3.3 million at Tumwater Falls Hatchery and 0.5 million at 

Percival Cove Pens. 250,000 yearlings are released from Percival Cove Pens. 

OPERATIONAL CONSIDERATIONS

• The program uses a variety of facilities, both in- and out-of-region, with extensive transfer of fish. 

• The operation in Percival Cove often has poor water quality resulting in poundage limits and 

early release of juveniles. 

• The program requires a waiver of the co-managers’ disease policy for rearing on surface water at 

Wallace Hatchery. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The Deschutes River fall chinook program is operated as a segregated harvest program consistent 

with its short- and long-term goals, and the program provides significant benefits to sport and 

commercial fisheries. Its location is ideal for significant educational and public outreach benefits.

 

39 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
66 Hatchery Reform Recommendations – February 2002 South Puget Sound 

B. Likelihood of attaining goals? 

Current facilities are inadequate to realize the goals of the program. Extensive transport is required 

among a number of facilities both in- and out-of-region increasing the risk of transfer of pathogens. 

Sub-yearlings are reared on surface water at Wallace Hatchery, requiring a waiver of the disease 

policy. Further, inadequate water and space result in less than optimal release time and condition and 

likely decrease survival rates. 

C. Consistent with goals for other stocks? 

The Deschutes River fall chinook program is operated as a segregated harvest program consistent 

with the goals for other stocks in the watershed. Risks from yearling production include potential 

predation on southern Puget Sound chinook, chum, and pink salmon and competition with coho and 

steelhead. 

RECOMMENDATIONS

• Obtain a memorandum of understanding (MOU) from NMFS addressing the potential 

Endangered Species Act status of chinook spawning naturally above Tumwater Falls, prior to 

implementing the long-term plans described below. 

• Develop long-term plans for rearing and release facilities that eliminate the need for out-of-basin 

transfers. This requires investment in new facilities in the Deschutes River basin. 

• Implement a transitional, in-region program that restricts fish and egg transfers, to be consistent 

with the co-managers’ disease policy. Consider incubation at Minter Creek and rearing at Coulter 

Creek as part of this transitional program. 

• Develop rearing and release locations that eliminate all net pen operations in Percival Cove. 

• Provide adequate water and pond space to allow fish to grow and be released at the optimal time 

and size for maximum survival advantage. 

• Develop appropriate pollution abatement or rearing strategies to meet local, state and federal 

clean water requirements. 

• Develop a strong educational component involving local partnerships, given the location of the 

drainage within a major urban area, the state capitol, and the City of Tumwater. 

COMMENTS

• The basin provides a significant opportunity to foster a research component focusing on the 

productivity of hatchery-origin chinook released to a natural spawning environment. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG and has taken the following actions: 

• Pursued discussions with the National Marine Fisheries Service regarding chinook spawning 

naturally above Tumwater Falls, but have been unable to secure an agreement. 

• Initiated the final phase of a scoping process leading to the selection and development of cost 

estimates for the preferred alternative for new facilities in the Deschutes Basin. 

• Reduced the reliance on out-of basin facilities by 40%. 

The Squaxin Island Tribe’s full comments are appended to this document. 
South Puget Sound Hatchery Reform Recommendations – February 2002 67 

Deschutes River Hatchery Steelhead 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability40 Low Low Low 

Habitat Limiting Limiting Limiting 

Harvest Opportunity Occasional Most Years Most Years 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Deschutes River hatchery steelhead program relies on annual outplants of Chambers Stock from 

Puyallup, Tokul or Eells Spring hatcheries. From 1975–96, this program was maintained primarily by 

adult returns to Eells Spring Hatchery. From 1997 until the present, this program has been maintained 

primarily through adult returns to Puyallup Hatchery. The objective of this program is to provide for 

harvest while avoiding adverse interactions with other fish stocks in the watershed. To this end, 

25,000 yearlings are released into the Deschutes drainage. Eggs are hatched and the hatch reared at 

Puyallup Hatchery. 

OPERATIONAL CONSIDERATIONS

• Fish are reared at Puyallup Hatchery, which is located in a region that has yet to be reviewed by 

the HSRG. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

Minimal harvest opportunity benefits are presently being obtained. This may be due to the low 

numbers of smolts being released or to the quality of smolts being released. 

B. Likelihood of attaining goals? 

If the future goal of increased harvest is to be realized, the two factors mentioned above will need to 

be examined. 

C. Consistent with goals for other stocks? 

There is the potential for competition with, and predation on, coho, cutthroat and chinook. 

 

40 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
68 Hatchery Reform Recommendations – February 2002 South Puget Sound 

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of “wild 

steelhead management zones” where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Develop on-site incubation and rearing with the new hatchery facility described in 

recommendations for Deschutes River fall chinook program. 

• Release hatchery yearling steelhead smolts between May 1 and May 15, at a target size of six to 

the pound, and at a condition factor of less than 1.0.

• Evaluate potential competition and predation on coho, cutthroat and chinook to determine 

appropriate program size. 

COMMENTS

• Increasing smolt quality and/or release numbers will probably be necessary to meet desired 

harvest opportunity goals. These benefits must be balanced against the risks to other species; 

however, due to a natural migrational blockage, the risk to native stocks is limited to nonmigratory species. 

MANAGERS RESPONSE

WDFW supports the recommendations and has initiated, with funding provided by the HSRG, studies 

to evaluate the risks posed by competition and predation by hatchery origin smolts. 
South Puget Sound Hatchery Reform Recommendations – February 2002 69 

SQUAXIN/SOUTH SOUND NET PENS AND INDEPENDENT 

TRIBUTARIES

Overview 

STOCK STATUS41

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

So. Sound Indep. Trib. Coho N M M M M M M M M M H H M

Squaxin/S Sound Net Pens Hatchery Coho Y L L L L L L L L M H H H

So. Sound Indep. Trib. Normal Chum N H H H H H H M/H H H H H H

So. Sound Indep. Trib. Summer Chum N H H H M/H H H M M H M M H

So. Sound Indep. Trib. Steelhead N M H H L L M L L M 0 0 0

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Stocks

HABITAT

This region consists of a complex system of streams, estuaries, and extensive marine inlets on the 

southwest terminus of Puget Sound. From south to north, Eld Inlet, Totten Inlet, Little Skookum Inlet, 

and Hammersley Inlet/Oakland Bay are the primary marine water bodies in this region. For all 

streams in this region, the extensive estuary mud flats along the inlets have been historically rich 

production areas for shellfish, as well as marine and anadromous fish.42 There are at least 36 

independent drainages to saltwater in WRIA 14 that have been identified as supporting anadromous 

salmonids, with several of the watersheds providing what would be considered as fair to good coho, 

chum, steelhead, and cutthroat habitat. Adult chinook presence is also documented in several of the 

larger watersheds, although these do not have “typical chinook habitat.” Collectively, the natural 

coho, chum, and cutthroat production is very significant. 

The larger watersheds of particular note include Schneider, Kennedy, Skookum, Mill/Goznell, 

Goldsborough, Johns, Cranberry, Deer, and Sherwood creeks. Kennedy Creek has perhaps the highest 

documented chum spawner density of any Puget Sound stream. Coho and chum spawner densities are 

also high in several of the other watersheds. Although there are habitat impairments identified in each 

of the watersheds, development densities are generally low and habitat conditions are generally in 

good condition when compared to other Puget Sound watersheds. Productivity is also enhanced by 

high quality estuarine habitat present throughout the sub-region’s marine inlets43. 

 

41 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.

42 Conservation Priorities: An Assessment of Freshwater Habitat For Puget Sound Salmon, The Trust For Public Land, Seattle, WA, November 2000.

43 Donald Haring, Washington Conservation Commission, March 19, 2001. 
70 Hatchery Reform Recommendations – February 2002 South Puget Sound 

HATCHERIES

South Sound Net Pens 

The Squaxin Island/South Sound Net Pen enhancement facility is a harvest-oriented program that has 

been in operation since the early 1970s. The complex is located in southern Puget Sound near 

Squaxin Island in Peale Passage. The program is co-managed by WDFW and the Squaxin Island 

Tribe. Under agreement, the Tribe provides labor and maintenance while the State supplies fish, feed, 

and technical assistance. The primary goal of the net-pen program is to provide for harvest 

opportunities of adult coho salmon in a terminal area fishery. Production from this facility provides 

harvest for Squaxin tribal fishermen exercising treaty fishing rights and recreational fishers in 

Southern Puget Sound. The current production goal is to rear 1.8 million coho smolts for delayed 

release in June at a size of 10 fish per pound. Historically, production at the pens has averaged 2.3 

million coho, but due to recent ocean conditions and poor survival the production goal was reduced.44

 

44 Will Henderson, Squaxin Island Tribe and Rich Eltrich, Washington State Department of Fish and Wildlife, July 2001.
South Puget Sound Hatchery Reform Recommendations – February 2002 71 

Squaxin/South Sound Net Pens Hatchery Coho 

Squaxin Tribe and Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability45 Low Low Low 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

Egg sources for this program include the Wallace River in the Skykomish drainage and the Minter 

Creek Hatchery stock that originated from Minter Creek and the Green and Skagit rivers. The purpose 

of this program is to provide pre-terminal and terminal sport harvest and terminal area treaty harvest 

in southern Puget Sound. To this end, 1.8 million yearlings at ten to the pound are released into Peale 

Passage. Eggs are collected at Wallace River Hatchery (Skykomish drainage) and incubated at 

Wallace River and Marblemount hatcheries (Skagit drainage). Rearing takes place at Wallace River 

(400,000) for direct transfer to the net pens and at Skookumchuck Ponds (1.4 million) (Chehalis 

drainage) for the component transferred through Marblemount Hatchery. 

OPERATIONAL CONSIDERATIONS

• This program relies on egg take, incubation, and rearing at multiple facilities in several drainages. 

• Fish are released at a larger size, and generally later, than freshwater coho yearlings. 

• The program has used a variety of coho stocks, primarily Issaquah Creek, southern Hood Canal, 

Skykomish River, and southern Puget Sound stocks. 

• The current production goal is 1.8 million fish, which is reduced from a previous average of 2.3 

million fish. 

• All released fish are marked to allow for assessment of harvest contribution from the hatchery 

release and evaluation of the status of natural stocks. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is generally consistent with the defined harvest goals. However, non-treaty harvest 

opportunities have been limited. 

 

45 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
72 Hatchery Reform Recommendations – February 2002 South Puget Sound 

B. Likelihood of attaining goals? 

The likelihood of attaining harvest goals for this program will be dependent on an overall 

improvement of survival from the net pen releases, as well as improved access to harvest by the nontreaty fishery. Use of non-local broodstock and multiple transfers of fish resulting from out-of-basin 

rearing may be contributing to lowered survival. Another risk that could affect the long-term success 

of this program is the current process of transferring these fish through several watersheds, which 

could interrupt the net pen program should a serious pathogen problem be identified in one of the 

rearing locations. This has the potential to halt transfers necessary to fulfill the current program. 

C. Consistent with goals for other stocks? 

The biological significance of naturally spawning coho stocks in the independent South Sound 

tributaries was rated as intermediate or high. Because of these ratings, there is reason to be concerned 

about the effects of the net pen program on these stocks, both from straying and ecological 

interactions. Straying risks include potential failure to meet goals for biological significance and 

population viability. Risks from ecological interactions include potential competition with other 

South Sound coho stocks, resulting in an overall loss of productivity. Risks to non-coho populations 

include potential predation on southern Puget Sound chinook, chum, and pink salmon and 

competition with steelhead. 

RECOMMENDATIONS

• Quantify the amount of straying from South Sound Net Pens to South Sound coho tributaries. 

• Compare the genetic and life history characteristics among South Sound, Skykomish and Minter 

Creek coho populations. 

• Compare rates of straying between in-region and out-of-region incubation and rearing. 

• During these evaluations, relocate incubation and rearing within the region to the extent that 

space exists at regional facilities. 

• Evaluate benefits and risks of using Skykomish stock versus a within-region stock, probably 

Minter Creek Hatchery. 

• During these evaluations, change the broodstock source for this program to a local broodstock. 

• Develop a long-term strategy based on the results of the analyses described above and other 

relevant information. 

• Do not increase the size of the program beyond the current level of 1.8 million fish, at least 

during this period when survival is depressed for many stocks possessing a yearling life history 

strategy. 

COMMENTS

• The co-managers are currently exploring the redefinition of South Sound coho regional 

management strategies through the Comprehensive Coho planning process. 

• Current survival rates (brood year 1988–94) have averaged 3.7 %, approximately 25% of the 

survival rate achieved during the 1970s and approximately 30% of the survival rates for brood 

years 1981–87. 

• Contribution of this program (based on expanded use of coded wire tags) to the South Sound 13D 

net fishery for the period 1985–98 has ranged from 46%–100%, averaging 63.8%. In 1999, that 

catch was the lowest on record (5,038 fish) and the program contribution was only 1.6% of the 

catch. 
South Puget Sound Hatchery Reform Recommendations – February 2002 73 

• The HSRG is concerned about the carrying capacity of southern Puget Sound, and its effect on 

current survival rates of all species with the yearling life history strategy, including natural and 

hatchery chinook, coho and steelhead. 

• This program’s out-of-region rearing also creates risks for stocks in the Skagit and Chehalis 

watersheds, and competition for hatchery resources. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. 

The Squaxin Island Tribe’s full comments are appended to this document. 
74 Hatchery Reform Recommendations – February 2002 South Puget Sound 

KEY PENINSULA

Overview 

STOCK STATUS46

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

White River Spring Chinook (Hupp Springs) Y H H ? L L ? L L ? L L ?

Minter Creek Hatchery Fall Chinook Y L L L L L L L L L H H H

Coulter Creek Hatchery Fall Chinook Y L L L L L L L L L H H H

Fox Island Net Pens Hatchery Fall Chinook Y L L L L L L L L M H H H

Minter Creek Coho Y M M M M M M M M M H H H

Fox Island Net Pens Hatchery Coho Y L L L L L L L L M H H H

Minter Creek Chum Y L L L H H H M M M H H H

Minter Creek Pink Y L L L L L L L L L 0 0 0

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Stocks

HABITAT

There are 46 independent, low-elevation drainages to saltwater with salmonid presence that flow into 

the Gig Harbor Peninsula/Key Peninsula/Islands portion of southeast WRIA 15, including over 58 

miles of stream known to be used by anadromous salmonids (with additional stream length used by 

cutthroat). Streams within this sub-region originate in the lowland hills of the Kitsap Peninsula and 

empty into several large inlets within western Puget Sound. Although this sub-region contains no 

major river systems, many of these streams historically supported substantial salmon runs. Currently, 

several stream systems contribute significantly to the salmon production of this sub-region, although 

nearly all watersheds on the eastern Peninsula have been impacted to some degree by land use.47

All of these drainages support cutthroat, most support coho and chum, many support steelhead, and 

some of the larger ones have documented adult chinook returns, although they do not have “typical 

chinook habitat.” Habitat conditions vary within and between streams, ranging from good to very 

poor. Habitat condition in several of the smaller streams is unknown. Collectively, and particularly 

when considered in conjunction with the streams in WRIA 14, these streams represent significant 

potential natural coho, chum, and steelhead production. 

The largest streams are Minter, Coulter, Rocky, Burley and Purdy creeks. Minter Creek is the largest 

of the watersheds in this sub-region (~10,000 acres) and enters the west shoreline of Carr Inlet. The 

 

46 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.

47 Conservation Priorities: An Assessment of Freshwater Habitat For Puget Sound Salmon, The Trust For Public Land, Seattle, WA, November 2000.
South Puget Sound Hatchery Reform Recommendations – February 2002 75 

watershed supports coho, chum, steelhead, cutthroat and chinook. The Minter Creek watershed is 

experiencing population growth and development pressure, and habitat condition varies from poor to 

good between different reaches. Coulter Creek enters the north end of Case Inlet, and supports natural 

coho, chum, steelhead, cutthroat and chinook. Much of the Coulter Creek watershed is operated as a 

private tree farm (Overton Tree Farm). Consequently, development within the watershed is low, there 

are few road encroachments on the stream channel, and freshwater and estuarine habitats are in 

generally good condition and thought to be very productive. 

The Burley Creek watershed enters Burley Lagoon at the north end of Carr Inlet, and supports coho, 

chum, steelhead, cutthroat and chinook (chinook are probably of hatchery origin). The watershed is 

experiencing population growth and development pressure, and habitat condition varies from poor to 

good between different reaches. Rocky Creek enters the east shoreline of Case Inlet, and supports 

natural coho, chum, steelhead, cutthroat and chinook. Habitat conditions in Rocky Creek are 

generally fair to good. Purdy Creek enters the east shoreline of Burley Lagoon at the north end of 

Carr Inlet, and supports coho, chum, steelhead, cutthroat and chinook (chinook are probably of 

hatchery origin). The watershed is experiencing population growth and development pressure, and 

habitat condition varies from good in the lower watershed to poor in some upstream reaches.48

HATCHERIES

Minter Creek Hatchery 

Minter Creek Hatchery is a harvest supplementation and stock recovery facility located on Minter 

Creek, a tributary to Carr Inlet, in south Puget Sound, approximately 10 miles west of Gig Harbor. 

The station was constructed in 1936 under a Works Progress Administration (WPA) contract, with 

the federal government furnishing materials and labor. It was operated as a research station until 

about 1960 when its primary function shifted to a harvest augmentation program. Beginning in 1993, 

the hatchery underwent a major renovation (mostly completed). Minter Creek Hatchery currently 

serves as the hub for several satellite facilities, including Coulter Creek Hatchery, Hupp Springs 

Hatchery, and the Fox Island Net Pens. Since the early 1980s, the hatchery has been involved in the 

restoration of the ESA-listed White River spring chinook. Minter Creek Hatchery now provides adult 

trapping, transportation and incubation support for Hupp Springs Hatchery. It also operates as a 

production facility for fall chinook, coho, pink and chum for various Puget Sound fisheries. Minter 

Creek Hatchery provides incubation and short-term rearing for other facilities, co-ops, and 

enhancement and educational projects in south Puget Sound. 

Coulter Creek Hatchery 

Coulter Creek Hatchery is located approximately two miles north of Allyn on State Highway 3. It 

operates as a harvest supplementation program. It was built in 1980 as part of a hatchery enhancement 

program to increase the production of chum salmon for an all citizen fishery. The hatchery is operated 

as a satellite of Minter Creek Hatchery and is supported by Minter. The Coulter Creek Hatchery 

program is designed to rear and transfer fall chinook to the Fox Island Net Pens, South Puget Sound 

Complex at Tumwater, to out-plant fingerling chinook on-site, and to provide yearling coho for the 

Agate Pass Net Pens, a cooperative project between WDFW and the Suquamish Tribe. The 

production program consists of 1.8 million fall chinook to be transferred to South Sound Complex, at 

Tumwater, at 150/lb, one million fall chinook to be released on station at 80/lb, and 350,000 yearling 

 

48 Donald Haring, Washington Conservation Commission, March 19, 2001. 
76 Hatchery Reform Recommendations – February 2002 South Puget Sound 

coho to be transferred to Agate Pass net pens at 25/lb. Coulter is also rearing 300,000 fall chinook for 

transfer to Fox Island Net Pens at 25/lb.49

Hupp Springs Hatchery 

Hupp Springs Hatchery was built in 1979. The hatchery is located on Minter Creek, approximately 

three-quarters of a mile upstream from Minter Creek Hatchery. The original program called for 

rearing and releasing chum and delayed release fall chinook. The program was quickly changed and 

dedicated to the restoration of the depleted White River spring chinook. Spring chinook adults are 

captured at Minter Creek Hatchery and held for transfer to Hupp Springs Hatchery. The maximum 

release capacity for the facility is approximately 90,000 yearling chinook and 250,000 sub-yearling 

chinook. This station supports the recovery program for the White River Spring Chinook, an ESAlisted stock.50

Fox Island Net Pens 

The Fox Island Net Pens are located in Echo Bay, on the north side of Fox Island, in Pierce County. 

The station was established in September 1975 and was designed to augment the sports fishery in 

southern Puget Sound by increasing residualization of fall chinook and coho. The current total release 

capacity is 320,000 yearling salmon per year. The Fox Island Net Pens were closed, effective July 1, 

2001.51

 

49 Dennis Popochock, Washington State Department of Fish and Wildlife, July 2001.

50 Sherman Davis, Washington State Department of Fish and Wildlife, July 2001.

51 Jon Lovrak, Washington State Department of Fish and Wildlife, July 2001.
South Puget Sound Hatchery Reform Recommendations – February 2002 77 

White River Spring Chinook (Hupp Springs) 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High ? 

Population Viability Critical Critical ? 

Habitat Inadequate Inadequate ? 

Harvest Opportunity Occasional Occasional ? 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The White River spring chinook (Hupp Springs) stock derives from fish collected in the Puyallup and 

White rivers from the late 1970s through the early 1980s, when the entire spring chinook run was 

trapped and moved into the hatchery or raised as captive brood. At one point, fewer than 30 fish per 

year remained. Captive brood were reared at the NMFS Manchester site and the South Sound net 

pens, to rapidly expand the program. This stock is maintained through adult returns to Minter Creek 

Hatchery. This stock is also maintained at White River Hatchery (Muckleshoot Tribe), which began 

with transfers from Hupp Springs’ production. The White River spring chinook stock is maintained 

outside of its natal drainage for conservation purposes. This belongs to, and is the only stock within, 

the South Puget Sound Spring Chinook GDU. The objective of this program has been to support the 

recovery of the White River chinook salmon through an integrated conservation program and to 

maintain the gene pool at the Minter Creek/Hupp Springs complex. To this end, 370,000 eggs from 

adults returning to Minter Creek Hatchery are collected to produce annual releases of 250,000 subyearlings and 85,000 yearlings, with eggs and fry beyond the goal being transferred to the White 

River acclimation ponds and White River Hatchery. The program uses Minter Creek Hatchery for 

adult trapping and egg incubation. Unfed fry are transported to Hupp Springs Hatchery for rearing 

until release. 

OPERATIONAL CONSIDERATIONS

• Returning adults are tagged and segregated from fall chinook salmon returning to Minter Creek. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The objective of this program has been to support the recovery of the White River chinook salmon 

through an integrated conservation program. The goal of an integrated program is to minimize the 

potential genetic divergence between the hatchery broodstock and the naturally spawning 

populations. However, no infusion of naturally spawning individuals into the broodstock has occurred 

in this program since the captive brood program was initiated three to four generations ago. This 
78 Hatchery Reform Recommendations – February 2002 South Puget Sound 

presents a significant risk of domestication and genetic divergence between the broodstock and 

populations targeted for restoration. Further, this continued infusion of domesticated genetic material 

might retard adaptation of hatchery-origin populations to the natural environment. 

B. Likelihood of attaining goals? 

This program has played an important role in the restoration of White River spring chinook, but 

continued infusion of genetic material from the three to four generation hatchery population into that 

once again present in the White River could retard adaptation of the latter population to the natural 

environment 

C. Consistent with goals for other stocks? 

Considerable effort has been expended to maintain the integrity of fall chinook salmon returning to 

Minter Creek. Risks to that stock from the White River spring chinook program appear to be within 

acceptable limits. 

RECOMMENDATIONS

• Discontinue the conservation program, unless this program is demonstrated to be critical to the 

conservation effort on White River spring chinook. 

• If the conservation program continues, implement protocols to reduce domestication and 

minimize genetic changes resulting from artificial propagation. 

• If the goals of the program change, the program should be reevaluated. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• The HSRG will evaluate the role of Hupp Springs in the current White River recovery program 

during its review of the Central Puget Sound region in 2002. 

• This program has played an extremely important role in the recovery of the White River during a 

period in which the stock was at an extreme risk of extirpation. However, the importance of the 

current program has changed with the reintroduction of naturally spawning populations in the 

White River drainage. 

MANAGERS RESPONSE

WDFW generally supports the recommendations of the HSRG, but notes that: 

• WDFW and the tribes need to evaluate the contribution of this program to the recovery of White 

River spring chinook. 

• Identification of the number of naturally origin spawners incorporated in the hatchery broodstock 

is a complex topic that will require additional analysis and discussion. 
South Puget Sound Hatchery Reform Recommendations – February 2002 79 

Minter Creek Hatchery Fall Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability52 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Minter Creek hatchery fall chinook program was derived from fish of Green River origin. There 

is no native fall chinook stock in Minter Creek. This program is maintained through adult returns to 

the hatchery trap. The objective of this program is to provide fish for harvest while avoiding adverse 

interactions with other fish stocks in the region. To this end, 1.8 million fingerlings are released 

annually into Minter Creek. Eggs are incubated at the hatchery, where the resulting fry are reared 

until release. 

OPERATIONAL CONSIDERATIONS

• None of the broodstock is passed into Minter Creek to spawn. 

• Releases are marked to allow harvest of hatchery fish while protecting naturally spawning fish. 

• Fish are not tagged. 

• Returns to the hatchery are currently surplus to hatchery broodstock needs because of a lack of a 

satisfactory level of harvest. 

• Change to an earlier run timing has occurred over the years, complicating the separation of this 

stock at the hatchery from returning adults of the White River spring chinook stock. 

• The number of programs and a water supply problem at Minter Creek Hatchery compromise the 

effectiveness of the fall chinook and other programs at the hatchery. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is consistent with the goals for the stock. 

B. Likelihood of attaining goals? 

The program is providing for harvest and is being operated in a segregated manner. 

 

52 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
80 Hatchery Reform Recommendations – February 2002 South Puget Sound 

C. Consistent with goals for other stocks? 

The program is generally consistent with the goals for other South Sound stocks. 

RECOMMENDATIONS

• Eliminate two programs (the pink and fall chum programs) at Minter Creek Hatchery (see 

relevant reviews for these programs). This will reduce constraints to the fall chinook program. 

• Reverse, over time, the problem of earlier run timing in the fall chinook stock to avoid 

compromising its ability to contribute to harvest and to achieve a better separation between the 

timing of its return and that of the White River spring chinook stock. 

• Upgrade the water supply system at the hatchery. 

COMMENTS

• Adjusting the run timing of fall chinook at Minter Creek Hatchery would reduce the level of adult 

handling currently required to separate them from the White River spring chinook, both of which 

return to the hatchery at the same time. It would also result in a stock more closely resembling the 

one from which it was derived. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. 
South Puget Sound Hatchery Reform Recommendations – February 2002 81 

Coulter Creek Hatchery Fall Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability53 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Coulter Creek hatchery fall chinook program relies on annual transfers of Minter stock, Coulter 

Creek Hatchery adult returns, and Tumwater Falls Hatchery as a backup. These fish were of Green 

River origin. This program’s objective is to produce fish for harvest and to do so in a manner that 

minimizes adverse effects on other local stocks. To this end, eggs are collected, incubated, and 

hatched at Minter Creek Hatchery. Resulting fry are reared at Coulter Creek Hatchery for transfer to 

Fox Island Net Pens (which have been closed) and the South Puget Sound Complex at Tumwater 

Falls (1.8 million fingerlings). Releases are also made onsite directly into Coulter Creek (one million 

smolts). 

OPERATIONAL CONSIDERATIONS

• Coulter Creek Hatchery was built in 1980 as part of a hatchery enhancement program to increase 

the production of chum salmon. 

• The facility is now being used to rear, transfer and release fall chinook. The hatchery has no 

incubation capability. 

• A dam provides an adult barrier and an impoundment to supply pumped water from Coulter 

Creek to two one-third acre rearing ponds. Due to pond design and fish health problems, an 

extended fall chinook rearing program was dropped. 

• Coulter Creek does not have a pollution abatement pond and uses a naturally impounded area for 

settling out pond waste materials. Coulter Creek meets NPDES discharge levels, but the addition 

of an abatement system would upgrade the facility. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The data indicate that there is a limited contribution to a terminal harvest. 

 

53 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
82 Hatchery Reform Recommendations – February 2002 South Puget Sound 

B. Likelihood of attaining goals? 

The program has been discontinued. 

C. Consistent with goals for other stocks? 

Because chum in Coulter Creek are managed for natural production, all returning chinook and chum 

adults are passed upstream. Returning chinook have a significant negative ecological impact as a 

result of redd superimposition on Coulter Creek chum salmon. Water quality at Coulter Creek in the 

fall and winter months can become a problem depending on the number of returning adults. 

RECOMMENDATIONS

• Use the resources dedicated to this program at Coulter Creek elsewhere to better achieve regional 

goals for chinook salmon. 

• Discontinue the release of chinook salmon on station (the HSRG has been informed that the 

release of chinook salmon into Coulter Creek has been discontinued since this recommendation 

was made). 

COMMENTS

• Coulter Creek also provides yearling coho for the Agate Pass Net Pen program, which will be 

reviewed as part of the Central Puget Sound regional review. 

MANAGERS RESPONSE

WDFW has implemented the recommendation of the HSRG to discontinue releases of chinook at 

Coulter Creek. 
South Puget Sound Hatchery Reform Recommendations – February 2002 83 

Fox Island Net Pens Hatchery Fall Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability54 Low Low Low 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Fox Island Net Pens hatchery fall chinook program relied on annual transfers from Minter Creek 

Hatchery. These fish were of Green River origin. The objective of this program was to provide fish 

for harvest and to do so in a manner that minimized adverse effects on other stocks. To this end, 

240,000 yearling fall chinook salmon were released into Echo Bay. Eggs were collected, incubated, 

and hatched at Minter Creek Hatchery. Unfed fry were transferred to Coulter Creek Hatchery for 

additional rearing and transfer to the net pens. 

OPERATIONAL CONSIDERATIONS

Not applicable (see Comments section below). 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program contributed to harvest. 

B. Likelihood of attaining goals? 

This program has been discontinued. 

C. Consistent with goals for other stocks? 

There was a concern about straying in South Sound and negative interaction such as predation on 

other stocks. 

RECOMMENDATIONS

Not applicable (see Comments section). 

 

54 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
84 Hatchery Reform Recommendations – February 2002 South Puget Sound 

COMMENTS

• WDFW has terminated the program, and discontinued use of the net pens. 

MANAGERS RESPONSE

None. 
South Puget Sound Hatchery Reform Recommendations – February 2002 85 

Minter Creek Coho 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Intermediate Intermediate Intermediate 

Population Viability At Risk At Risk At Risk 

Habitat Limiting Limiting Limiting 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest and Education 

Type Integrated 

PROGRAM DESCRIPTION

The Minter Creek coho stock derived historically from Minter Creek, and the Green and Skagit rivers. 

The inflow of Green and Skagit river fish stopped around 1980. This stock has been maintained by 

adult returns to Minter Hatchery for the past 25 years. Minter Creek coho belong to the Puget Sound/ 

Strait of Georgia ESU. The purpose of the program is to provide harvest, while minimizing adverse 

interactions with other local stocks. To this end, approximately 1.4 million yearlings are released 

annually on-station. Eggs are collected, incubated, hatched and reared at Minter Creek Hatchery. One 

million eyed eggs are collected for the Nisqually Hatchery coho program; 450,000 are collected for 

the Agate Pass net pens. 

OPERATIONAL CONSIDERATIONS

• Run timing is increasingly early. 

• All releases are mass-marked (adipose fin clipped). 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is consistent with the harvest and education goals, but does not have the broodstock 

management plan needed to achieve goals of an integrated program. 

B. Likelihood of attaining goals? 

The program is providing significant harvest benefits, and also educational benefits (providing 65 

schools with aquariums of eyed eggs). Increasingly early egg-take timing, decreasing size of returning 

adults and other domestication effects could decrease the viability of the population over time. 

C. Consistent with goals for other stocks? 

Magnitude of yearling releases poses some risk to local chum stocks. 
86 Hatchery Reform Recommendations – February 2002 South Puget Sound 

RECOMMENDATIONS

• Collect sufficient gametes across entire run-timing, cull as needed to assure proportionate normal 

timed egg-take for rearing. 

• Introduce an average of 10% naturally spawning fish into the hatchery broodstock each year for 

on-station releases. 

• Upgrade the water supply system at the hatchery. 

COMMENTS

• The Minter Creek coho program plays an integral role for meeting this region’s goals. 

• The HSRG and the managers discussed reducing the on-station releases from approximately 1.4 

million to approximately one million. Subsequently, WDFW decided to make this change in the 

program. 

• Minter Creek also provides coho for the Agate Pass Net Pen program, which will be reviewed as 

part of the Central Puget Sound regional review. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG but notes that: 

• Identification of the number of naturally origin spawners incorporated in the hatchery broodstock 

is a complex topic that will require additional analysis and discussion; 

• Additional funds will be required to upgrade the water supply system at the hatchery. 
South Puget Sound Hatchery Reform Recommendations – February 2002 87 

Fox Island Net Pens Hatchery Coho 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability55 Low Low Low 

Habitat Inadequate Inadequate Limiting 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Fox Island Net Pens hatchery coho program relied on annual transfers from Minter Creek 

Hatchery. This program used Minter Creek stock and operated from the early 1970s through 2001. 

The purpose of the program was to provide for harvest while minimizing adverse interactions with 

other local stocks. To this end, 40,000 (at ten fish per pound) and 10,000 age two-plus coho were 

released into Echo Bay. Eggs were collected, incubated, and hatched at Minter Creek Hatchery, 

where rearing until transfer to the net pens also occurred. 

OPERATIONAL CONSIDERATIONS

None. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program contributed to harvest. 

B. Likelihood of attaining goals? 

See above comment. 

C. Consistent with goals for other stocks? 

There was a concern about straying in the Sound and negative interactions, such as predation on other 

stocks. 

RECOMMENDATIONS

Not applicable (See Comments section). 

 

55 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
88 Hatchery Reform Recommendations – February 2002 South Puget Sound 

COMMENTS

• WDFW has terminated the program, and discontinued use of the net pens. 

MANAGERS RESPONSE

None. 
South Puget Sound Hatchery Reform Recommendations – February 2002 89 

Minter Creek Chum 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability Healthy Healthy Healthy 

Habitat Limiting Limiting Limiting 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Integrated 

PROGRAM DESCRIPTION

The original Minter Creek fall chum program began with introductions from Hoodsport Hatchery on 

Hood Canal. In the late 1980s, that stock was replaced by introduction of Elson Creek fish, a South 

Sound stock, for a period of five years. The program is currently maintained by returns to Minter 

Creek Hatchery. Minter Creek chum belong to the South Puget Sound Fall Chum GDU. There are 

eleven other stocks within this GDU. The objective of the program is to provide fish for harvest, 

while minimizing genetic divergence from the naturally spawning stock. To this end, two million fry 

at 450 fish per pound are released annually into Minter Creek. The eggs are incubated at the hatchery 

and fry are released on-site. 

OPERATIONAL CONSIDERATIONS

• Returns surplus to hatchery needs are passed upstream to spawn in Minter Creek. 

• Releases from the hatchery are unmarked. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is being operated in a manner consistent with its short- and long-term goals. 

B. Likelihood of attaining goals? 

The program has provided fish for harvest, but this opportunity has been underused. 

C. Consistent with goals for other stocks? 

The program is generally consistent with the goals for other stocks, but its very great success, coupled 

with the lack of a suitably intense harvest, is resulting in water quality problems at Minter Creek 

Hatchery that adversely affect coho and chinook programs at the hatchery. 
90 Hatchery Reform Recommendations – February 2002 South Puget Sound 

RECOMMENDATIONS

• Suspend the chum program at Minter Creek until such time as a need for the program is 

identified. 

• Manage chum salmon in Minter Creek for natural reproduction and to minimize unnecessary 

water quality problems at the hatchery. 

COMMENTS

• Hatchery capacity at Minter Creek would be more effectively used to achieve the managers’ 

regional goals if the fall chum program was suspended. 

• Cessation of the chum program at Minter Creek Hatchery would have implications for co-op 

programs that depend on Minter Creek for their chum salmon supply. Solutions to this problem 

would have to be sought. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG and has taken the following actions: 

• Reduced the size of the program by 75%. 

• Proposed to the Washington State Legislature the termination of this program. 
South Puget Sound Hatchery Reform Recommendations – February 2002 91 

Minter Creek Pink 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability Critical Critical Critical 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity None None None 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Minter Creek pink program began with introductions from South Prairie Creek (Puyallup River 

drainage) brood stock, beginning in 1989. This program is maintained by returns to the Minter Creek 

Hatchery. Minter Creek pinks belong to the Puyallup Pink GDU. The objective of the program is to 

establish an introduced stock. To this end, 90,000 fry are released into the Minter Creek drainage 

annually. Eggs are incubated at Minter Creek Hatchery, where they are hatched and released at 450 

fish per pound or smaller. 

OPERATIONAL CONSIDERATIONS

• There are no naturally spawning pink salmon in the Key Peninsula sub-region. The stock has a 

low biological significance. 

• The number of adults is insufficient to maintain an effective population size of 1,000. 

• Fish are released with no mark or tag. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The goals for this stock do not justify the program. Although this is described as a conservation 

program, there are no conservation goals for this stock. 

B. Likelihood of attaining goals? 

Conservation benefits are minimal or unknown. Because of the way broodstock is collected, the 

program does create a risk of domestication to the stock. 

C. Consistent with goals for other stocks? 

The program is generally consistent with the goals for other South Sound stocks. 
92 Hatchery Reform Recommendations – February 2002 South Puget Sound 

RECOMMENDATIONS

• Terminate the program because no evidence has been presented that it is contributing or will 

contribute to its conservation goal. 

• Allow returning fish to pass upstream and attempt to spawn naturally. 

COMMENTS

• Since there is no infusion of new (naturally spawning) genetic material, there is no evidence that 

the program is actually integrated. 

• This facility has more important programs to focus on. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG and will terminate the program beginning with 

the 2003 brood. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 93 

Stillaguamish/Snohomish 

Overview 

This region includes the watersheds contained by the Stillaguamish and Snohomish rivers and Tulalip 

Bay. For the purposes of this review, the Scientific Group and the regional managers divided the 

region into three sub-regions and then reviewed the hatchery programs involving each identified subregional salmonid stock (for example, North Fork Stillaguamish summer chinook). The review 

included a consideration of the program’s effects on all other hatchery and naturally spawning subregional salmonid stocks. The sub-regions identified for this region include: 

1. Stillaguamish River Watershed 

2. Snohomish River Watershed 

3. Tulalip Bay and Independent Tributaries 

This chapter provides region-wide recommendations for the Stillaguamish/Snohomish region, a 

general overview of each sub-region, followed by reviews and recommendations for each salmonid 

stock that has an associated hatchery program. 

FISHERIES

Chinook, coho and chum salmon harvest management in the Stillaguamish/Snohomish region is 

directed primarily towards the needs of natural production and secondarily for harvest of surplus 

hatchery production. Odd-year pink salmon harvest management is based on natural production; there 

is no hatchery production for pink salmon in this region. In addition to the normal odd-year pinks, the 

Snohomish supports an even-year run. Currently this population supports no directed fisheries. 

Winter steelhead harvest management is directed primarily towards the needs of natural production 

and secondarily for harvest of hatchery production. Summer steelhead harvest management is 

directed towards the needs of natural production and harvest of hatchery production. Sea-run 

cutthroat management is based entirely on natural production. 

CONSERVATION

All Puget Sound chinook are currently managed under the Puget Sound Comprehensive Chinook 

Management Plan: Harvest Management Component, March 23, 2001. The intent of this plan is to 

maintain exploitation rates on natural chinook populations at or below levels that will allow them to 

rebuild as habitat conditions improve to allow greater production. Puget Sound coho salmon are 

currently managed under exploitation rate guidelines and escapement breakpoints being developed for 

the co-managers’ Comprehensive Coho Management Plan. Natural origin chum salmon in the region 

have been managed for fixed escapement goals, with different goals set for odd- and even-year 

returns. Beginning with the 2000 management year, the management objectives were revised to add a 

harvest rate ceiling to these escapement goals. Odd-year pinks are managed so that the expected 

natural spawning escapement exceeds the goals for each of the rivers in the region. Even-year pink 

salmon are managed to allow the population to continue to expand. The goal of regional winter 

steelhead management is to consistently exceed the established escapement goal. The priority for 

regional summer steelhead is to place the needs of the naturally spawning fish first. Under the 
94 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

management strategy for sea-run cutthroat, minimum fish size limits were set so that the majority of 

females (more than 50%) would be allowed to spawn at least once. Harvest under this scenario is 

allowed only where stocks are thought to be healthy and such harvest is consistent with management 

objectives. 56

HABITAT

The geology of Stillaguamish basin is a complex combination of continental and alpine glacial 

material, and marine/non-marine interglacial deposits that have been influenced by volcanism, 

faulting and erosion. The upper North Fork Stillaguamish is dominated by Darrington Phyllite which 

is a metamorphic rock type that is particularly prone to erosion (a major problem in this watershed). 

Clay, silt and sand deposits of glacial and lake origin are the main source of significant sediment 

production in the watershed. In the steeper sloped areas, these deposits are particularly prone to 

landslides, which are a significant problem for salmonids living in this drainage. Over one third of the 

Stillaguamish watershed is in the rain-on-snow zone area (1,001–2,999 feet in elevation). As a result 

of the low elevation nature of this watershed and the extensive land use modifications, ten of the 

largest eleven annual peak flows on record occurred between 1980 and 1995.57

The future condition of habitat in this basin will depend primarily on social, political and economic 

factors, which are difficult to predict. Weather conditions will also influence habitat conditions. An 

optimistic forecast would assume that the general public and stakeholder groups would fully support 

salmon recovery goals and actions, and demand political action for implementation of recovery plans. 

There is reason to hope that we will be going down the optimistic road that will eventually lead to 

improved habitat quality, but that road will be slow and have lots of obstacles to overcome before we 

get to our destination. Ten years might not be long enough to see habitat improvement, but hopefully 

habitat improvement will not take much longer. In fifty years, the hope is the habitat will be in better 

shape than it is now. 

Formal long-term habitat goals have not yet been established for the Stillaguamish Basin. The 

Stillaguamish Technical Advisory Group (STAG) published the Technical Assessment for Chinook 

Salmon Recovery in the Stillaguamish Watershed on July 12, 2000. This document contains three 

habitat recovery objectives for the Stillaguamish Watershed: 1) maintain and restore natural 

watershed processes; 2) maintain a dispersed and interconnected network of high quality habitat that 

addresses the needs of all life history stages of chinook; and 3) monitor and evaluate certain land use 

activities so that they can be adapted (where possible) to achieve specific objectives outlined in the 

document. 

Long-term habitat goals for the Snohomish Basin are currently being developed. The Initial 

Snohomish River Basin Chinook Salmon Conservation/Recovery Technical Work Plan published 

October 6, 1999, by the Snohomish Basin Salmonid Recovery Technical Committee, recommends 

five habitat management concepts and principles that form the foundation of the work plan. These 

are: 1) emphasize protection and reconnection of habitat; 2) use historical information to guide 

today’s decisions; 3) preserve and restore the natural ecosystem processes; 4) use monitoring and 

assessment to guide adaptive management; and 5) preserve options for the future. 

 

56 Kit Rawson, The Tulalip Tribes and Curt Kraemer, Washington State Department of Fish and Wildlife, September 2001.

57 Kip Killebrew, Stillaguamish Tribe; includes citations of Thomas et al. 1997, 2496 Report, Perkins and Collins, 1997, STAG, 2000, and Collins, 1997.
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 95 

The work plan also identifies nine major habitat problems in the basin with recommended actions to 

address those problems. The Technical Committee has also produced the Snohomish River Basin 

Chinook Salmon Habitat Evaluation Matrix. This report evaluated seven major habitat conditions 

within 62 sub-basins in the Snohomish Basin. Performance criteria and interim recovery goals were 

developed to establish three categories of habitat status: properly functioning, at risk, and not properly 

functioning. The Technical Committee is currently working on a similar project covering all salmonid 

species within the watershed. For chinook salmon, the habitat conditions in the majority of all subbasins was considered to be at risk or not properly functioning.58

 

58 Mike Chamblin, Washington State Department of Fish and Wildlife, September 2001.
96 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 97 

STILLAGUAMISH

Overview 

STOCK STATUS59

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

NF Stillaguamish Summer Chinook Y H H H L/M L/M H L L H 0 L M

SF Stillaguamish Chinook N H H H L L H L M H L L M

NF Stillaguamish Chum Y H H H H H H M M H M M M

SF Stillaguamish Chum Y H H H H H H M M H M M M

Stillaguamish Coho Y H H H M M H M M H L M M

Deer Creek Stillaguamish Coho N H H H L M H L M H L L M

NF Stillaguamish Pink N H H H H H H M M H M M M

SF Stillaguamish Pink N H H H H H H M M H M M M

NF Stillaguamish Hatchery Summer Steelhead Y L L L L L L L L L H H H

NF Stillaguamish Deer Creek Summer Steelhead N H H H M M H L M H 0 L M

SF Stillaguamish Hatchery Summer Steelhead Y L L M L? L? L? M M H 0 L M

SF Stillaguamish Other Summer Steelhead N L L M H H H M M H 0 L M

SF Stillaguamish Canyon Summer Steelhead N H H H M M H L M H 0 L M

Stillaguamish Natural Winter Steelhead N H H H M M H M M H L M M

Stillaguamish Hatchery Winter Steelhead Y L L L L? L? L? M M H H H H

Stillaguamish Cutthroat N H H H H H H M M H 0 L L

Stillaguamish Char N H H H M M H M M H L L M

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Stocks

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

HABITAT

The Stillaguamish River drains an area of approximately 438,365 acres and includes more than 4,618 

miles of streams and rivers. The river enters Puget Sound near the town of Stanwood, 16 miles north 

of Everett. This watershed includes more than 890 miles of anadromous stream habitat, just less than 

one-third of the total stream network. The headwaters are in the North Cascades, a topographically 

diverse area characterized by peaks and valleys carved by glacial activity. The South Fork 

Stillaguamish drainage begins at Three Fingers Peak (6,854 feet). Above the town of Silverton, the 

South Fork loses about 2,000 feet in elevation in three miles and then opens up to a valley floor. The 

river then flows 26 miles through this gradually widening valley, which is bordered by high 

mountains and ridges. Elevation drops 1,000 feet to the head of Robe Canyon, then another 600 feet 

in the eight miles to the mouth of Canyon Creek. Below Canyon Creek, the South Fork Stillaguamish 

flows an additional 12 miles northwesterly through a canyon and then over Granite Falls. The South 

Fork Stillaguamish continues an additional four miles through a narrow floodplain to its confluence 

with the North Fork. 

 

59 This table contains ratings for all the salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the 

Components of This Report section of the Introduction.
98 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

The North Fork Stillaguamish headwaters form at an elevation of about 4,550 feet. The first 16 miles 

of the North Fork Stillaguamish, including the major tributaries of Squire, Boulder, French and Deer 

creeks, flows through narrow valleys with steep gradients. Near the present-day city of Darrington, 

the North Fork Stillaguamish emerges from the higher mountains and enters a wide valley 

characterized by braided channel, back channel sloughs, and ox-bow lakes. Its confluence with the 

South Fork Stillaguamish occurs at an elevation of 52 feet. The mainstem gradually slopes downward 

as it meanders through a wide floodplain to Port Susan.60

HATCHERIES

Whitehorse Ponds 

Whitehorse Ponds are located 1.5 miles upstream of the mouth of Whitehorse Springs Creek, a 

tributary to the North Fork Stillaguamish River at river mile 28 from its confluence with the 

mainstem Stillaguamish River. The purpose of the facility is to produce winter and summer-run 

steelhead and rainbow trout for harvest. In addition, the facility works in cooperation with the 

Stillaguamish Tribe on a Stillaguamish summer chinook recovery program. The facility is closely 

linked with the WDFW Arlington Hatchery, on which it depends for incubation and initial rearing of 

steelhead and rainbow.61

Harvey Creek and Johnson Creek Hatcheries 

The Stillaguamish Tribe’s Harvey Creek Hatchery is located two miles upstream of the mouth of 

Harvey/Armstrong Creek, which is located 15.3 miles upstream of the mouth of the Stillaguamish 

mainstem. The Stillaguamish Tribe also has an acclimation pond located on Johnson Creek, which is 

a tributary of the North Fork Stillaguamish. The US Navy has a small hatchery located on Jim Creek, 

which is a tributary of the South Fork Stillaguamish. There are chinook, chum, steelhead and coho 

programs sited at these Stillaguamish Tribe hatcheries.62

Arlington Hatchery 

The Arlington Hatchery was constructed by the WPA and started operating in 1939. It is located nine 

miles east of Arlington on Highway 530. It currently rears rainbow and cutthroat trout for inland 

recreational fisheries. In addition, it supports the winter and summer steelhead programs at 

Whitehorse Ponds, providing early rearing of these fish. Arlington Hatchery’s major program is the 

hatching, rearing and planting of rainbow trout. The facility produces approximately 160,000 “legal” 

rainbow, 120,000 fingerling rainbow and 45,000 fingerling cutthroat trout. These fish are planted 

primarily in Snohomish and Island counties, but Skagit and King counties also get plants of these 8–

13 inch rainbow trout.63

 

60 Mike Chamblin, Washington State Department of Fish and Wildlife, September 2001.

61 Chuck Lavier, Washington State Department of Fish and Wildlife, September 2001.

62 Kip Killebrew, Stillaguamish Tribe, September 2001.

63 Darrell Mills, Washington State Department of Fish and Wildlife, September 2001.
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 99 

North Fork Stillaguamish Summer Chinook 

Stillaguamish Tribe and Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability Critical/At Risk Critical/At Risk Healthy 

Habitat Inadequate Inadequate Healthy 

Harvest Opportunity None Occasional Most Years 

Hatchery Program:

Purpose Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The North Fork Stillaguamish summer chinook stock derives from, and is maintained by, annual 

brood stock collection in the North Fork Stillaguamish River and adult returns to Whitehorse 

Hatchery. This program began in 1986 and is included in the Stillaguamish and Skagit Chinook 

GDU. This is an integrated conservation program with the goal of assisting with recovery of summer 

chinook salmon in the North Fork Stillaguamish River. To this end, 65 males and 65 females are 

collected for broodstock each year, and 220,000 smolts are released annually into the North Fork 

Stillaguamish River from Whitehorse Ponds. The long-term goal is to restore this population to a high 

level of viability so that it can support terminal fisheries in most years. This is a Pacific Salmon 

Treaty indicator stock. 

OPERATIONAL CONSIDERATIONS

• The program attempts to achieve a natural origin recruit escapement of 700 fish for four 

consecutive years. If achieved, the managers will assess the ability of the natural population to 

rebuild itself without hatchery supplementation. 

• Adult fish are collected for broodstock by small-mesh gill nets from the principal spawning areas 

of the North Fork of the Stillaguamish River. The proportion of natural-origin fish among the 

collected broodstock has ranged from 47.6% (1998) to 71.9% (1995) during the years 1993–98. 

• Adult fish are spawned at the Harvey Creek Hatchery (HCH) in a five-by-five modified matrix. 

• Fertilized eggs are incubated and hatched at the HCH, with initial rearing at Harvey Creek. 

• Early rearing densities of juveniles at HCH exceed fish health guidelines. 

• Pre-smolt juveniles are transferred to Whitehorse Ponds (WP) for tagging, acclimation and final 

rearing prior to release into the North Fork Stillaguamish River. 

• Summer chinook pre-smolts are on reuse water at WP from ponds rearing steelhead. This is 

particularly a problem in low-flow, drought years. 

• Summer chinook fingerlings at WP are transferred to ponds previously occupied by rainbow 

trout, but the gravel bottom of the pond precludes cleaning, drying, or disinfecting between 

transfers. 
100 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is consistent with short-term and long-term goals. The program appears to be reducing 

the risk of demographic extinction of summer chinook salmon in the North Fork Stillaguamish River. 

The demographic benefits of this program outweigh the risks. The greatest risk imposed by the 

program is the removal of natural-origin adults from their spawning areas. Recruits per spawner 

exceed 2.0 in most years, thus the program is conferring a net demographic benefit. The numbers of 

adults trapped in some years was lower than desired (11 and 44 females in 1995 and 1999, 

respectively), thus raising some concerns regarding a possible Ryman-Laikre64 effect when the 

progeny representing those brood years returned and spawn naturally in the North Fork Stillaguamish. 

B. Likelihood of attaining goals? 

The program has a high likelihood of achieving its goals, particularly if pre-spawning mortality and 

disease transmission can be controlled, and potentially reduced, at HCH. 

C. Consistent with goals for other stocks? 

The program appears to be having little effect on other species in the Stillaguamish River. 

RECOMMENDATIONS

• Improve existing facilities at Harvey Creek Hatchery and Whitehorse Ponds to increase 

likelihood of success for this conservation program. 

• Consider ways to reduce the ten percent pre-spawning mortality of adults held at HCH. 

• Develop a complete program to control pathogen transmission at HCH during adult spawning. 

• Provide additional rearing space at HCH to reduce juvenile densities. 

• Address water quality and quantity problems at WRP via program re-prioritization and/or 

additional water supply and/or plumbing redesign. Summer chinook, because of their high 

biological significance, should have top priority for water at Whitehorse. Consequently, conflicts 

for space and water between summer chinook and other stocks (e.g. steelhead, rainbow trout) 

should be resolved. This could include a dedicated final rearing and acclimation pond for summer 

chinook at Whitehorse that mimics natural rearing characteristics. 

• Increase security measures at HCH and WP, including improved predator control. These issues 

are particularly important because of the high biological significance of the North Fork 

Stillaguamish summer chinook stock. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

• Monitor juvenile growth, distribution, post-release survival, and the length-frequency/age-class 

distributions of hatchery- and natural-origin fish constituting adult recruits. 

COMMENTS

• The “critical” to “at risk” viability of this stock is related to poor habitat conditions associated 

with landslides, siltation and flooding. 

 

64 Ryman, N. and L. Laikre. 1991. Effects of supportive breeding on the genetically effective population size. Conservation Biology 5: 325-3329.
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 101 

• This is a valuable program that has the potential to provide very important long-term conservation 

benefits. 

• The five-by-five modified factorial mating design is appropriate, because this method has the 

indirect effect of maximizing the genetic effective number of breeders for a given number of male 

and female spawners. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG but notes that: 

• Additional funding will be required to improve the existing facilities at Harvey Creek Hatchery 

and Whitehorse Rearing ponds. 

• Number of fish released should be carefully reviewed to assure the objectives of the program are 

achieved. 

The Stillaguamish Tribe generally agrees with the recommendations of the HSRG (the Tribe’s full 

comments are appended to this document) and has taken the following steps: 

• Beginning in 2002, all adult broodstock will be inoculated to help reduce pre-spawning 

mortalities. 

• During 2002, grant proposals will be submitted to both the BIA (cyclical maintenance and 

rehabilitation) and NWIFC (hatchery reform) to make significant improvements to the existing 

spawning shed location and reduce disease transmission risks. 

• Funding has been secured through the HSRG hatchery reform grant process to expand early 

rearing capacity at the Stillaguamish Tribe’s Harvey Creek Hatchery. Additional early rearing 

capacity should be online by the fall of 2002. 

• The co-managers are working diligently towards acquiring additional first pass water and 

improved plumbing for summer chinook reared at the WDFW Whitehorse Hatchery, with the 

goal of having additional water available by the spring of 2003. 

• The rearing ponds at both hatcheries have had recent upgrades to their predator control 

equipment. The WDFW Whitehorse rearing pond will have an electronic counter installed to 

accurately enumerate releases and losses of summer chinook as the fish leave the pond. Should 

predator losses continue to be significant, additional measures will be taken to further reduce 

predator access to the acclimation pond. 

• The Stillaguamish Technical Advisory Group and Stillaguamish Implementation and Review 

Group are developing specific habitat improvement objectives and habitat restoration projects 

needed to recover natural chinook productivity throughout the Stillaguamish watershed. 

• The Stillaguamish Tribe and WDFW are implementing monitoring and evaluation programs that 

include coded wire tagging, morphometric analysis, smolt trap outmigration characterizations, 

extensive spawning ground surveys and genetic analysis. 
102 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

North Fork Stillaguamish Chum 

Stillaguamish Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability Healthy Healthy Healthy 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Most Years Most Years Most Years 

Hatchery Program:

Purpose Harvest 

Type Integrated 

PROGRAM DESCRIPTION

The Stillaguamish North Fork chum stock (hatchery run) derives from brood stock collected 

primarily from Squire and Ashton creeks on the North Fork Stillaguamish, with some introductions 

from Jim Creek on the South Fork Stillaguamish. This program began in 1979. Throughout the 1980s, 

there were intermittent additions of wild-origin fish. By 1987, this hatchery program was selfsustaining. Currently, this stock is maintained by adults returning annually to Harvey Creek Hatchery, 

and by naturally spawning broodstock, every three to five years. This stock belongs to the North 

Puget Sound Fall Chum GDU. There are eleven other chum stocks in this GDU. The objective of the 

program is to provide fish for harvest while minimizing the genetic divergence of the hatchery stock 

from that of the naturally spawning stock. Additional hatchery program objectives identified include: 

1) Increase harvest opportunity using a native derived stock; 2) dilute the harvest impact of preterminal fisheries on natural Stillaguamish River spawners; 3) provide a stable source of eggs and fry 

for reseeding under-used tributary habitat. To these ends, 650,000 fed fry (500,000 at Harvey Creek; 

25,000 at Eagle Creek; 50,000 at Maxwelton Creek; 50,000 at Church Creek) are released into the 

mainstem and North Fork Stillaguamish. All eggs are collected and eyed at Harvey Creek. Eggs are 

hatched and the hatch reared at Harvey, Eagle, Maxwelton and Church creeks. 

OPERATIONAL CONSIDERATIONS

• The program is designed to collect natural broodstock every three to five years, but this has not 

been accomplished since the inception of the program. 

• The program has been limited by high rearing densities and water quality problems contributing 

to cold water disease, and environmental and bacterial gill disease.

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The harvest benefit from this program appears to be minimal, with the program contributing less than 

two percent of the overall harvest for the Stillaguamish sub-region. There was no apparent 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 103 

contribution of this program toward diluting pre-terminal harvest of the Stillaguamish natural origin 

chum. There is also a potential genetic risk to North and South Fork Stillaguamish chum salmon 

populations, considering the manner in which broodstock is collected for supplementation of natural 

stock (no yearly infusion of genes from naturally spawning stock). 

B. Likelihood of attaining goals? 

Given the current healthy status of the natural chum runs and the relatively small size of this program, 

the likelihood of achieving a significant harvest benefit is low. The likelihood of contributing to 

dilution of pre-terminal harvest, given current harvest management approaches, also appears low. 

C. Consistent with goals for other stocks? 

No negative effects were noted on goals for other natural stocks in the basin. There is a concern that, 

because of facility limitations, there is a significant risk of pathogen transmission between stocks of 

fish on-site. There is also a concern about using the Stillaguamish stock for supplementation of 

Maxwelton Creek on Whidbey Island. No information was provided about stock status or goals in this 

area. This program may well provide some benefits to artificial and natural coho and steelhead 

populations as a food source. 

RECOMMENDATIONS

• Suspend this program because of minimal harvest benefits and healthy natural stocks. 

• Develop a plan to reinstate the program should the natural stock status change for the worse. 

• Modify several operational procedures in the event the program is restarted: 

o Change the approach to maintaining integration with the natural chum stock to 

incorporate naturally spawning broodstock each year. 

o Collect stocks used for supplementation from either the North or South Fork, 

depending on the location of the tributary planned for supplementation. 

o Develop facilities and procedures to reduce the risk of pathogen transmission 

between stocks of fish on-site. 

o Improve facilities to reduce early rearing densities. 

• Review stock status and goals for the recipient watershed prior to continuing the use of 

Stillaguamish stock outside the Stillaguamish watershed.

COMMENTS

• In recent years, the natural chum stocks have been at or above escapement goals, with harvest 

ranging from 20,000–100,000 fish annually. 

• WDFW and the Tribes have communicated their decision to modify the North Fork Stillaguamish 

chum program in a manner consistent with the above recommendations. The program will be 

converted from an integrated harvest to an educational program. The details of this change will be 

provided in the Managers Response. 

MANAGERS RESPONSE

The Tribes and WDFW have agreed with the HSRG that the North Fork Stillaguamish chum program 

as outlined in October is not meeting its goals as an integrated harvest program and we have taken the 

following steps: 

• Program size reduced to 200,000 fry and goal changed to an integrated education program. 
104 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

• HSRG recommendations for broodstock collection and reduced rearing densities have been 

incorporated into the new program. 

• During 2002, grant proposals will be submitted to both the BIA (cyclical maintenance and 

rehabilitation) and NWIFC (hatchery reform) to make significant improvements to the existing 

spawning shed location and reduce disease transmission risks. 

• The co-managers will again evaluate the appropriateness of using Stillaguamish chum for the 

Maxwelton supplementation program and discontinue the program if the stock is not appropriate. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 105 

South Fork Stillaguamish Chum 

Stillaguamish Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability Healthy Healthy Healthy 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Most Years Most Years Most Years 

Hatchery Program:

Purpose Harvest and Education 

Type Integrated 

PROGRAM DESCRIPTION

The Stillaguamish South Fork chum stock (wild run) derives from brood stock captured in Jim and 

Siberia creeks in the South Fork of the Stillaguamish River. This program began in 1984 and is 

maintained by adult brood stock, primarily from Jim Creek Hatchery, with periodic introductions 

from the Stillaguamish Hatchery chum stock. This stock belongs to the North Puget Sound Fall Chum 

GDU. There are eleven other chum salmon stocks in this GDU. The objective of the program is to 

provide fish for harvest while minimizing the genetic divergence of the hatchery stock from that of 

the naturally spawning stock. To this end, 25,000 unfed fry are released from the Indian Ridge egg 

box. Eggs are collected and eyed at the Harvey Creek Hatchery. 

OPERATIONAL CONSIDERATIONS

None. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The primary benefit of this program appears to be its educational value, given the healthy status of the 

stock.

B. Likelihood of attaining goals? 

See comments in A, above, relating to program benefits. 

C. Consistent with goals for other stocks? 

In general, the program appears to be too small to have any adverse impacts, but many of the 

concerns noted for the North Fork program also apply, including stock choice and risk of pathogen 

transmission between stocks of fish at Harvey Creek Hatchery. 
106 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

RECOMMENDATIONS

• Evaluate this program principally as an education program. 

COMMENTS

• In recent years the natural chum stocks have been at or above escapement goals, with harvest 

ranging from 20,000–100,000 fish annually. 

• WDFW and the Tribe have communicated their decision to modify this program to address the 

concerns in Benefits and Risks, Part C, above. 

MANAGERS RESPONSE

The Stillaguamish Tribe generally agrees with the recommendations of the HSRG and has taken the 

following steps: 

• We will return to broodstocking 100% of the chum needed for the program from Jim and Siberia 

creeks, which run immediately adjacent to the Indian Ridge facility and are tributaries of the 

South Fork Stillaguamish. 

• The eggs will be incubated at the Harvey Creek hatchery and then returned to the facility egg box 

for hatching and release. 

• During 2002, grant proposals will be submitted to both the BIA (cyclical maintenance and 

rehabilitation) and NWIFC (hatchery reform) to make significant improvements to the existing 

spawning shed location and reduce disease transmission risks. 

• Funding has been secured through the hatchery reform grant process to expand early rearing 

capacity at the Stillaguamish Tribe’s Harvey Creek Hatchery. Additional early rearing capacity 

should be on line by the fall of 2002. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 107 

Stillaguamish Coho 

Stillaguamish Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability At Risk At Risk Healthy 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Occasional Most Years Most Years 

Hatchery Program:

Purpose Harvest and Conservation 

Type Integrated 

PROGRAM DESCRIPTION

The Stillaguamish coho stock derives from hatchery and wild fish returning to Harvey and Jim 

creeks. This program began in 1986 and is maintained by adult returns to Harvey Creek Hatchery and 

Jim Creek. The Stillaguamish coho stock belongs to the Puget Sound/Strait of Georgia ESU. The 

objectives of the program are to provide fish for harvest and to aid in the recovery of the natural 

stock, while minimizing the genetic divergence of the hatchery stock from that of its naturally 

spawning counterparts. Eggs for both programs are collected, incubated, hatched and early-reared at 

Harvey Creek Hatchery. 25,000 yearlings are released from Johnson Creek Pond into the North Fork 

Stillaguamish or from Harvey Creek Hatchery into the mainstem. 20,000 yearlings are released from 

Jim Creek Hatchery into the South Fork Stillaguamish. This stock has been suggested as a candidate 

for use as an indicator stock for the Stillaguamish River. 

OPERATIONAL CONSIDERATIONS

• Current broodstock collection methods involve mixing gametes from multiple stocks. 

• The stock is tagged and marked. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

Conservation need and benefits are questionable under present operating conditions. 

B. Likelihood of attaining goals? 

Likelihood of achieving benefits in future could be increased with different broodstock selection 

methods, if the conservation need increased. The program is likely to meet modest harvest 

expectations. 

C. Consistent with goals for other stocks? 

The program appears to be consistent with goals for other stocks. 
108 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

RECOMMENDATIONS

• Put the program on “standby” status, with a plan for how and when to restart if a conservation 

need is more clearly indicated. 

• If the program is continued, increase the number of smolts released and introduce an average of 

10% naturally spawning fish into the hatchery broodstock each year for on-station releases. Use a 

single source for broodstock and do not mix broodstock from multiple sub-stocks or drainages 

within the drainage. 

• Evaluate whether an annual trapping and tagging operation on a naturally spawning stock would 

be less costly and more effective. There is some question about the efficiency of using this 

yearling smolt coho program as an indicator stock. 

• Address long-term habitat improvement issues. The hatchery program will be successful only if 

the post-release environment is able to support the population. 

COMMENTS

• The HSRG’s preference is for the program to be placed on standby because the program is too 

small to provide a significant conservation or harvest benefit. 

• WDFW and the Tribe have indicated that they will pursue a four-year program to assess the 

accuracy of using a naturally spawning stock as an indicator stock. However, this approach is not 

consistent with the above recommendation to trap and mark naturally-produced juveniles. 

MANAGERS RESPONSE

Based on the recommendations of the HSRG, the Stillaguamish Tribe has taken the following steps to 

modify this program: 

• Program goal has been modified from integrated recovery program to integrated harvest/recovery. 

• HSRG recommendations regarding the size of the program, spawning protocols and broodstock 

source have been incorporated. 

• Release location will be consistent with supporting sustainable fisheries. 

• Program fish would be more representative of naturally spawning Stillaguamish coho than the 

current multi-generational hatchery stock. 

• Program fish would be available to provide broodstock for reseeding under utilized or newly 

opened habitat. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 109 

North Fork Stillaguamish Hatchery Summer Steelhead 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability65 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The South Fork Stillaguamish hatchery summer steelhead program derives from Skamania Hatchery 

(lower Columbia River) fish transplants. This program began in 1959 and has been maintained for the 

past 20 years from adult returns to Reiter Ponds (Skykomish drainage). The objective of this program 

is to provide for harvest, while avoiding adverse interactions with other local stocks. To this end, 

70,000 yearlings are released from Whitehorse Ponds into the North Fork of the Stillaguamish River. 

Eggs are collected and eyed at Reiter Pond on the Skykomish River. Eggs are hatched and early 

reared at Arlington Hatchery.

OPERATIONAL CONSIDERATIONS

• Releases are marked. 

• Program requires inter-facility transfers of eggs and fish. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The Program is operated in a manner consistent with goals. 

B. Likelihood of attaining goals? 

Uncertain, no data on harvest provided. 

C. Consistent with goals for other stocks? 

There are potential genetic interactions (outbreeding depression), predation, and competition with 

other steelhead stocks, particularly naturally spawning stocks. There are also disease risks, due to the 

rearing environment. 

 

65 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
110 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of “wild 

steelhead management zones” where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Focus on water quality and quantity, improving smolt quality, considering aspects of 

environmental enhancement in rearing units. 

• Increase water flows at the Whitehorse Ponds. 

• Revise spawning procedures to include single-family mating or five-by-five matrix spawning. 

• Release hatchery yearling steelhead smolts between May 1 and May 15, at a target size of six to 

the pound, and at a condition factor of less than 1.0.

COMMENTS

• Data concerning harvest benefits are lacking. WDFW values the fishing opportunity created by 

this program. 

MANAGERS RESPONSE

WDFW generally supports the recommendations of the HSRG but notes that: 

• Implementing a regional system of wild steelhead management zones has a number of 

implications that will require discussion with the affected tribes and the Fish and Wildlife 

Commission. 

• Proposed spawning protocol may be difficult to implement because sperm is collected for 

virology tests. 

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 

• The Tulalip Tribes will want to review the concept of wild steelhead management zones and the 

selection of particular zones before this concept is implemented. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 111 

South Fork Stillaguamish Hatchery Summer Steelhead 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Medium 

Population Viability66 Low? Low? Low? 

Habitat Limiting Limiting Healthy 

Harvest Opportunity None Occasional Most Years 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION 

The South Fork Stillaguamish hatchery summer steelhead program derives from Skamania Hatchery 

(lower Columbia River) fish transplants. This program began in 1959 and has been maintained for the 

past 20 years from adult returns to Reiter Ponds (Skykomish drainage). The objective of this program 

is to provide for harvest while avoiding any adverse interactions with other local stocks. To this end, 

20-30,000 yearlings are out-planted from Reiter Ponds into the South Fork above Granite Falls, and 

10,000 are outplanted into Canyon Creek. Eggs are collected and eyed at Reiter Pond on the 

Skykomish River. Eggs are hatched and early-reared at Arlington Hatchery. 

OPERATIONAL CONSIDERATIONS

• Releases are marked. 

• The program requires inter-facility transfers of eggs and fish. 

• The program uses an HSRG-approved steelhead rearing and release process (hatchery yearling 

steelhead smolts are released between May 1 and May 15, at a target size of six to the pound, and 

have a condition factor of less than 1.0).

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is operated in a manner consistent with goals. 

B. Likelihood of attaining goals? 

Uncertain, no data on harvest provided. 

 

66 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
112 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

C. Consistent with goals for other stocks? 

There are potential genetic interactions (outbreeding depression), predation, and competition with 

other steelhead stocks, particularly naturally spawning stocks. There are also disease risks, due to the 

rearing environment. There are particular concerns regarding the outplanting of hatchery fish in 

Canyon Creek. 

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of “wild 

steelhead management zones” where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Focus on water quality and quantity, improving smolt quality, considering aspects of 

environmental enhancement in rearing units. 

• Increase water flows at the Whitehorse Ponds. 

• Revise spawning procedures to include single-family mating or five-by-five matrix spawning. 

• Consider alternative strategy focused on colonization of the upper watershed. 

COMMENTS

• Data concerning harvest benefits are lacking. WDFW values the fishing opportunity created by 

this program. 

MANAGERS RESPONSE

WDFW generally supports the recommendations of the HSRG but notes that: 

• Implementing a regional system of wild steelhead management zones has a number of 

implications that will require discussion with the affected tribes and the Fish and Wildlife 

Commission. 

• Additional funds will be required to increase water flows at Whitehorse Hatchery. 

• Proposed spawning protocol may be difficult to implement because sperm is collected for 

virology tests. 

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 113 

• The Tulalip Tribes will want to review the concept of wild steelhead management zones and the 

selection of particular zones before this concept is implemented. 
114 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Stillaguamish Hatchery Winter Steelhead 

Washington Department of Fish and Wildlife and Stillaguamish Tribe 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability67 Low? Low? Low? 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Stillaguamish hatchery winter steelhead program derives from transplants from South Tacoma 

Hatchery (Chambers Creek stock) in the 1960s. Since the 1980s, this stock has been maintained from 

returnees to Whitehorse Pond on the Stillaguamish River and supplemented with primarily Tokul 

Creek Hatchery (Snohomish drainage) or Reiter Pond winter steelhead (Skykomish drainage). The 

objective of this program is to provide for harvest, while avoiding any adverse interactions with other 

local stocks. To this end, eggs are collected and eyed at Whitehorse Ponds, and then hatched and 

early reared at Arlington Hatchery (for Whitehorse Ponds release) and Harvey Creek Hatchery (for 

Johnson Creek release). 130,000 yearlings (115,000 at Whitehorse Ponds, 15,000 at Johnson Creek 

Hatchery) are released into the North Fork Stillaguamish. Releases of up to 25,000 Snohomish River 

winter steelhead stock from Reiter Pond are outplanted into the Stillaguamish (Pilchuck Creek and 

Canyon Creek). 15,000 yearlings are released from the Masonic Park acclimation pond into the South 

Fork Stillaguamish. 

OPERATIONAL CONSIDERATIONS

• All releases are marked. 

• The program requires inter-facility transfers of eggs and fish. 

• The program uses an HSRG-approved steelhead rearing and release process (hatchery yearling 

steelhead smolts are released between May 1 and May 15, at a target size of six to the pound, and 

have a condition factor of less than 1.0).

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is operated in a manner consistent with goals. 

 

67 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 115 

B. Likelihood of attaining goals? 

This program provides one of a few reliable harvest opportunities for tribal and sport fishers in the 

region. Harvest catch is low (<0.4%) relative to the size of the program, even though opportunity for 

harvest is high (60–70% of the winter run steelhead harvest). 

C. Consistent with goals for other stocks? 

There are potential genetic interactions (outbreeding depression), predation, and competition with 

other steelhead stocks, particularly naturally spawning stocks. There are also disease risks, due to the 

rearing environment. 

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of “wild 

steelhead management zones” where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Two potential wild steelhead management zones are above Granite Falls and Deer Creek. 

• Focus on water quality and quantity, improving smolt quality, considering aspects of 

environmental enhancement in rearing units. 

• Increase water flows at the Whitehorse Ponds. 

• Revise spawning procedures to include single-family mating or five-by-five matrix spawning. 

• Resize this program to reduce fish densities during early rearing until rearing conditions at the 

hatchery can be improved. 

• Focus on smolt quality and eliminating disease problems to improve survival and better achieve 

harvest goals. 

COMMENTS

None. 

MANAGERS RESPONSE

WDFW generally supports the recommendations of the HSRG but notes that: 
116 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

• Implementing a regional system of wild steelhead management zones has a number of 

implications that will require discussion with the affected tribes and the Fish and Wildlife 

Commission. 

• Additional funds will be required to increase water flows at Whitehorse Hatchery. 

• Implementing the proposed spawning protocol may be difficult because sperm is collected for 

virology tests. 

• The portion of this winter run steelhead program conducted by the Stillaguamish Tribe has been 

officially terminated. 

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 

• The Tulalip Tribes will want to review the concept of wild steelhead management zones and the 

selection of particular zones before this concept is implemented. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 117 

SNOHOMISH

Overview 

STOCK STATUS68

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Snohomish/Snoqalmie Chinook N H H H M M H M M H L L M

Snohomish/Skykomish Summer Chinook Y H H H L/M L/M M M M M L L M

Snohomish Coho N H H H M H H M M M M M M

Snohomish/Skykomish Hatchery Coho Y H H H M H H M M M M M M

Snohomish/SF Skykomish Coho N M M M H H H M M H M M M

Snohomish/Snoqalmie Coho N H H H H H H H H H M M M

Snohomish Odd Pink N H H H H H H H H H M M M

Snohomish Even Pink N H H H H H H M M H 0 L M

Snohomish/Skykomish Fall Chum N H H H H H H H H H M M M

Snohomish/Snoqualmie Fall Chum N H? H H H? H H M? M H M M M

Snohomish/Wallace Fall Chum N H H H H H H H H H M M M

Snohomish/Skykomish Winter Steelhead N H H H H H H M M H L M M

Snohomish/Pilchuck Winter Steelhead N H H H H H H M M H L M M

Snohomish/Snoqualmie Winter Steelhead N H H H H H H M M H L M M

Snohomish Hatchery Winter Steelhead Y L L L L? L? L? M M H H H H

Snohomish/Tolt Summer Steelhead N H H H H H H M M H 0 L L

Snohomish/NF Skykomish Summer Steelhead N H H H M M H M M H 0 L L

Snohomish/SF Skykomish Summer Steelhead N M M M H H H M M H 0 L L

Snohomish Hatchery Summer Steelhead Y L L L L? L? L? M M H H H H

Snohomish Cutthroat N H H H H H H M H H M M M

Snohomish Char N H H H H H H M M H M M M

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Stocks

HABITAT

The Snohomish River basin drains a 1,780 square mile area and is the second largest watershed 

draining into Puget Sound. The basin has three distinct physiographic regions: the Skykomish River 

Basin, the Snoqualmie River Basin and the Snohomish River Valley. Over 1,730 tributary rivers and 

streams have been identified in the basin, providing over 2,718 linear miles of drainage. 

The South Fork Skykomish River originates near the summit of Stevens Pass and flows west and 

northwest some 32 miles through mountainous terrain, to its confluence with the North Fork 

Skykomish near the town of Index. The Beckler, Foss and Miller Rivers, Money and Index creeks are 

some of the larger tributaries of the South Fork. The mainstem Skykomish River continues generally 

west for about 30 miles, to its junction with the Snoqualmie River. From the Skykomish Forks 

 

68 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.
118 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

downstream for about six miles, the channel is confined, with a relatively steep gradient. From the 

vicinity of Gold Bar downstream to Sultan, the channel widens and the gradient decreases, forming 

numerous gravel bars and side channels in this braided reach. Major tributaries of this section include 

the Wallace and Sultan rivers. Downstream from Sultan, the river meanders some 14 miles through a 

wide floodplain with a moderate to gentle gradient, where it meets the Snoqualmie River to form the 

Snohomish River. Woods, Elwell and McCoy creeks are the larger tributaries in this section. 

The Snoqualmie River originates in the high cascades and consists of three forks; the South, Middle 

and North Forks. Approximately five miles above Snoqualmie Falls, the combined North and Middle 

Fork have their confluence with the South Fork. From Snoqualmie Falls, plunging 268 feet, the 

Snoqualmie River travels 36 miles northwest through a broad and flat valley to the confluence of the 

Skykomish River. The Tolt and Raging rivers, Tokul, Patterson, Griffin, Harris, and Cherry creeks 

are main tributaries to the Snoqualmie River. 

The mainstem Snohomish River meanders 20.5 miles through a broad valley floor, where it enters 

Puget Sound at Everett. The Pilchuck River is the largest tributary, entering the river at the town of 

Snohomish. Three major sloughs—Ebey, Union and Steamboat—diverge from the main Snohomish 

channel in the lower eight miles. The Snohomish River is tidally influenced upstream to about river 

mile 14.69

HATCHERIES

Wallace River Hatchery 

The Wallace River Hatchery is located between the confluence of May Creek and the Wallace River, 

near the town of Startup. The hatchery was originally known as the Skykomish Hatchery and dates 

back to 1907. It is the only hatchery facility rearing chinook within the Snohomish River Basin. The 

Wallace River Hatchery rears both summer chinook, for local release, and fall chinook in support of 

the Tumwater Falls program (see South Sound, Deschutes River sub-region). Both of these programs 

are harvest-oriented. During the 1970s, three chum salmon spawning channels were installed at this 

hatchery. Sediment and disease issues eventually caused the channels to fail as spawning and initialrearing habitat. They were asphalted and converted into rearing ponds, which remain in use today. 

The 1980s saw the construction of a bank of concrete raceways, a bank of standard ponds, and an 

adult trapping facility on the Wallace River side of the hatchery. The hatchery incubates and rears 

Reiter Ponds summer steelhead production from the time the eggs are eyed until the fish reach a size 

of 70 fish per pound, at which time they are transferred back to Reiter Ponds for final rearing. In 

addition, Wallace River Hatchery receives winter steelhead fingerlings from Tokul Creek Hatchery, 

at 150 fish per pound that are eventually destined for Reiter Ponds. These fish are transferred to 

Reiter Ponds at the same time as summer steelhead, usually in October when the fish are 

approximately 70 fish per pound. 

Reiter Ponds Hatchery 

The Reiter Ponds Hatchery is located on the main stem of the Skykomish River at river mile 46, just 

east of the town of Gold Bar. Original construction took place in 1973–74 and included the rearing 

 

69 Mike Chamblin, Washington State Department of Fish and Wildlife, September 2001.
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 119 

ponds, migrant fish traps and residence. Additional construction in 1988 included an incubation 

building, adult holding pond and fish ladder. The purpose of the facility is to provide winter- and 

summer-run steelhead for harvest. The operation of the hatchery is closely linked to WDFW’s 

Wallace River and Tokul Creek hatcheries, because Reiter Ponds is limited in its ability to incubate 

eggs, having only eight shallow troughs and no intermediate starting ponds. Typically, eggs are eyed 

at Reiter Ponds and then shipped to either Tokul Creek Hatchery (if winter-run eggs are taken) or 

Wallace River Hatchery (summer-run) for final incubation and initial fry rearing. The fish then return 

to Reiter Ponds in the fall (October) for final rearing and spring release. 

Tokul Creek Hatchery 

Tokul Creek Hatchery is situated 2.5 miles east of Fall City and 2.5 miles west of the town of 

Snoqualmie. The hatchery is adjacent to Tokul Creek, a tributary of the Snoqualmie River. Tokul 

Creek enters the Snoqualmie River immediately below Snoqualmie Falls, the upper limit for 

anadromous salmonids. Tokul Creek Hatchery is a harvest-oriented facility that produces winter-run 

steelhead and various trout species for the local fisheries. The facility was constructed in the early 

1900s.70

 

70 Doug Hatfield, Washington State Department of Fish and Wildlife, September 2001.
120 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Snohomish/Skykomish Summer Chinook 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability Critical/At Risk Critical/At Risk At Risk 

Habitat Limiting Limiting Limiting 

Harvest Opportunity Occasional Occasional Most Years 

Hatchery Program:

Purpose Harvest 

Type Integrated 

PROGRAM DESCRIPTION

The Snohomish/Skykomish summer chinook stock derives from wild fish collected at Sunset Falls on 

the Skykomish River in the early 1970s. This stock is maintained by adult returns to Wallace River 

Hatchery (on the Wallace River, a tributary to the Skykomish River). The Snohomish/Skykomish 

summer chinook stock belongs to the South Puget Sound, Hood Canal, and Snohomish Summer+Fall 

GDU. This GDU is composed of multiple stocks from throughout Puget Sound and Hood Canal. This 

program’s objectives include providing for harvest, while avoiding adverse interactions with other 

stocks in the watershed. A second objective is to provide 200,000 eyed summer chinook eggs 

annually to the Tulalip summer chinook program. To this end, one million fingerlings and 250,000 

yearlings are released annually into the Wallace River. The eggs are incubated at the Wallace River 

Hatchery and the resulting progeny are reared at and released from the hatchery as fingerlings and 

yearlings. This stock is an indicator stock for Puget Sound summer chinook. 

OPERATIONAL CONSIDERATIONS

• Broodstock used is native to the Skykomish River. 

• Fingerling and yearling releases mimic the life history strategies exhibited by naturally spawning 

Skykomish summer chinook. 

• Releases are non–volitional. 

• Fingerlings are double-index tagged, consistent with the role of a US/Canada indicator stock 

(200,000 fingerlings receive a coded-wire tag and adipose clip; another 200,000 receive only a 

coded-wire tag). 

• Adults surplus to program needs are allowed to spawn naturally in the Wallace River, or used for 

other purposes. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 121 

The program is generally consistent with the goals for the stock. However, current broodstock 

management creates a risk of domestication. 

B. Likelihood of attaining goals? 

The program is meeting its goals by providing modest but important harvest in pre-terminal and 

terminal fisheries. It is useful as an indicator stock for summer chinook and is successfully providing 

eyed eggs for Tulalip Hatchery. 

C. Consistent with goals for other stocks? 

Evidence indicates that the program results in minimal interaction with Snoqualmie fall chinook, but 

straying into the Skykomish River may have an adverse effect on Bridal Veil and Sultan River 

chinook stocks.

RECOMMENDATIONS

• Improve broodstock management to ensure that the hatchery stock remains truly integrated with 

the naturally spawning stock. Introduce an average of 10% naturally spawning fish into the 

hatchery broodstock each year for on-station releases. Sunset Falls currently appears to be the 

best choice for this broodstock source. 

• Use a spawning protocol involving single pair matings or five-by-five matrix matings to 

maximize the effective population size. 

• Consider environmental enhancement to improve the adult return rate. 

• Eliminate the rearing of fall chinook for the Deschutes program in South Sound, in coordination 

with changes proposed for southern Puget Sound region (program contravenes existing policy on 

fish transfers between fish health management zones). 

• Eliminate the rearing of steelhead in river water at Wallace River Hatchery as soon as possible 

(losses, particularly with summer steelhead, are unacceptably high). 

• Consider providing ground water for incubation and early rearing at Wallace River Hatchery. 

• Upgrade rearing ponds at Wallace River Hatchery to permit volitional releases. 

• Upgrade the broodstock collection facility to facilitate sorting of naturally spawning and hatchery 

adults at Wallace River Hatchery. 

• Upgrade the pollution abatement facility at Wallace River Hatchery. 

COMMENTS

• Better integration of the hatchery summer chinook population with its naturally spawning 

counterparts will mean that hatchery strays will pose a reduced risk to natural chinook 

populations in the Skykomish River (e.g., Bridal Veil and Sultan Creek populations). 

• Elimination of fall chinook and steelhead rearing at Wallace River Hatchery should allow 

available hatchery facilities and staff to be used more effectively on remaining programs, or may 

permit other needed programs to be conducted at the hatchery. 

• Upgrading facilities at the hatchery will provide for future flexibility. 

• If and when the Tulalip program is switched to summer chinook, this program will provide 1.5 

million eggs annually for that program. 

MANAGERS RESPONSE

WDFW generally supports the recommendations and has taken the following actions: 
122 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

• Reduced by 40% the rearing of fall chinook for the Deschutes program in South Sound. 

• Prioritized upgrading the pollution abatement facility. 

WDFW notes that: 

• Identification of the number of naturally origin spawners incorporated in the hatchery broodstock 

is a complex topic that will require additional analysis and discussion; 

• Additional funding will be required to upgrade the facilities as recommended. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 123 

Snohomish/Skykomish Hatchery Coho 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance High High High 

Population Viability71 Medium High High 

Habitat Limiting Limiting Limiting 

Harvest Opportunity Most Years Most Years Most Years 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Snohomish/Skykomish hatchery coho program derives from wild fish trapped in the lower 

Snohomish basin, with supplementation from the Wallace River Hatchery (on the Wallace River, a 

tributary to the Skykomish River). The stock has been maintained from returnees to the Wallace 

River Hatchery on the Skykomish River since the early 1900s. The goal of this program is segregated 

harvest augmentation. A secondary goal is to provide a tagged index stock for assessment of regional 

contribution to distant (Canadian) fisheries. To this end, 4.3 million eggs are collected. Smolts 

sufficient to sustain broodstock at Wallace River Hatchery are released. Harvest augmentation at 

Tulalip Bay and at South Sound is supported. Tulalip Tribal Hatchery receives 1.3 million eggs 

annually for fishery augmentation program at Tulalip Bay. Marblemount Hatchery receives 1.7 

million annually for South Sound harvest augmentation. The South Sound Net Pens receive 400,000 

yearling coho annually for harvest augmentation. Other small programs are also supported, in 

addition to 150,000 smolt releases at Wallace. 

OPERATIONAL CONSIDERATIONS

• The surplus hatchery production is provided for harvest in Tulalip Bay and in the South Sound, in 

isolation from harvest of naturally spawning stock. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals?

This program is consistent with goals and objectives. The conservation risks posed by this program to 

naturally-spawning salmon in the region are relatively small. Evidence from spawning ground 

surveys in which marked fish were counted and from surveys in which scales were collected 

(allowing discernment from pattern analysis of hatchery-origin fish) suggests that straying outside the 

 

71 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
124 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Wallace River is relatively small and that inter-crossing with naturally spawning-spawning coho is 

minimal. In addition, the size of the program is small relative to the size of the stock.

B. Likelihood of attaining goals?

Historical success suggests strong likelihood of meeting objectives.

C. Consistent with goals for other stocks? 

Transfers of this stock to South Sound programs are not consistent with conservation goals, as 

Skykomish coho are not locally adapted to the South Sound. 

RECOMMENDATIONS

• Maintain a large effective population size in the Skykomish coho broodstock. The rationale for 

this recommendation includes: 1) the sustained protection of the productivity of the Skykomish 

coho program; and 2) amelioration of any risk posed by inter-crossing of program coho with 

naturally spawning coho in the basin. Gametes taken for support of the broodstock, for release at 

Wallace, should be a representative sample of the entire return and include equal representation 

of 500 or more spawners. 

• Consider converting this program from a segregated to an integrated program, to address 

concerns about natural spawning. 

COMMENTS

None. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 125 

Snohomish Hatchery Winter Steelhead 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability72 Low? Low? Low? 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Snohomish hatchery winter steelhead stock derives from Chambers Creek origin winter steelhead 

that came from Tokul Creek Hatchery (Snohomish drainage) and Reiter Ponds (Skykomish drainage) 

around the time of World War II. This stock has been maintained from adult returns to Tokul Creek 

Hatchery and Whitehorse Pond on the Stillaguamish River since the late 1970s. The purpose of this 

three-faceted program is to provide for harvest, while avoiding adverse interactions with other stocks 

in the watershed. To this end: 

1. 270,000 yearlings are released into the Skykomish River (80–110,000 at Reiter Ponds, 20,000 at 

Wallace River Hatchery, and the remainder at various other Skykomish River release sites). Eggs 

for this purpose are collected from adults returning to Tokul Creek Hatchery, where they are also 

incubated and the hatch early reared. Wallace River Hatchery provides intermediate and final 

rearing for the group released into Wallace River and intermediate rearing for the group released 

from Reiter Ponds. 

2. 185,000 yearlings are released into the Snohomish basin (80-90,000 from Tokul Creek Hatchery 

and the remainder from various other release sites). Eggs for this purpose are collected and 

incubated at Tokul Creek Hatchery, where the resulting progeny are reared until release. 

3. 15,000 yearlings are released into the Pilchuck River. Eggs for this purpose are collected and 

eyed at Whitehorse Ponds, hatched and early reared at Arlington Hatchery, then reared to release 

at Whitehorse Ponds. 

OPERATIONAL CONSIDERATIONS

• Released fish are marked. 

• Returning adults surplus to broodstock needs are forced to remain in the river at Tokul Creek and 

Reiter Ponds, to provide for sports fishing. 

 

72 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
126 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

• Early spawn timing of the hatchery stock minimizes genetic interaction with naturally spawning 

winter steelhead. 

• The program requires inter-facility transfers of eggs and fish. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is being operated in a manner consistent with its short- and long-term goals. It is 

providing for valuable harvest. Interbreeding of the hatchery stock with the naturally spawning stock 

is minimized by the differences in spawn timing. 

B. Likelihood of attaining goals? 

There is a strong likelihood that program goals will continue to be met, although recent trends in adult 

returns have shown an unexplained decline. 

C. Consistent with goals for other stocks? 

There is the potential for genetic interaction with naturally spawning winter steelhead, but this is 

likely to be insignificant for the reason stated in A, above.

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of “wild 

steelhead management zones” where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Manage the hatchery stock to maintain its current spawn timing. 

• Revise the spawning protocol to use single pair matings or five-by-five matings, to help ensure an 

effective-size spawning population. 

• Release hatchery yearling steelhead smolts between May 1 and May 15, at a target size of six to 

the pound, and a condition factor of less than 1.0.

• Continue to use the weir at Tokul Creek Hatchery to trap all salmonids and transport naturally 

spawning salmonids above the weir, so that these fish can take advantage of existing spawning 

habitat (an exception to the upstream transport would be naturally spawning salmonids deemed 

by the managers to pose an unacceptable risk to fish stocks held at Tokul Creek hatchery). 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 127 

• Obtain an additional one cubic foot per second of spring water at Tokul Creek Hatchery for 

incubation and early rearing. 

• Expand the Reiter Ponds facility to provide for incubation and early rearing of winter and 

summer steelhead, so that the need for rearing at Wallace River Hatchery is eliminated. 

COMMENTS

• Reasons for the decline in adult winter steelhead returns should be investigated if this decline 

continues. 

• Establishment of wild steelhead management zones should reduce the chances of ecological and 

genetic interactions with hatchery steelhead and help to ensure the availability of founding stocks 

for hatchery purposes should the need for such stocks arise. 

• Upgrade the water supply at Tokul Creek Hatchery and expand rearing capabilities at Reiter 

Ponds, for more efficient production of steelhead. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG but notes that: 

• Implementing the proposed spawning protocol may be difficult because sperm is collected for 

virology tests. 

• Additional funding will be required to upgrade the facilities as recommended. 

• Implementing a regional system of wild steelhead management zones has a number of 

implications that will require discussion with the affected tribes and the Fish and Wildlife 

Commission. 

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 

• The Tulalip Tribes will want to review the concept of wild steelhead management zones and the 

selection of particular zones before this concept is implemented. 
128 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Snohomish Hatchery Summer Steelhead 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability73 Low? Low? Low? 

Habitat Limiting Limiting Healthy 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Snohomish hatchery summer steelhead stock derives from Reiter Ponds (Skamania origin) along 

with an unknown contribution of indigenous stock. This program began in 1974. Since the 1980s, this 

stock has been maintained from adult returns to Reiter Ponds (on the Skykomish River). The purpose 

of this program is to provide for harvest, while avoiding adverse interactions with other stocks in the 

watershed. To this end, 250,000 yearlings are released annually into the Skykomish River (80–

110,000 at Reiter Ponds, the remainder at various other release sites along the Skykomish River). The 

eggs are incubated at Wallace River Hatchery, and the resulting progeny early reared there. Final 

rearing and release are at Reiter Ponds. 

OPERATIONAL CONSIDERATIONS

• Yearlings are marked prior to release. 

• Adults surplus to broodstock needs are forced to remain in the river to provide a recreational 

fishery. 

• Spawn timing of the hatchery stock overlaps that of naturally spawning summer steelhead, but the 

overlap is apparently decreasing because of current hatchery broodstock collection practices. 

• Interactions with naturally spawning summer steelhead are minimized by releasing hatchery fish 

in the mainstem, well downstream of areas in the basin typically used by naturally spawning 

summer steelhead. 

• Properly timed hatchery releases appear to be vacating the basin rapidly (within a week of 

release). 

• The program requires inter-facility transfers of eggs and fish. 

 

73 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 129 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

The program is being operated in a manner consistent with short- and long-term goals. It is providing 

a high contribution to harvest, and precautions mentioned above are being taken to minimize 

interactions with naturally spawning summer steelhead. 

B. Likelihood of attaining goals? 

There is a strong likelihood that the program will continue to meet its goals. Its contributions to 

harvest show no tendency to decline and spawn timing overlaps with naturally spawning summer 

steelhead have been substantially reduced. 

C. Consistent with goals for other stocks? 

The program appears to be operating in a manner consistent with the goals for other stocks.

RECOMMENDATIONS

• Implement System-wide Recommendations regarding establishing a regional system of “wild 

steelhead management zones” where streams are not planted with hatchery fish and are instead 

managed for native stocks. Fishing for steelhead in these zones would not be incompatible with 

this approach, but no hatchery-produced steelhead should be introduced. Such zones would 

reduce the risk of naturally spawning fish interbreeding with hatchery fish, and provide native 

stocks for future fisheries programs. 

• Select streams to represent a balance of large and small streams, productivity, etc. Hatchery 

production may need to be increased in streams selected for hatchery harvest. The HSRG 

encourages the use of locally-adapted stocks for those streams. 

• Minimize interaction with naturally spawning steelhead when implementing a segregated 

steelhead program through such tools as differential timing and a decision on benefits versus risks 

on outplanting in freshwater habitat. In addition, adult collection procedures should be designed 

to capture as many adults from the returning segregated population as possible. 

• Organize a workshop to develop this concept. 

• Include monitoring and evaluation as a basic component of the concept, for both wild steelhead 

management zones and hatchery harvest streams. 

• Maintain current broodstock collection practice, as it will help to further reduce overlaps in 

spawn timing with naturally spawning summer steelhead. 

• Revise the spawning protocol to use single pair matings or five-by-five matings, to help ensure an 

effective-size spawning population. 

• Release hatchery yearling steelhead smolts between May 1 and May 15, at a target size of six to 

the pound, and a condition factor of less than 1.0.

• Continue to use the weir at Tokul Creek Hatchery to trap all salmonids and transport naturally 

spawning salmonids above the weir, so that these fish can take advantage of existing spawning 

habitat (an exception to the upstream transport would be naturally spawning salmonids deemed 

by the managers to pose an unacceptable risk to fish stocks held at Tokul Creek hatchery). 

• Obtain an additional one cubic foot per second of spring water at Tokul Creek Hatchery for 

incubation and early rearing. 

• Expand the Reiter Ponds facility to provide for incubation and early rearing of winter and 

summer steelhead, so that the need for rearing at Wallace River Hatchery is eliminated. 

• Upgrade facilities for spawning and handling of adult steelhead. 
130 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

• Provide improved predator control at rearing ponds. 

COMMENTS

• Currently, summer steelhead broodstock collection at Reiter Ponds uses only the first 500 fish 

that return, a procedure that likely accounts for the decreasing overlap in spawn timing with that 

of naturally spawning summer steelhead. 

• Establishment of the wild steelhead management zones should reduce the chances of ecological 

and genetic interactions with hatchery steelhead and should help to ensure the availability of 

founding stocks for hatchery purposes should the need for such stocks arise. 

• Upgrading facilities at Reiter Ponds should result in more efficient production of steelhead. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG but notes that: 

• Implementing the proposed spawning protocol may be difficult because sperm is collected for 

virology tests. 

• Additional funding will be required to upgrade the facilities as recommended. 

• Implementing a regional system of wild steelhead management zones has a number of 

implications that will require discussion with the affected tribes and the Fish and Wildlife 

Commission. 

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 

• The Tulalip Tribes will want to review the concept of wild steelhead management zones and the 

selection of particular zones before this concept is implemented. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 131 

TULALIP BAY AND INDEPENDENT TRIBUTARIES

Overview 

STOCK STATUS74

ShortTermLongTermShortTermLongTermShortTermLongTermShortTermLongTerm

Tulalip Bay Hatchery Spring Chinook Y L L L L L L L L L H H H

Tulalip Bay Hatchery Summer Chinook Y L L L L L L L L L H H H

Tulalip Bay Hatchery Fall Chinook Y L L L L L L L L L H H H

Tulalip Bay hatchery Coho Y L L L L L L L L L H H H

Tulalip Bay Hatchery Chum Y L L L L L L L L L H H H

Other Cutthroat N H H H L L L L M M 0 0 L

Other Hatchery Coho Y L L L L L L L L L H H H

Harvest 

Opportunity

(0 = None, L = 

Occasional, M = Most 

years, H = Each year)

Now

Goals

Now

Goals

Now

Goals

Now

Goals

Hatchery Program?

Biological 

Significance

(L=Low, M 

=Intermediate, 

H =High)

Population 

Viability

(L=Critical, M = At Risk,

H = Healthy)

Habitat

(L = Inadequate, M = 

Limiting,

H = Healthy)

Stocks

HABITAT

No information provided. 

HATCHERIES

Tulalip Bay (Bernie Kai-Kai Gobin) Hatchery 

The Tulalip (Bernie Gobin) Salmon Hatchery is located at the north end of Tony’s Marsh on the 

Tulalip Indian Reservation, near the point where the East and West forks of Tulalip Creek meet. The 

pond is created by a large dam near Tulalip Bay and is several acres in size. It drains to Tulalip Bay 

via the lower facility pond and a series of valves, raceways, pipes and a fish ladder. The hatchery 

rears and releases spring, summer and fall chinook, as well as coho and chum to provide commercial 

and ceremonial opportunity for tribal members. The hatchery also provides commercial and 

recreational opportunity in non-Indian fisheries. 

Everett Net Pens 

Community volunteers, in cooperation with WDFW, operate a marine coho net pen in the City of 

Everett to provide recreational fishing opportunity and to keep the local community engaged in state 

and regional fishery matters.75

 

74 This table contains ratings for all salmonid stocks in the sub-region, as provided by the managers. For definitions of these ratings, see the Components 

of This Report section of the Introduction.

75 Darrell Mills, Washington State Department of Fish and Wildlife, September 2001.
132 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Tulalip Bay Hatchery Spring Chinook 

Tulalip Tribes 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability76 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Tulalip Bay hatchery spring chinook program relied on annual outplants from adult returns to the 

Marblemount Hatchery (on the Skagit River). This stock originates from the Sauk River tributary (on 

the Skagit River). This program began with brood year 1993 and was suspended in brood year 1999. 

The purpose of the program was to provide for harvest while avoiding adverse interactions with other 

local stocks. To this end. 40,000 yearlings were released at Bernie Kai-Kai Gobin Salmon Hatchery 

into Tulalip Bay. Eggs were collected and eyed at Marblemount Hatchery. Eggs were hatched, and 

the hatch reared and released at the Bernie Kai-Kai Gobin Salmon Hatchery. 

OPERATIONAL CONSIDERATIONS 

• Tulalip Bay has no habitat for natural salmon production. It is strictly a terminal area for harvest 

of hatchery produced salmon. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is consistent with the goals. 

B. Likelihood of attaining goals? 

The likelihood of attaining goals is low, since Tulalip Bay facilities currently lack rearing space and 

sufficient cold water to rear spring chinook successfully.

C. Consistent with goals for other stocks? 

This program may affect other stocks through genetic or ecological interactions. 

 

76 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 133 

RECOMMENDATIONS

• Determine whether returns from the summer chinook program are sufficient to meet the 

ceremonial purposes. If not, facilities at Tulalip Bay must be upgraded to provide appropriate 

rearing conditions for spring chinook. 

COMMENTS

None. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. 

The Tulalip Tribes support the recommendations of the HSRG. 
134 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Tulalip Bay Hatchery Summer Chinook 

Tulalip Tribes and Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability77 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Tulalip Bay hatchery summer chinook program relies on annual outplants from adult returns to 

the Wallace River Hatchery on the Skykomish River. This stock originates from the Skykomish 

River. The Tulalip Bay hatchery summer chinook program is a two generation trial to determine if 

program goals can be met by switching from fall to summer chinook and basing the program on an 

in-region stock. The summer chinook salmon program began in brood year 1998. The purpose of this 

program is to provide for harvest, while avoiding adverse interactions with other local stocks. To this 

end, 200,000 eggs are obtained from the integrated broodstock program at the Wallace River 

Hatchery. Incubation, rearing and release as sub-yearlings occur at the Bernie Kai-Kai Gobin Salmon 

Hatchery. 

OPERATIONAL CONSIDERATIONS

• Tulalip Bay has no habitat for natural salmon production. It is strictly a terminal area for harvest 

of hatchery produced salmon. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

B. Likelihood of attaining goals? 

C. Consistent with goals for other stocks? 

As this is a new program, harvest benefits and potential straying risks cannot yet be evaluated. The 

most significant potential risk is the effect of introgression of hatchery strays on the distinct and 

relatively small naturally spawning Snoqualmie fall chinook population. The opportunity for nontreaty harvest could be increased through adipose fin clip mass marking. 

 

77 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 135 

RECOMMENDATIONS

• Design studies that evaluate different approaches to manage potential straying problems, while 

proceeding with the evaluation of the summer chinook program. Such approaches might include 

(but not be limited to): reducing straying to areas other than the Skykomish, for example, by 

incubating and initial rearing of Tulalip bound fish at Wallace, and/or through the use of 

morpholine drip at Tulalip and at Skykomish to improve homing to these destinations. It is also 

possible that habitat in the Snoqualmie is unsuitable for the summer chinook life history pattern 

and/or that separation in spawning timing and location prohibits introgression with Snoqualmie 

fall chinook. Evaluation of the current program should continue, so that more information about 

the magnitude and consequences of straying can be obtained. 

• Include adipose fin clip mass marking to help this program achieve the goal of maximizing 

harvest rate and to assess straying. 

• Implement a Skykomish brood stock program consistent with the goals of the Snohomish summer 

chinook population. Introduce an average of 10% naturally spawning fish into the hatchery 

broodstock each year for on-station releases. 

COMMENTS

• The HSRG commends the managers in this region for recognizing the potential risks due to 

straying and for conducting well designed studies to evaluate them. 

MANAGERS RESPONSE

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 

• The co-managers believe that the otolith mark is the only type of mass mark suitable for assessing 

straying when the simultaneous contribution of several different hatchery stocks to natural 

spawning areas is of interest and the hatchery stocks must therefore receive a unique mark. 

• During the period of feasibility testing for the suitability of the summer chinook stock for rearing 

at Tulalip, 100,000 fish per year are receiving a coded wire tag and adipose fin clip. During this 

period, the co-managers believe the otolith mark is the only mass mark this group should receive, 

not additional adipose fin clips. 

• If and when the summer chinook become the broodstock of choice at Tulalip Hatchery, then the 

co-managers believe it would be appropriate to discuss whether to mass mark all or part of the 

production with an adipose fin clip. 

WDFW generally supports the recommendations and notes that: 

• Identification of the number of naturally origin spawners incorporated in the hatchery broodstock 

is a complex topic that will require additional analysis and discussion. 
136 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Tulalip Bay Hatchery Fall Chinook 

Tulalip Tribes and Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability78 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Tulalip Bay hatchery fall chinook program relied on annual outplants from adult returns to the 

Wallace River Hatchery on the Skykomish River. This stock originates from Green River. Currently 

this program is supported by Green River-origin fish returning to Samish Hatchery on the Samish 

River and from adults returning to Wallace River Hatchery after August 15. This program began in 

the mid-1970s.The purpose of this program is to provide for harvest while avoiding adverse 

interactions with other local stocks. To this end, the program releases 1.5 million fingerlings annually 

into Tulalip Bay. Eggs are eyed, hatched, and the hatch reared and released at Bernie Kai-Kai Gobin 

Salmon Hatchery. 

OPERATIONAL CONSIDERATIONS

• Tulalip Bay has no habitat for natural salmon production. It is strictly a terminal area for harvest 

of hatchery produced salmon. 

• Since the fall chinook program at Wallace is discontinued, this source of brood stock is no longer 

available. 

• The agreement between the co-managers states that if not enough eggs can be collected at 

Wallace, eggs will come from another Green River stock. 

• Skykomish summer chinook is also being studied as a possible alternative brood for this program. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is consistent with the goals for this stock. 

 

78 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 137 

B. Likelihood of attaining goals? 

The program has provided reliable harvest opportunities each year. The Tulalip Bay fall chinook 

program has provided valued harvest opportunities in particular by providing access to harvestable 

hatchery fish when other marine fisheries must remain closed to protect depressed natural 

populations. The opportunity for non-treaty harvest opportunity could be increased through adipose 

fin clip mass marking. 

C. Consistent with goals for other stocks? 

The primary concern with this program is the straying of fall chinook that escape fisheries in Tulalip 

Bay (and elsewhere) and migrate into the Snohomish River. Preliminary study results suggest that 

straying into the Snoqualmie River may be significant. The Snoqualmie fall chinook is a genetically 

distinct population which, although relatively stable, is of low enough abundance to warrant concern 

about the rate of contribution of hatchery fish to the spawning population. 

RECOMMENDATIONS

• Consider summer chinook as a substitute for out-of-basin-origin fall chinook as a brood stock 

choice for this program. 

• Reduce or suspend the program pending the outcome of the ongoing straying study, to avoid 

potential impacts on the Snoqualmie fall chinook population. 

• Include adipose fin clip mass marking, to help this program achieve the goal of maximizing 

harvest rate and to assess straying. 

COMMENTS

• The managers in this region are commended for recognizing the potential risks due to straying, 

for conducting well designed studies to evaluate these risks, and for developing potential 

alternative programs. 

MANAGERS RESPONSE

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 

• During the period of feasibility testing for the suitability of the summer chinook stock for rearing 

at Tulalip, 100,000 fall chinook per year are receiving a coded wire tag and adipose fin clip. 

During this period, the co-managers believe the otolith mark is the only mark this group should 

receive, not additional adipose fin clips. 

• The co-managers believe that the program should continue at current levels until such time as 

data from the summer chinook evaluation indicates otherwise. Some mixture of summers and 

falls may be used to achieve program goals in the interim, based on discussions and agreement 

between the Tulalip Tribes and WDFW. 

WDFW generally supports the recommendations and notes that: 

• The co-managers believe that the program should continue at current levels until such time as 

data from the summer chinook evaluation indicates otherwise. Some mixture of summers and 

falls may be used to achieve program goals in the interim, based on discussions and agreement 

between the Tulalip Tribes and WDFW. 
138 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Tulalip Bay Hatchery Coho 

Tulalip Tribes 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability79 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Tulalip Bay hatchery coho program relies on annual outplants from adult returns to the Wallace 

River Hatchery (on the Skykomish River). This stock originates from the Skykomish River. This 

program began in the mid 1970s. The purpose of this program is to provide for harvest while avoiding 

adverse interactions with other local stocks. To this end, the program releases one million yearling 

smolts each year into Tulalip Bay, where returning adults are harvested at the highest possible rate. 

Incubation, rearing and release occur at the Bernie Kai-Kai Gobin Salmon Hatchery. 

OPERATIONAL CONSIDERATIONS

• Tulalip Bay has no habitat for natural salmon production. It is strictly a terminal area for harvest 

of hatchery produced salmon. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is consistent with harvest goals. 

B. Likelihood of attaining goals? 

The program has provided harvest opportunities each year and is likely to continue to do so. The 

opportunity for non-treaty harvest opportunity could be increased through adipose fin clip mass 

marking. 

C. Consistent with goals for other stocks? 

 

79 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 139 

Information about straying is sparse, however even with a moderate straying rate, the contribution of 

Tulalip hatchery coho to naturally spawning escapement would be small, due to the low abundance of 

hatchery fish relative to the natural escapement. 

RECOMMENDATIONS

• Investigate the contribution of hatchery fish to natural spawning. 

• Manage the brood stock maintenance program at Wallace River Hatchery consistent with the 

goals for the Skykomish coho population. 

• Consider integrating naturally spawning fish into the brood stock. 

• Include adipose fin clip mass marking to help this program achieve the goal of maximizing 

harvest rate and to assess straying. 

• Design and implement a study to assess the contribution of hatchery fish to natural spawning 

populations. 

COMMENTS

None. 

MANAGERS RESPONSE

The Tulalip Tribes generally support the recommendations of the HSRG (the Tribes’ full comments 

are appended to this document), but have the following to add: 

• This program currently includes coded wire tags and adipose fin clips on 50,000 smolts per year 

and mass marking of an additional 250,000–300,000 smolts per year with adipose fin clips 

subject to agreement between Tulalip and WDFW. 

WDFW generally supports the recommendations and notes that: 

• Identification of the number of naturally origin spawners incorporated in the hatchery broodstock 

is a complex topic that will require additional analysis and discussion. 
140 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Tulalip Bay Hatchery Chum 

Tulalip Tribes 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability80 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Tulalip Bay hatchery chum stock derives from Quilcene Hatchery plants (Walcott Slough stock 

on Hood Canal) from 1975–78. This stock was genetically marked through selective breeding of 

individuals with particular allelic genotypes, resulting in progeny with elevated frequencies of rare 

genotypes. Genotypic marking took place over a complete generation cycle and was completed in the 

mid 1990s. This stock is maintained by genetically marked adult returns to Tulalip Hatchery on 

Tulalip Creek. The purpose of this program is to provide for harvest while avoiding adverse 

interactions with other local stocks. To this end, eggs are incubated, hatched, reared and released at 

Bernie Kai-Kai Gobin Salmon Hatchery. The annual egg take goal is eight million, with a release 

goal of 7.5 million smolts. 

OPERATIONAL CONSIDERATIONS

• Tulalip Bay has no habitat for natural salmon production. It is strictly a terminal area for harvest 

of hatchery produced salmon. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is consistent with harvest goals. 

B. Likelihood of attaining goals? 

This program meets its goals with no apparent adverse impact, although evaluation of straying into 

natural populations should continue so that this potential risk can be properly managed. 

C. Consistent with goals for other stocks? 

 

80 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 141 

The Tulalip chum population is genetically mass marked. Study results so far indicate no significant 

straying of these fish into the Stillaguamish or Snohomish basins. 

RECOMMENDATIONS

• Resume allozyme genetic analysis for this program for the purpose of monitoring contribution of 

hatchery fish to harvest (i.e. monitoring benefits), and naturally spawning populations (potential 

effects on naturally spawning stocks). 

COMMENTS

• This is an example of a successful program that meets its goals, while effectively managing 

potential risks. 

• The managers in this region are commended for recognizing the potential risks due to straying 

and for conducting well designed studies to evaluate them. 

MANAGERS RESPONSE

WDFW supports the recommendations of the HSRG. No response yet received from the Tulalip 

Tribes. 

The Tulalip Tribes support the recommendations of the HSRG. 
142 Hatchery Reform Recommendations – February 2002 Stillaguamish/Snohomish 

Other Hatchery Coho 

Washington Department of Fish and Wildlife 

Stock Goals: Current Short-Term Long-Term 

Biological Significance Low Low Low 

Population Viability81 Low Low Low 

Habitat Inadequate Inadequate Inadequate 

Harvest Opportunity Each Year Each Year Each Year 

Hatchery Program:

Purpose Harvest 

Type Segregated 

PROGRAM DESCRIPTION

The Other hatchery coho program is used for a cooperative project and relies on annual outplants 

from Wallace River Hatchery on the Skykomish River. This stock originates from the Skykomish 

River. The purpose of this program is to provide for harvest while avoiding adverse interactions with 

other local stocks. To this end, 70,000 yearlings are released into Puget Sound (50,000 at Possession 

Point; 20,000 at Port Gardner Bay, Snohomish River mouth). Eggs are collected and incubated at 

Wallace River Hatchery, where they are reared prior to final rearing and release into saltwater. 

OPERATIONAL CONSIDERATIONS

• The net pen consists of one deep net pen where coho are acclimated, reared and released. Smolts 

are transferred from the Wallace River Hatchery. 

BENEFITS AND RISKS

A. Consistent with short-term and long-term goals? 

This program is consistent with the goals. 

B. Likelihood of attaining goals? 

Continued harvest opportunity is expected from this program. There is also an education benefit. 

C. Consistent with goals for other stocks? 

Straying from net pens can pose genetic risks to adjacent native stocks. However, there is a low risk 

here because of the source of the broodstock, the relatively small release numbers, and the viability or 

health of the adjacent native population to which straying may occur. 

 

81 In the case of a segregated harvest program, population viability ratings are low, medium and high and refer to the stock’s ability to sustain itself in 

the culture environment. 
Stillaguamish/Snohomish Hatchery Reform Recommendations – February 2002 143 

RECOMMENDATIONS

• Do not significantly increase release numbers. 

COMMENTS

None. 

MANAGERS RESPONSE

WDFW supports the recommendation of the HSRG. 

Appendices Hatchery Reform Recommendations – February 2002 145 

Appendices 

Appendix A: Jamestown S’Klallam Tribe Full Comments 

Jamestown S’Klallam Tribe Responses to HSRG Report 

My comments are provided with the two stated goals of hatchery reform in 

mind: 

 Help recover and conserve naturally spawning populations 

 Support sustainable fisheries 

Comments offered here are limited to the recommendations provided for 

Dungeness Chinook, Dungeness Hatchery Coho, Dungeness Fall Pink and 

Dungeness Hatchery Winter Steelhead. 

I would like to emphasize that many of the recommendations listed by the 

HSRG are those that the co-managers have been discussing for years. There 

are also new and interesting recommendations from the HSRG that we are 

anxious to attempt and implement. However, resources necessary to 

accomplish these recommendations are scarce. We welcome the support of 

and partnership with the HSRG in our attempts to reform the hatchery 

programs in the Eastern Straits region. 

Dungeness Chinook

The HSRG recommends that studies be initiated to understand the 

freshwater life history patterns of resident chinook. By resident we assume 

the HSRG means the natural, locally adapted chinook population of the 

Dungeness River. Studies such as these were initiated in 1997 and our 

understanding of freshwater life history has improved. Much more work is 

needed. Downstream migration of chinook through the lower river must be 

sampled on a regular basis beginning as early as April and extending into 

the fall months. This can be accomplished by a passive sampling apparatus 

such as a rotary trap or by active sampling means such as seining. The river 

reach under tidal influence and the Bay must also be regularly sampled. A 
146 Hatchery Reform Recommendations – February 2002 Appendices 

long-term commitment both in terms of effort and funding is required for 

this study. 

Hatchery release strategies must be evaluated through analysis of coded 

wire tag data as it becomes available. July and August releases of zero age 

chinook do not seem to contribute well to adult returns. With increasing 

returns to the river in 2001, it may be somewhat premature to discount a 

given release strategy until available coded wire tag data has been analyzed. 

Yearling chinook releases will be evaluated with coded wire tagging studies 

beginning this year. Early indications are that this rearing strategy will 

significantly increase the release to return rates of Dungeness chinook. 

A recovery plan that moves managers beyond the captive broodstock 

program is needed. Efforts to develop this plan will begin this year. 

Plans to develop well water sources for Dungeness Hatchery are underway. 

Should adequate quantities of ground water be found, incubation and early 

rearing conditions at Dungeness Hatchery can be greatly improved. 

Related to the acquisition of adequate well water is Canyon Creek, the 

existing secondary water supply for Dungeness Hatchery. Should the 

Department of Fish and Wildlife find adequate water and funding to utilize 

ground water as an alternative to Canyon Creek, restoration efforts should 

immediately begin. The water intake dam should be removed in a manner 

that maximizes restoration opportunity both upstream and downstream of 

the structure. Stream channel and riparian restoration projects should be 

planned, funded and accomplished as soon as practical. A restored Canyon 

Creek represents a major tributary habitat in the Dungeness River system, 

particularly for natural production of coho, steelhead and cutthroat. 

Opening the Dungeness River side channel across from the Hatchery poses 

some major questions from a river hydrology and channel stability point of 

view. This issue needs the attention of experts in the field before pursuing a 

main river channel alteration. 

Dungeness Hatchery Coho

Dungeness Bay and the Dungeness River have been home to Indian salmon 

fisheries for thousands of years. S’Klallam village sites have historically been 
Appendices Hatchery Reform Recommendations – February 2002 147 

located on the shore of the Bay because of the rich diversity of fish and 

shellfish resources. The Dungeness Bay hatchery coho fishery is the last 

remaining commercial salmon fishery with Jamestown S’Klallam Tribal 

member participation. One of two goals for the hatchery reform effort is to 

find ways of supporting sustainable fisheries. This fishery is of great 

importance to the Jamestown S'Klallam Tribe and deserves the support of 

the HSRG. 

Little is know about the status of natural coho in the Dungeness River 

system. While the life history of coho in general and of the regional 

populations in particular is fairly well understood, the Dungeness River 

system has been so greatly altered that the population’s response to the 

lack of quality spawning habitat, limited summer rearing area and 

treacherous over-wintering conditions is not understood. A straightforward 

estimate of coho production from the Dungeness is needed along with an 

accurate estimate of the annual spawning population size. This can be 

accomplished through spawning surveys and with smolt tagging or marking 

and some of the same lower river sampling projects needed for studies of 

juvenile chinook migration. 

Concerns about the effect of large number of hatchery coho smolts being 

released into the system are valid. The life history studies needed for 

chinook can be adapted to monitor the migration of hatchery coho through 

the lower river, to ensure the rapid migration that is intended is occurring. 

More importantly, managers need to learn what the hatchery coho do when 

they reach the estuary. Seining operations can be an effective means of 

monitoring fish communities in the near-shore environment of Dungeness 

Bay. 

Evaluating whether the hatchery coho program could become an integrated 

program depends heavily on managers understanding more about the 

natural population, what the population size is, how productive the stock is, 

what the limits to production are in the basin, and whether adequate 

broodstock could be obtained on an annual basis. 

Efforts to assess the spawning activity of coho salmon in the basin, where 

they spawn, what the origin of spawners is, whether hatchery coho 

spawners disturb chinook and/or pink salmon redds and displace natural 

coho spawners, have begun. This is particularly true in years of high marine 

survival when coho returns number in the tens of thousands and a 
148 Hatchery Reform Recommendations – February 2002 Appendices 

significant portion of the hatchery run bypasses the Hatchery and spawns in 

the wild. 

Dungeness Fall Pink

Assessing risks of producing fall pink salmon in the hatchery is appropriate. 

However, an assessment will undoubtedly show the habitat these fish utilize 

for spawning is highly unstable. Given the preferences for spawning habitat 

these fish exhibit there is little opportunity for production improvement or 

perhaps continued existence of the stock without some degree of 

intervention and the use of salmon culture technology. Perhaps this is where 

the assessment effort would be most valuable. 

In 2001, analytical tools used in the genetic separation of summer and fall 

pink salmon broodstock improved measurably. Different marking and 

tagging methods of cultured fish are being considered for possible use with 

Dungeness fall pinks. The co-managers are continually seeking 

improvements with these and other methods and techniques. 

Dungeness Hatchery Winter Steelhead

Wild steelhead management zones may be attempted in this and other 

regions. The size of the region and the quantity of hatchery fish released 

should be evaluated carefully given the propensity of hatchery origin 

steelhead to stray. Also, management jurisdictions must be given 

consideration with this approach. One of the goals of the reform effort is to 

support sustainable fisheries. Some Tribes, whose local river system may 

become designated as a wild production system, may lose a sustainable 

winter fishery and may not have fishing access to those rivers where 

hatchery production would more often provide that sustained fishery. 

A prescribed release time and size may or not be appropriate for some 

hatchery steelhead stocks. Perhaps an analysis of available size and time of 

release data would be in order. Regional differences may exist in what is 

thought to be optimal release or migration timing. 

Much more than removing the dam, a restored Canyon Creek likely 

represents some of the best tributary spawning habitat in the basin for coho, 

steelhead and cutthroat. 
Appendices Hatchery Reform Recommendations – February 2002 149 

As with coho and chinook, were Dungeness Hatchery able to use ground 

water of sufficient quantity and quality in place of the existing surface water 

from Canyon Creek, all aspects of egg incubation and initial rearing would 

become much more manageable. 
150 Hatchery Reform Recommendations – February 2002 Appendices 

Appendix B: Nisqually Tribe Full Comments 

MEMORANDUM

TO: HSRG Members 

FROM: David A. Troutt, Natural Resources Director 

DATE: January 16, 2002 

RE: Comment on the Final Report of the HSRG 

 I have carefully reviewed the draft Final Report of the Puget Sound and Coastal 

Washington Hatchery Reform Project and would like to provide both general and specific 

comments. These comments are intended to be constructive and maintain the separation, and 

therefore integrity, of the independent scientific review and closely related policy decisions 

needed to implement the suggested changes. 

 I would like to compliment the HSRG for the excellent product represented in this draft 

report. From organization to detailing specific recommendations, this report is well thought out 

and should find use amongst a number of audiences. Considering the technical nature of the 

subject, you have done an excellent job in presenting the information in a way that will find 

broad acceptance and appeal. Given the importance of this project and the focus hatcheries have 

been subject to over the recent past, it is only through an open, honest, and scientifically credible 

review of our current practices will we make significant progress toward recovery in these 

dynamic ecosystems; and, equally important, acceptance in the turbulent court of public opinion. 

 One of our goals in this report should be to avoid crossing that somewhat gray area 

between science and policy that has lead to the criticism of efforts like this in the past (i.e. NMFS 

and its Salmon Recovery Science Review Panel). I have reviewed this document with this intent 

in mind, but you should also consider this objective in your final deliberations over this report. 

Nothing will spell the end of a scientific endeavor faster than a trespass into policy. 

On to specific comments: 

Page 6, Egg-Take Timing. The HSRG should recommend consideration of removing policy 

constraints to promote the desired outcome. 

Chambers Bay Fall chinook section – We concur with the recommendations 
Appendices Hatchery Reform Recommendations – February 2002 151 

Garrision chum – we concur with the analysis and further recommend discontinuing the 

program. 

The level of priority given to pink protection in the Nisqually should be complimented by actions 

taken outside of the basin. Mention should be given to protection strategies throughout their life 

cycle. Finally, the determination of a high priority is clearly a policy call. We need this report to 

reflect the risk of our current strategy and call for a change, not determine the ranking of this 

concern versus other concerns. 

Recommendations on McAllister – Whether we agree or not with this notion, how the property is 

dealt with and where the potential proceeds are spent is clearly a policy decision and should be 

removed from this document. 

I hope that these suggestions are found useful and productive as we move on to the next phase in 

this project. Thanks again for your hard work and commitment to this project and to the 

improved management and recovery of salmon in this region. 
152 Hatchery Reform Recommendations – February 2002 Appendices 

Appendix C: Squaxin Island Tribe Full Comments 

Squaxin Island Tribe 

Comments on HSRG Recommendations for South Puget Sound Region 

January 7, 2002 

Deschutes River Hatchery Fall Chinook 

Recommendation 1: Obtain a Memorandum of Understanding (MOU) from NMFS addressing 

potential Endangered Species Act status of Chinook spawning naturally above Tumwater Falls, 

prior to implementing the long-term plans described below. 

The Tribe is strongly supportive of this recommendation. We have continually raised this issue 

with the State, and together we have approached NMFS in the past to address this issue. To date 

we have not been successful in getting NMFS to establish a formal position on the issue. 

Hopefully with this recommendation we can renew our efforts. 

Recommendation 2: Develop long-term plans for rearing and release facilities that eliminate the 

need for out-of-basin transfers. This requires investment in new facilities in the Deschutes River 

basin. 

The Tribe is supportive of this recommendation. We are working closely with the State and their 

consultant to develop a programmatic approach and Master Plan proposal for facilities that 

would provide for all life history stage rearing within the basin. 

Recommendation 3: Implement a transitional, in-region program that restricts fish and egg 

transfers, to be consistent with the co-managers disease policy. Consider incubation at Minter 

Creek and rearing at Coulter Creek as part of this transitional program. 

The Tribe is supportive of this goal while recognizing that there are short-term obstacles to 

overcome. While there is certainly opportunity in reprogramming the Coulter Creek facility for 

this purpose now that on-station release of Chinook has been discontinued there, it is unlikely 

that this change alone can accommodate the full range of production. We are committed to 

investigating a full range of interim alternatives while moving expeditiously toward 

implementation of a new, in-basin facility. 

Recommendation 4: Develop rearing and release locations that eliminate all net pen operations in 

Percival Cove. 
Appendices Hatchery Reform Recommendations – February 2002 153 

The Tribe is supportive of this recommendation and has advocated such in the Capital Lake 

Adaptive Management Steering Committee. 

Recommendation 5: Provide adequate water and pond space to allow fish to grow and be 

released at the optimal time and size for maximum survival advantage. 

With the development of the new facility plan for the Deschutes, the Tribe has the expectation 

that it will accommodate optimal production strategies for the Chinook program. 

Recommendation 6: Develop appropriate pollution abatement or rearing strategies to meet local, 

state and federal clean water requirements. 

It is the Tribe’s expectation that the new facility will be state-of-the art in terms of treating and 

reusing available water resources. It will be our goal to exceed all relevant water quality 

standards and statutes. 

Recommendation 7: Develop a strong educational component involving local partnerships, given 

the location of the drainage within a major urban area, the state Capitol and the City of 

Tumwater. 

The Tribe is working closely with the State, the City of Tumwater, Trout Unlimited, and other 

local partners to achieve a positive climate for supporting the development of a new facility that 

maximizes the opportunity for public education. 

Squaxin / South Sound Net Pens Hatchery Coho 

Recommendation 1: Quantify the amount of straying from South Sound Net Pens to South Sound 

Coho tributaries. 

The Tribe is involved with several efforts that are aimed, at least in part, at further clarification 

of Net Pen Coho contribution to naturally spawning coho production. We have conducted adult 

trapping programs on three local coho tributaries and are continuing this effort on one of these 

where an adult trap is practical to maintain without flooding over a complete spawning season. 

All fish are marked and increasing numbers will be coded wire tagged such that spawning 

assessments will be better able to detect hatchery fish presence on the spawning grounds. The 

Tribal fishery is being intensively sampled including scale analysis to ascertain the hatchery and 

wild composition of the commercial catch. Consistent efforts at these types of studies will be 

necessary to achieve a dependable level of quantification. 

Recommendation 2: Compare the genetic and life history characteristics among South Sound, 

Skykomish and Minter Creek coho populations. 
154 Hatchery Reform Recommendations – February 2002 Appendices 

A better understanding of any existing distinctions between these coho stocks is warranted. Due 

to decades of out planting using Minter Creek fish, it is unclear if there exists any distinct South 

Sound stock that is different from Minter Creek. Coho are notoriously hard to determine distinct 

genetic characteristics between stocks. Still, life history attributes deserve more detailed 

attention and should also include performance characteristics regarding the production setting, 

especially considering the concerns expressed by the HSRG about survival rates. There also 

exists CWT data from different stocks utilized in the past, which can be analyzed to further 

evaluate contribution to the programs intended goals. 

Recommendation 3: Compare rates of straying between in-region and out-of-region incubation 

and rearing. 

Examination of these rearing strategies is currently underway. Fish reared at Minter Creek and 

transferred directly to the net pens will be compared with similar fish reared at Wallace and 

transferred directly to the pens. Additionally, we will be examining groups of different brood 

origin (Minter Creek and Skykomish) that are reared under identical strategies and conditions. 

Recommendation 4: During these evaluations, relocate incubation and rearing within the region, 

to the extent that space exists at regional facilities. 

The Squaxin Island Tribe remains concerned about the effect of this recommendation. We have 

strong reservations that this proposal does not fully consider the intent of the program. While we 

support the intent to minimize fish transfers, and the effects from straying, we believe it is 

premature to follow this recommendation without further examination of its outcomes. Our 

contention that out of basin rearing actually helps to reduce straying should be considered in 

light of additional information. Even so, it may be possible to reduce transfers and the basins 

impacted by improving infrastructure at a central location. It is our position that this 

recommendation would clearly benefit from additional discussion. We will certainly pursue this 

discussion within the co-manager Core Group proposed below, and would also like to suggest 

that the HSRG reserve some time to revisit this issue in the future when there is better 

information available upon which to base a recommendation. 

Recommendation 5: Evaluate benefits and risks of using Skykomish stock versus a within-region 

stock, probably Minter Creek hatchery. 

The Tribe and the State are currently undertaking this evaluation with a direct comparison of 

performance of these two stocks in the production setting. Brood from both facilities will be 

reared simultaneously at the same facilities throughout their rearing history and will be evaluated 

by means of CWTs recovered from adults in the fishery, at the hatcheries, and recovered on the 

spawning grounds. In addition, the management issues implicit in the broodstock discussion will 

be evaluated in a workgroup proposed as an extension of the Comprehensive Coho process. This 

Core Group will allow the co-managers to fully discuss all the management implications 
Appendices Hatchery Reform Recommendations – February 2002 155 

including in addition to the enhancement issues presented in the HSFG report, harvest 

management issues relating to terminal and pre-terminal fisheries, habitat protection, 

supplementation and restoration efforts incumbent in projects like the Goldsborough Creek dam 

removal, and ecosystem loading concerns (also identified by the HSRG). 

Recommendation 6: During these evaluations, change the broodstock source for this program to 

a local broodstock. 

The co-managers are already in partial compliance with this recommendation as the 2001 brood 

will be approximately one half Minter Creek broodstock. In order to maintain the validity of the 

comparison between broods, this regime will be maintained for a minimum of three years. There 

is also a risk in shifting to the Minter Creek stock too abruptly, that there may not be sufficient 

brood stock available to supply the additional egg take needs. Minter Creek is within an area 

that is managed for hatchery production; therefore the harvest level is higher than the Skykomish 

system, which is managed for natural production. The management regime at Skykomish 

assures a surplus of hatchery fish available at broodstock, while Minter Creek can be influenced 

by the harvest regime. Two years ago Minter Creek barely had enough escapement to supply its 

on-station needs, even with additional fishery restrictions implemented. This is a consideration 

that must be built into management plans to assure there are enough adults returning to Minter 

Creek to supply the enhancement goals. 

Recommendation 7: Develop a long-term strategy based on the results of the analyses described 

above and other relevant information. 

As noted above, the regional co-managers will convene a workgroup under the auspices of 

Comprehensive Coho to further elucidate the management issues for southern Puget Sound coho 

and develop a comprehensive approach for harvest, habitat and hatchery issues. This Core 

Group will work in an integrated fashion to address regional issues and will include the bestinformed and most involved scientists in developing the management strategy. 

Recommendation 8: Do not increase the size of the program beyond the current level of 1.8 

million fish, at least during the period when survival is depressed for many stocks possessing a 

yearling life history strategy. 

It is the intention of the co-managers to maintain the current reduced production level until we 

can develop a better evaluation of the survival depression observed in recent years. To that end, 

we are participating in the development of a trophic level model (ECOPATH) of southern Puget 

Sound in an attempt to determine whether any regime shifts have altered productivity of this 

region. We are currently pursuing funding to assess the residency period and survival of coho 

smolts in South Sound once they are released from the net pens. This information will also be 

useful in calibration of the trophic production model. 
156 Hatchery Reform Recommendations – February 2002 Appendices 

Appendix D: Stillaguamish Tribe Full Comments 

Suggested Changes, Recommendations and 

Responses to the Draft HSRG Regional Review 

Stillaguamish North Fork Summer Chinook Manager’s Response

Recent fish health information has documented elevated pre-spawning mortalities in male 

chinook broodstock as being caused by BKD. Beginning in 2002, all adult broodstock will be 

inoculated to help reduce prespawning mortalities. 

During 2002 grant proposals will be submitted to both the BIA (cyclical maintenance and rehab) 

and NWIFC (hatchery reform) to make significant improvements to the existing spawning shed 

location and disease transmission risks. 

Funding has been secured through the HSRG hatchery reform grant process to expand early 

rearing capacity at the Stillaguamish Tribe’s Harvey Creek hatchery. Additional early rearing 

capacity should be on line by the fall of 2002. 

The co-managers are working diligently towards acquiring additional first pass water and 

improved plumbing for summer chinook reared at the WDFW Whitehorse hatchery with the goal 

of having additional water available by the spring of 2003. 

The rearing ponds at both hatcheries have had recent upgrades to their predator control 

equipment. The WDFW Whitehorse rearing pond will have an electronic counter installed to 

accurately enumerate releases and losses of summer chinook as the fish leave the pond. Should 

predator losses continue to be significant, additional measures will be taken to further reduce 

predator access to the acclimation pond. 

The Stillaguamish Technical Advisory Group and Stillaguamish Implementation and Review 

Group are developing specific habitat improvement objectives and habitat restoration projects 

needed to recover natural chinook productivity throughout the Stillaguamish watershed. 

The Stillaguamish Tribe and WDFW are implementing monitoring and evaluation programs that 

include coded wire tagging, morphometric analysis, smolt trap outmigration characterizations, 

extensive spawning ground surveys and genetic analysis. 
Appendices Hatchery Reform Recommendations – February 2002 157 

North Fork Stillaguamish Chum Managers Response

The Tribes and WDFW have agreed with the HSRG panel that the North Fork Stillaguamish 

chum program as outlined in October is not meeting its goals as an integrated harvest program. 

Our proposal is to change the goal of the program to an integrated education program. During the 

time that chum salmon are returning to the Stillaguamish Tribe’s Harvey Creek hatchery, we 

have 600 to 1000 students from local school districts coming to the facility to observe both 

hatchery spawning and natural chum spawning that occurs in the stream adjacent to the hatchery. 

During their visit to the facility they also learn about the habitat and water quality requirements 

for healthy salmon populations and how humans have impacted salmon habitat. 

The proposed integrated education program would involve downsizing the current integrated 

harvest program from 650,000 to a release of 200,000 chum fry at 400-600 fish per pound. This 

release would result in an annual return of 200 to 300 adults back to the hatchery. We would 

augment these returning hatchery fish each year with 10-20% wild chum exclusively from the 

North Fork Stillaguamish. 

With the addition of a doubling of our current early rearing capacity scheduled to be in place by 

the fall of 2002, we can operate this chum program with no direct impacts to the chinook 

program and meet our target rearing densities of .25 pounds/cubic ft/inch for all species reared at 

this facility. 

Using other species of salmon returning and rearing at the facility is not feasible for the 

following reasons. When we are spawning chinook in August and early September, students 

either have not returned from summer vacation or have just started school. Most of the classes 

that come for tours in late November and early December are studying about salmon as part of 

their class work and the field trips compliment that learning. Both our current coho program and 

the proposed modifications to that program don’t provide enough fish for spawning for all the 

classes and coho rarely spawn in the stream adjacent to the hatchery, but instead move up higher 

in the watershed. 

In addition to educational component to the program, the hatchery chum program provides a 

stable source of carcasses for the Sarvey Wildlife Care Center for use in the rehabilitation of 

injured wild animals. The hatchery chum program also makes eggs and carcasses available for 

tribal members who no longer fish and want fish for eating and smoking. 

During 2002 grant proposals will be submitted to both the BIA (cyclical maintenance and rehab) 

and NWIFC (hatchery reform) to make significant improvements to the existing spawning shed 

location and disease transmission risks. 
158 Hatchery Reform Recommendations – February 2002 Appendices 

Funding has been secured through the HSRG hatchery reform grant process to expand early 

rearing capacity at the Stillaguamish Tribe’s Harvey Creek hatchery. Additional early rearing 

capacity should be on line by the fall of 2002. 

The co-managers will again evaluate the appropriateness of using Stillaguamish chum for the 

Maxwelton Supplementation program and discontinue the program if the stock is not 

appropriate. 

South Fork Stillaguamish Chum Managers Response

This program is operated at the corrections facility in conjunction with educational staff at the 

facility. The individuals at this facility are used for stream restoration and fire control activities. 

Having them actively involved in the care and release of salmon helps them understand the 

connection between what they learn in their classes and the work that they carry out in the field. 

The proposed changes for the program are that we will return to broodstocking 100% of the 

chum needed for the program from Jim and Siberia creeks, which run immediately adjacent to 

the Indian Ridge facility and are tributaries of the South Fork Stillaguamish. The eggs will be 

incubated at the Harvey Creek hatchery and then returned to the facility egg box for hatching and 

release. 

During 2002 grant proposals will be submitted to both the BIA (cyclical maintenance and rehab) 

and NWIFC (hatchery reform) to make significant improvements to the existing spawning shed 

location and disease transmission risks. 

Funding has been secured through the HSRG hatchery reform grant process to expand early 

rearing capacity at the Stillaguamish Tribe’s Harvey Creek hatchery. Additional early rearing 

capacity should be on line by the fall of 2002. 

Stillaguamish Coho Managers Response

The HSRG panel noted that one of the reasons they recommended putting this program into 

standby was because the run was healthy. Yet in the matrix, the stock status was noted as at risk. 

The SASSI status for this stock is depressed. 

George Pess and others have noted significant losses of coho habitat. Off channel habitat has 

been critically diminished. Beaver ponds, sloughs and tidelands account for the majority of 

habitat lost in the last century. Between 67% to 91% of these habitats have been eliminated due 

to human land use altercations (Pess et al., 1999). Approximately 37% of summer and 21% of 

winter coho loss in tributaries is due to blocking culverts (Pess et al., 1999). 
Appendices Hatchery Reform Recommendations – February 2002 159 

From 1992 to 2001, Stillaguamish tribal fishermen have only been able to have directed coho 

fisheries 3 out of 10 years and escapement levels have been met only 4 out 12 years during the 

1988 –99 period (Drotts, per.comm.). Wild Stillaguamish coho have been and continue to be one 

of the key weak stock drivers limiting mixed stock coho fisheries throughout the Pacific 

Northwest region. 

The HSRG scientific panel had a number of alternatives and recommendations concerning the 

current coho program. The tribe has reviewed those alternatives. The proposal is to modify the 

existing integrated recovery program to an integrated harvest/recovery program, where each year 

we capture 100% of our broodstock from the Fortson Creek fish ladder, which is a tributary of 

the North Fork Stillaguamish. This tributary has a consistently strong run of coho that occurs in 

the middle of the time period that coho are returning and spawning in the North Fork 

Stillaguamish. 

Up to 45 pairs of coho would be captured each year, spawned using a 5 X 5 matrix cross and 

early reared at the Harvey Creek hatchery. Additional rearing would occur at the tribe’s North 

Fork (Johnson Creek) hatchery (9,600 cu/ft.; 300GPM). These fish (50K) would be coded wire 

tagged for four consecutive years to evaluate the existing North Sound multi-generational 

hatchery indicator stock programs and how well they represent naturally spawning North Fork 

Stillaguamish coho. 

The fish would then be transferred in April to a net pen located in Warm Springs Slough for final 

acclimation and release during mid-May. The Warm Springs Slough is an isolated slough located 

in Port Susan 3⁄4 mile south of the mouth of Stillaguamish River, which receives freshwater 

drainage from agricultural fields. The water is pumped year round over the sea dike into the head 

of the slough. 

Adult CWT tagged wild origin program coho would return primarily to the Warm Beach Slough 

with any strays returning to either the North Fork (Johnson Creek) hatchery or Fortson Creek. 

Returning tagged fish could be culled out of traps situated at both locations. In addition, both 

Fortson Creek and Johnson Creek would be surveyed to enumerate straying levels from the net 

pen. The returning hatchery adults would be available to tribal members and sports fishermen in 

an extreme terminal fishery at Warm Beach Slough with restricted fishing boundaries, which 

would minimize the interception of returning natural spawning coho. 

Adults from the net pen that stray back to either to the Johnson Creek hatchery or the Fortson 

Creek trap would be available as a broodstock source if needed. If the returning adults were not 

needed for broodstock, then they would be given to tribal members, sold to a buyer, used by the 

wildlife recovery center or returned to local streams for nutrient recycling. 

This program modification would address a number of concerns the HSRG raised about the 

existing coho program that the tribe operates. We would be increasing the number of fish 

released and using 100% wild origin broodstock. Additionally, this program would provide a 

limited consistent directed harvest located in an area that would minimize the capture of wild 
160 Hatchery Reform Recommendations – February 2002 Appendices 

coho during years when the run is too weak for directed in river harvests. The program would 

provide additional tagged fish which are more wild in origin than the current multi-generational 

hatchery stocks currently used as surrogate indicator stocks for North Puget Sound wild coho 

populations, and coho broodstock would be available to use for reseeding under utilized or newly 

opened up habitat. 

Why can’t we capture outmigrant wild coho smolts to create an indicator stock? During the 

operation of smolt trap in the Stillaguamish mainstem during 2001 only 3,500 wild coho smolt 

were captured for the whole trapping season (Griffith, per. comm.). Results from outmigrant 

smolt trapping done by the Tulalip Tribes in the mid-1980’s documented the time, difficulty and 

cost associated with capturing enough wild outmigrant coho for tagging (Nelson et al., 1997.) 

Capturing wild coho broodstock and then rearing their progeny in a large pond would be much 

more efficient then trying to capture wild outmigrant smolts. 

Please note that the winter run steelhead program for the Stillaguamish Tribe has been officially 

terminated. 

Thank you for taking the time to review these proposed modifications 

Kip Killebrew 

Stillaguamish Tribe 
Appendices Hatchery Reform Recommendations – February 2002 161 

Appendix E: Tulalip Tribes Full Comments 

Tulalip Tribes Responses to HSRG Regional Review 

Snohomish Wild Summer Steelhead 

HSRG wild steelhead management zones. As indicated in the text, the citation of Pilchuck Creek and the 

Tolt River are examples only. The Tulalip tribes will want to review the concept of wild steelhead 

management zones and the selection of particular zones before this concept is implemented. Also, it 

should be noted that Pilchuck Creek is in the Stillaguamish system. 

Tulalip Summer Chinook 

The HSRG states that the program should include mass marking to help maximize harvest rates and 

assess straying. It should be noted that the Tulalip summer chinook are mass-marked with thermal marks 

on otoliths. The co-managers believe that this is the only type of mass mark suitable for assessing straying 

when the simultaneous contribution of several different hatchery stocks to natural spawning areas is of 

interest and the hatchery stocks must therefore receive a unique mark. A visible mass mark, such as an 

adipose finclip, is necessary for these fish to contribute to selective fisheries. During the period of 

feasibility testing for the suitability of the summer chinook stock for rearing at Tulalip, 100,000 fish per 

year are receiving a CWT and AD/clip. During this period, the comanagers believe this is the only mass 

mark this group should receive. If and when the summer chinook become the broodstock of choice at 

Tulalip hatchery then the comanagers believe it would be appropriate to discuss whether to mass mark all 

or part of the production with an adipose finclip. 

The co-managers appreciate the commendation from the HSRG regarding the otolith marking and 

recovery studies. It should be noted that, as well as stray rates, this study is being used to document the 

contribution of Tulalip hatchery fish to the terminal fishery. This allows us to manage terminal sport and 

net fisheries as selective fisheries using time and area management instead of selective retention 

regulations. This adds an important option to the toolkit for responsible management of hatchery fish. 

Tulalip Hatchery fall chinook 

See above comments on Tulalip summer chinook. During the period of summer chinook evaluation it 

should be noted that 100,000 Tulalip fall chinook per year are receiving a CWT and AD/clip. 

The co-managers believe that the program should continue at current levels pending the outcome of the 

study of the feasibility of switching Tulalip chinook production to the summer broodstock. 

Tulalip Bay Hatchery Coho 

The HSRG suggests that this program “include mass marking”. It should be noted that this program 

currently includes CWT and Ad/clips on 50,000 smolts per year and mass marking of an additional 

250,000 to 300,000 smolts per year with Ad/clips subject to agreement between Tulalip and WDFW. 
Puget Sound and Coastal Washington 

Hatchery Reform Project 

May 2005 Update 

What is Hatchery Reform? 

Hatchery Reform affects more than just hatcheries. It 

requires a new approach to managing salmon and 

steelhead—one that begins with goals for and 

understanding of the status of wild stocks and then 

designing hatchery programs consistent with 

conservation and harvest goals for those stocks. Far 

from seeing hatcheries as a substitute for habitat, 

hatchery reform recognizes that healthy, abundant 

habitat is essential to the success of hatchery programs 

that seek to meet these goals. The size and health of 

natural populations and the habitat on which they 

depend controls what hatcheries can do to boost 

natural spawning and/or provide a harvestable 

surplus. Hatchery reform means managing a holistic, 

science-based system that results in more adult fish 

returning to both maintain healthy, fit natural 

populations and provide harvest opportunities. 

The Hatchery Reform Project: Salmon 

Conservation & Sustainable Fisheries 

In 2000, with bipartisan support, the US Congress 

established the Puget Sound and Coastal Washington 

Hatchery Reform Project. Led by independent 

scientists and supported by state, tribal, federal and 

private sector leaders, the project is a science-based 

reform of our hatchery system to achieve two goals: 

1. Helping to conserve naturally spawning 

salmon and steelhead populations; and 

2. Supporting sustainable fisheries. 

The History of Hatcheries 

Puget Sound and the Washington coast are home to 

the world’s largest salmon hatchery system—over 100 

hatcheries, some dating back to the 1800s. These 

hatcheries provide about 75 percent of the fish caught 

in Puget Sound, are important to commercial fishing 

and to meeting tribal treaty harvest obligations, and 

are the linchpin of $854 million recreational and $145 

million commercial annual fishing economies in 

Washington (the eighth and seventh largest in the 

nation, respectively). 

When Puget Sound chinook and Hood Canal summer 

chum salmon were listed as threatened under the 

federal Endangered Species Act in 1999, outdated 

hatchery practices were recognized as one of the 

causes for the decline, along with habitat loss and 

over-fishing. It was clear that the time had come to 

rethink the role of hatcheries and to redesign the 

system to meet today’s needs and challenges. 

A Unique Partnership 

The Hatchery Reform Project brings together a unique 

combination of independent science, manager 

involvement, political support and third-party project 

coordination/facilitation that has proven to be a 

highly effective formula. The partnership is guided by 

the assumption that the best way to help the state and 

tribes succeed in moving their hatchery system 

forward is to let the scientists focus on science and the 

managers on management. The scientific 

recommendations assess benefits and risks, but leave 

the “how-to’s” to the managers. 

Independent Science 

The heart of the project is the Hatchery Scientific 

Review Group (HSRG), an independent scientific 

panel established by Congress that systematically 

reviewed more than 200 hatchery programs in Puget 

Sound and coastal Washington, and has provided a set 

of scientific tools for implementing reforms and 

rethinking the way salmon and steelhead are managed. 

Coordination with Policymakers 

The Hatchery Reform Coordinating Committee is 

made up of the federal, state, and tribal entities 

responsible for implementation of the HSRG’s 

principles and recommendations. They include the 

Northwest Indian Fisheries Commission (NWIFC), 

Washington Department of Fish and Wildlife 
Puget Sound and Coastal Washington Hatchery Reform Project 

May 2005 Update 

2

(WDFW), US Fish and Wildlife Service (USFWS) and 

NOAA Fisheries. Members of the original 

Congressional Hatchery Science Advisory Team and 

Long Live the Kings are also on the committee. 

Third-Party Facilitation & Project Management 

The salmon conservation organization Long Live the 

Kings (LLTK) was designated by Congress as the 

project’s independent third party. LLTK’s roles 

include providing facilitation and project coordination 

to the HSRG and the Hatchery Reform Coordinating 

Committee, and helping the managers communicate 

hatchery reform progress to Congress, state legislators, 

stakeholder groups and the public. LLTK retained the 

law firm of Gordon, Thomas, Honeywell to serve with 

LLTK staff on the facilitation team. 

Hatchery Reform Principles & 

Recommendations 

From 2001–03, the HSRG reviewed over 200 hatchery 

programs at over 100 hatcheries in 10 regions of Puget 

Sound and coastal Washington (see map above). These 

reviews were held in the regions. The HSRG worked 

with the regional managers to ensure a clear 

understanding of stock, habitat and harvest 

management goals and premises in each watershed, via 

briefing books, field tours and face-to-face meetings. 

In April 2004, the HSRG published a report 

containing over 1,000 recommendations for change at 

individual hatcheries, along with 18 recommendations 

to be applied across the entire system. The HSRG also 

provided three principles to guide hatchery 

management in the future: 

3. Goals for all stocks must be quantified and 

expressed in terms of values to the 

community (harvest, conservation, education, 

research, etc.) 

4. The purpose, operation and management of 

each hatchery program must be scientifically 

defensible and consistent with current scientific 

knowledge. 

5. Decisions must be informed and modified by 

continuous evaluation and new scientific 

information. 

As a foundation for reform, the HSRG recommended 

that hatchery managers change their measure of 

success from the number of juvenile fish released, to 

the number of adult fish returning to sustain the stock 

and provide fishing opportunities. This means 

focusing on quality over quantity, understanding the 

carrying capacity of the freshwater and marine 

environments into which fish are released, and other 

scientifically sound hatchery practices. 

Central to the HSRG’s work is the concept that 

hatchery fish must be managed either as part of a wild 

population (genetically integrated) or as a wholly 

separate population (genetically segregated). 

Segregated programs are for use primarily where the 

goal is to provide fishing opportunities, and where 

interactions between these fish and wild populations 

can be limited. Integrated programs are most 

appropriate where conservation is a primary goal, or 

for harvest programs where the potential for genetic 

interactions between hatchery and wild fish make this 

the best strategy for meeting regional stock goals. 

A properly integrated program maintains fish that are 

adapted to the natural environment, in that the natural 

spawners drives the adaptation of the composite 

population. Therefore, these fish may be appropriate 

for helping to rebuild declining wild populations. They 

should also survive in greater numbers than fish from 

a poorly integrated program, meaning more fish may 

available for harvest or conservation. 

Successful integrated programs require healthy 

naturally-spawning populations and the functional 
Puget Sound and Coastal Washington Hatchery Reform Project 

May 2005 Update 

3

habitats that sustain them. In this context, a hatchery 

should not be seen as a substitute for habitat, but 

rather as an extension of it—a productive tributary of 

the watershed in which it resides. 

Most importantly, the HSRG’s principles and 

recommendations make it clear that hatcheries can no 

longer be designed, operated and evaluated in 

isolation. In order to properly evaluate the benefits 

and risks from a hatchery program, it is necessary to 

examine it in the context of the watershed in which it 

resides. Only within this context can it be determined 

if a hatchery program is an appropriate tool for 

helping to reach harvest and conservation goals for a 

given stock and, if so, what size and type of program is 

called for. 

This approach goes beyond hatcheries, representing a 

new model for watershed-focused, science-based 

management of salmon and other natural resources, 

one that takes into account all the factors that affect a 

species. 

Tools for Reform 

The HSRG has developed a set of tools to help the 

managers operationalize the new approach and apply 

available science to decision making. 

Scientific Framework 

Organizes the current state of knowledge about how 

actions associated with hatcheries affect the 

environment and fish resources. Forms the basis for 

all of the HSRG’s tools, processes and 

recommendations. First published in 2000, after 

review by over 200 scientists and stakeholders. 

Updated in 2004. 

Benefit/Risk Assessment Tool 

Adapted from a tool developed by the co-managers, 

allows the user to evaluate the relative benefits and 

risks associated with specific actions and choices in 

hatchery management. Central to the regional review 

effort. 

Hatchery Operational Guidelines 

Describe operational practices most likely to meet 

conditions for success, as defined in the Scientific 

Framework. 

Applied Research Program 

A competitive grant program funding research 

projects to address knowledge gaps identified in the 

Scientific Framework. 

Emerging Issues in Hatchery Reform 

White papers on emerging issues critical to 21stcentury hatchery management, such as the effects of 

changing ocean conditions on fisheries, preventing 

hatchery fish from preying on wild fish, and methods 

for preserving genetic diversity and fitness in hatchery 

populations. 

All H Analyzer (AHA) Management Tool 

Allows managers to explore the likely results—in 

terms of numbers of adult fish returning to sustain 

natural populations and provide harvest—of 

alternative actions and strategies in habitat, hatchery 

and harvest management. Provides accountability by 

documenting goals, assumptions, hypotheses and 

decisions. 

Managing for Success and Accountability 

Will provide managers with a practical and costeffective set of variables to monitor, in order to ensure 

hatchery programs are accountable for their results, 

successfully meeting goals, and adaptively managed to 

improve performance and adjust to changing 

circumstances. Currently under development. 
Puget Sound and Coastal Washington Hatchery Reform Project 

May 2005 Update 

4

Implementing Hatchery Reform 

Implementing the HSRG’s recommendations and 

putting into practice the new approach to salmon and 

steelhead management will require capital investment, 

a commitment to new hatchery practices, and 

accountability to ensure goals are being achieved. The 

state and tribal co-managers have agreed with the vast 

majority of the recommendations and have 

implemented many of them. They are working with 

the HSRG and the facilitation team to design a 

strategy for changing the way hatcheries are managed, 

and incorporating hatchery reform into other salmon 

recovery and harvest management processes. 

In 2004, that work included technical discussions that 

resulted in new management tools and papers refining 

key hatchery reform concepts; regional workshops 

where guidelines for integrated and segregated 

hatchery programs and tools such as AHA were 

applied to regional case studies; co-manager decisionmaking meetings on implementing reform in each 

region; and work by the HSRG to prepare manuscripts 

for the peer-reviewed scientific literature. 

In 2005, the co-managers are continuing to use AHA; 

wrapping up regional decision-making meetings; and 

incorporating the recommendations into recovery 

plans and other management documents and 

processes. The HSRG is completing its tools and 

scientific publications; developing an agenda to guide 

hatchery-related research; and preparing for a 

workshop on hatchery reform to be held in the second 

half of the year. 

Implementation of the 1,000 program-specific 

recommendations continues. The state, tribal and 

federal managers have developed databases for 

tracking the status of each recommendation. They 

report that over one-third have been completed. 

Examples include: 

• Species Preservation: The Elwha Fish Restoration 

Team is evaluating options for preserving 

Elwha chinook during removal of dams and is 

incorporating HSRG recommendations for 

improved stock management. 

• Revised Program Management: Hatchery runs of 

chinook and coho returning to Tulalip Bay 

have been revised to reduce genetic risks and 

further assess stray rates. 

• Discontinued Programs: Hatchery programs for 

Dungeness fall pink, Garrison Springs chum, 

Fox Island hatchery coho and chinook, 

Minter Creek chum and pink, and Tulalip Bay 

hatchery spring chinook have been 

discontinued. 

• Hatchery Closure: The McAllister Creek 

Hatchery on the Nisqually River was closed 

due to poor fish survival, water quality and 

disease transfer issues. 

• Facility Improvements: Improvements for water 

quality, rearing and predator control are being 

implemented to increase the success of the 

chinook conservation program at Whitehorse 

and Harvey Creek facilities on the 

Stillaguamish River. 

The Hatchery Reform Coalition 

LLTK has convened a coalition of organizations to 

build a constituency for hatchery reform. The 

Mountaineers, Northwest Sportsfishing Industry 

Association, Puget Sound Anglers, Recreational 

Fishing Alliance, National Trout Unlimited, 

Washington Council of Trout Unlimited, Wild 

Steelhead Coalition and other recreation, sports fishing 

and conservation organizations have signed a letter of 

support for hatchery reform as recommended by the 

HSRG. That coalition is meeting regularly and features 

20 regional and national organizations and advocates, 

with a combined membership base greater than 

300,000. 

For more information on the Hatchery Reform Project, visit 

www.hatcheryreform.org, call LLTK at 206-382-9555 x. 25, 

or email mkern@lltk.org. 
The All-H Hatchery Analyzer (AHA) 

Hatchery Reform Technical Discussion Paper, August 20051

Background 

Management decisions about salmon and steelhead hatchery programs are best made in the context of the 

particular circumstances in a given watershed. This requires understanding the current and expected future 

status of all natural and hatchery stocks in an ecosystem—along with the habitat on which they depend—as 

well as harvest and conservation goals. Only within this context can it be determined if a hatchery program is 

an appropriate tool for helping to reach harvest and conservation goals for a given stock and, if so, what size 

and type of program is appropriate. 

This represents a new, watershed-based approach to management of anadromous salmonids, one that takes into 

account all the factors that affect a species (sometimes referred to in the case of salmonids as the “H’s”—

habitat, harvest and hatcheries). Recognizing this, the state and tribal co-managers of Washington’s salmon 

and steelhead asked the Hatchery Scientific Review Group (HSRG) to work with them to develop tools for 

managing hatcheries in this new context. 

Technical discussions in 2004 with Washington State Department of Fish and Wildlife (WDFW) and 

Northwest Indian Fisheries Commission (NWIFC) scientists resulted in one such tool—the “All-H Hatchery 

Analyzer” (AHA). AHA was applied to 27 case studies in a series of technical workshops in Puget Sound and 

coastal Washington during the summer of 2004. It is being refined during technical discussions in 2005 among 

scientists from the HSRG, WDFW, NWIFC and individual treaty tribes. 

Purpose 

AHA is a hatchery management planning tool, built on recent work by HSRG, WDFW, NWIFC, NOAA 

Fisheries and other scientists.2

 AHA is used to project the effects of artificial propagation on the target stock, 

given details about brood sources, survival rates and general information about the productivity and capacity of 

natural habitat and overall harvest rates on natural- and hatchery-origin fish. 

AHA provides a way to explore the genetic implications of alternative broodstock management strategies and 

enables planners to compare alternative scenarios for incorporating natural-origin broodstock into hatchery 

programs, as well as different program sizes. AHA projects the effects of various hatchery scenarios, under 

differing harvest and habitat assumptions, on the productivity and abundance of associated natural spawners of 

natural and hatchery origin, in terms of whole population performance. 

AHA allows salmon and steelhead managers to: 

• Use current habitat productivity/capacity, harvest rates and hatchery operations in a watershed to consider 

what will result from that set of factors, in terms of the number of adult fish returning to the habitat, 

harvest and hatchery, and the amount of influence the natural environment has on integrated 

natural/hatchery populations. 

 

1

 This paper was produced by the Hatchery Reform Technical Discussion Group, which has included John Barr, Lee 

Blankenship, Don Campton, Trevor Evelyn, Tom Flagg, Connie Mahnken, Lars Mobrand Lisa Seeb, Paul Seidel and Bill 

Smoker, Hatchery Scientific Review Group; Alan Chapman, Lummi Indian Nation; Ken Currens and Terry Wright, Northwest 

Indian Fisheries Commission; Chris Weller, Point No Point Treaty Council; Kip Killebrew, Stillaguamish Tribe; Kit Rawson, 

Tulalip Tribes; and Andy Appleby, Heather Bartlett, Craig Busack and Jim Scott, WDFW. 2

 See for example: 

Ford, M.J. 2002. Selection in captivity during supportive breeding may reduce fitness in wild. Conserv. Biol. 16:815-625 

Lynch, M., and M. O’Hely. 2001. Supplementation and the genetic finess of natural populations. Conservation Genetics 2: 363-

378. 
The All-H Hatchery Analyzer (AHA) 

Hatchery Reform Technical Discussion Paper, August 2005 

2

• Examine how these results could be modified in the short- and long-terms if habitat, harvest and/or 

hatchery programs are changed. 

• Confirm current conditions, describe a goal for the long-term future of the population, and develop one or 

more scenarios for achieving or moving toward that goal. 

• Apply a scientific approach in the face of the uncertainty always present in natural resource management. 

• Move from general management guidelines to strategies specifically tailored to unique watershed 

conditions and circumstances. 

AHA is important, because it: 

• Uses the best available scientific information to predict implications, and quantifies/tracks fish produced 

naturally and in hatcheries, fish removed for harvest or hatchery broodstock, and the likely genetic 

interactions of hatchery and natural fish spawning in the natural environment. 

• Fosters accountability, by documenting goals, assumptions, scientific hypotheses, relationships, 

management decisions and the rationale behind these decisions. The assumptions can then be verified by 

monitoring and evaluation; the hypotheses can be tested by research. In this way, AHA can be used to help 

identify areas where better science will make a difference in decision making. 

• Tests a key hypothesis about whether fitness loss can be addressed without losing demographic benefits 

from hatcheries.3

 

• Can be used in conjunction with detailed habitat models, such as SHIRAZ or EDT, and more detailed 

harvest models, such as FRAM, if more detail of habitat and harvest management is required.4

Current Status and Next Steps 

• Participants in the Hatchery Reform Technical Discussion Group are currently discussing AHA and 

considering possible refinements. The group encourages salmonid managers and others to do case studies 

using AHA and welcomes informal feedback, to help improve it. 

• The HSRG is in the process of preparing a manuscript for publication in a peer reviewed journal, where 

AHA will be used to analyze the implications of integrated hatchery programs in western Washington. The 

methods section of this journal article will also serve to describe and document AHA for peer review. The 

draft manuscript will be made available electronically once it is submitted for publication. 

• AHA is being used by co-managers in Puget Sound and coastal Washington to develop short-term harvest, 

habitat and hatchery strategies that can lead to the recovery of important natural stocks and sustainable 

fisheries. 

• As part of the Northwest Power and Conservation Council’s sub-basin planning process, AHA is being 

used to bring together hatchery strategies with the habitat components of sub-basin plans. 

• AHA will be used to document the assumptions made about harvest, habitat and hatchery programs in the 

Managing for Success (MFS) tool currently being developed to support adaptive management, monitoring 

and evaluation. 

 

3

 Because this is an area of uncertainty, the effects of fitness gain or loss can be adjusted or turned off in AHA. 4

 For more information on these models, see: 

Lestelle, L. C., L. E. Mobrand, and W. E. McConnaha. 2004. Information Structure of Ecosystem Diagnosis and Treatment 

(EDT) and Habitat Rating Rules for Chinook Salmon, Coho Salmon, and Steelhead Trout. Mobrand Biometrics, Inc., 

Vashon Island, WA, 27 pages. 

Model Evaluation Workgroup. 2004. Fishery regulation assessment model (FRAM): An overview for Chinook and coho, 39 

pages (Available from Northwest Indian Fisheries Commission, 6730 Martin Way E., Lacey, WA 98516). 

Mobrand, L. E., J. A. Lichatowich, L. C. Lestelle, and T. S. Vogel. 1997. An approach to describing ecosystem performance 

“hrough the eyes of salmon.”Canadian Journal of Fisheries and Aquatic Sciences 54:2964-2973.Sharma, R., A. B. Cooper, 

and R. Hilborn. 1997. A quantitative framework for analysis of habitat and hatchery practices on pacific salmon. Columbia 

River Inter-Tribal Fish Commission, Scientific, Seattle, 58 pages. 

Scheuerell, MD, R Hilborn, MH Ruckelshaus, KK Bartz, K Lageux, A Hass, and K Rawson. (in review). SHIRAZ: a model 

framework for incorporating fish-habitat relationships in conservation planning. Canadian Journal of Fisheries and Aquatic 

Sciences. 
The Hatchery Reform Coalition 

October 2005 

In 2002, Long Live the Kings (LLTK) convened a number of conservation, 

recreation and sport fishing organizations to lend support to the Puget Sound 

and Coastal Washington Hatchery Reform Project and the Hatchery Scientific 

Review Group (HSRG). The HSRG was in the middle of a three-year, regional 

review of over 200 hatchery programs in Puget Sound and on the coast, and 

was just beginning to articulate its vision about how the hatchery system 

could be reformed to meet the twin goals of providing fish for harvest and 

helping to conserve naturally-spawning populations. 

Since that time, the HSRG has completed its review and published the 

results, and the Hatchery Reform Coalition has grown to feature 18 regional 

and national organizations and advocates with a combined membership base 

of over 300,000 (see list on the back of this sheet). The Coalition includes 

organizations that are not always on the same side on all issues, but all have 

agreed that the HSRG’s principles and recommendations (available at 

www.hatcheryreform.org) represent the right way to proceed with managing 

the hatchery system. Now, Coalition members are working together to build 

a constituency for hatchery reform. 

The Coalition provided a letter for the April 2004 release of the HSRG’s report 

pledging to support the state and tribal co-managers’ hatchery reform 

implementation efforts, given that they are guided by the recommendations 

of the HSRG. In June 2004, a majority of Coalition members signed a letter 

of support for a Northwest Indian Fisheries Commission request to Congress 

for tribal hatchery rehabilitation funding through the Bureau of Indian Affairs. 

In 2005, Coalition members signed two additional letters in support of tribal 

hatchery rehabilitation funding and one to the Washington State Legislature 

in support of hatchery reform implementation funding for the Washington 

State Department of Fish and Wildlife. 

The Coalition will continue to work to see that resources are available to 

implement hatchery reform, and that the co-managers’ reform efforts are 

consistent with the principles and recommendations of the HSRG. 

For more information on the Hatchery Reform Project and the recommendations of 

the HSRG, visit www.hatcheryreform.org. For more information on the Hatchery 

Reform Coalition, call LLTK at 206-382-9555 x. 25 or email mkern@lltk.org 
HATCHERY REFORM COALITION MEMBERS 

October 2005 

Gestin Suttle, Friends of Issaquah Salmon Hatchery 

Gary Loomis, G. Loomis Rods/Fish First 

Buzz Ramsey, Luhr Jensen 

Norm Winn, The Mountaineers 

Jeff Curtis and Kaitlin Lovell, National Trout Unlimited 

Liz Hamilton and Carl Burke, NW Sportsfishing Industry Association 

Peter Bergman and Frank Haw, Northwest Marine Technology 

Tony Floor, Northwest Marine Trade Association 

Clint Muns, Puget Sound Anglers 

Jim Martin, Berkeley Conservation Institute 

Corey Freeman and Mike Gilchrist, Recreational Fishing Alliance 

Scott Weedman, Three Rivers Marine 

Dick Burge and Nate Mantua, Wild Steelhead Coalition 

Heather Rowton, Washington Forest Protection Association 

Mark Cedergreen, Westport Charterboat Association 

Bill Robinson, Fish Advocate 

Terry Turner, Fish Advocate 

Frank Urabeck, Fish Advocate 
HTTP/1.1 404 Object Not Found Server: Microsoft-IIS/5.0 Date: Wed, 14 Jun 2006 

12:57:22 GMT MicrosoftOfficeWebServer: 5.0_Pub Connection: close Content-Type: 

text/html 

404 Object Not Found

Fisheries Magazine, 

June 2005, Vol. 30 No. 6

Featured articles are available below in PDF form! 

Feature: Fisheries 

Management

Hatchery Reform in 

Washington State: 

Principles and Emerging 

Issues

An examination of 100 

facilities and 200 programs in 

Washington state revealed 

three principles of hatchery 

reform—explicit goals for each 

program, adaptive responses 

to new information, and 

scientifically defensible 

programs. 

Hatchery Scientific Review 

Group: Lars E. Mobrand, John 

Barr, Lee Blankenship, Donald 

E. Campton, Trevor T. P. Evelyn, Tom A. Flagg, Conrad V. W. 

Mahnken, Lisa W. Seeb, Paul R. Seidel, and William W. Smoker

Feature: Endangered Fishes

Prospects for Recovering Endemic Fishes Pursuant to the 

U.S. Endangered Species Act

For some endangered fish species, recovery may be an 

unobtainable goal. The authors argue that the restricted range 

and specialized habitat of many endemic, spring-dwelling fishes 

necessitates continuing protection. 
Jack E. Williams, Catherine A. Macdonald, Cindy Deacon 

Williams, Hal Weeks, Georgina Lampman, and Don W. Sada

Essay: Endangered Species

Moving Forward from Recovery under the U.S. 

Endangered Species Act to Long-term Conservation of 

Inland Cutthroat Trout

The authors present their opinion on conflicts in current 

recovery programs and offer a new paradigm for moving 

forward from the present, seemingly intractable recovery 

process to long-term conservation of cutthroat trout. 

Bruce E. May and Lynn R. Kaeding

Forum: Economics Growth

Analysis of Customs Trade Data to Characterize 

Importation of Live Bait 

An analysis of customs data reveals what we do and don’t 

know about live bait importations into the United States. 

Julie A. Thompson and Shawn K. Alam

Column: President’s Hook

What Your Colleagues Are Doing for You

Every year AFS members enthusiastically take on tasks that 

benefit the entire Society. Here’s a look at the Standing 

Committees and their activities this year. 

Barbara A. Knuth

Column: Director’s Line

NOAA Fisheries, regional councils hold second annual 

meeting on fisheries management

Reauthorization of Magnuson-Stevens, ecosystem-based 

management, and the use of science by fisheries management 

councils were the featured topics at a recent NOAA-sponsored 

conference in Washington, DC. 

Jessica Geubtner and Alesia Read

Fisheries 2001-2004

Fisheries Archive 

See the Archive for related Fisheries articles on topics of interest.

Fisheries Electronic Manuscript Submission
2003 Fisheries Guide for 

Authors Calendar of Events

Guide for Reviewers Case History Guidelines

Name of Fishes Changes Job Postings

AFS Fish Name SpellChecker

Download a .pdf version of the Fisheries Media Kit:

● Fisheries Rate Card

● Advertising Insertion Order and Frequency Agreement

HTTP/1.1 404 Object Not Found Server: Microsoft-IIS/5.0 Date: Wed, 14 Jun 2006 12:57:22 GMT 

MicrosoftOfficeWebServer: 5.0_Pub Connection: close Content-Type: text/html 

404 Object Not Found
HSRG/WDFW/NWIFC Technical Discussion Paper #1: 

Integrated Hatchery Programs 

June 21, 2004 

Genetic and ecological interactions have been at the center of the debate over benefits 

and risks of hatchery programs (e.g., NRC 1993; HSRG 2004; Williams et al. 2003). The 

two options for managing these risks are either to minimize interaction through 

segregation (isolation) of the hatchery population from the natural population or to 

manage the hatchery population as an integral, benign component of a composite 

hatchery-natural population. All salmon and steelhead hatchery programs must be 

classified either as integrated or segregated by intent. These classifications lead directly 

to a series of genetic and ecological management guidelines for each of the two types of 

programs. How well programs meet this intent will vary; this variation provides an 

important measure for evaluating the biological risks posed by hatchery programs on 

natural populations. 

The purpose of this summary is to provide a definition of an integrated hatchery program, 

describe operational guidelines for implementation, and identify some of the implications 

and constraints imposed by the guidelines. 

Definition of an Integrated Hatchery Program 

The terms integrated and segregated describe the intended reproductive relationship of 

hatchery populations to naturally spawning populations. An integrated hatchery program 

is associated with a specified natural population from which gene flow occurs. The goal 

of an integrated program is to demographically increase the abundance of fish 

representing a natural population (two environments, one gene pool). 

Formal Definition: A hatchery program is an Integrated Type if the intent is for the 

natural environment to drive the adaptation and fitness of a composite population of fish 

that spawns both in a hatchery and in the wild. 

Theoretical Premise for Integrated Programs 

For a natural/hatchery composite population at equilibrium (Ford 2002), the influence of 

the hatchery and natural environments on the adaptation of the composite population is 

determined by the proportion of natural-origin broodstock in the hatchery (pNOB1

) and 

the proportion of hatchery-origin fish in the natural spawning escapement (pHOS). The 

larger the ratio pNOB/(pHOS+pNOB), the greater the strength of selection in the natural 

environment relative to that of the hatchery environment (Figure 1). In order for the 

natural environment to dominate selection, this ratio must exceed 0.5 (Campton, Busack 

and Currens, personal communication). Furthermore, the greater the difference between 

the hatchery and natural stock components (e.g., in run timing) and the “less natural” the 

hatchery environment (e.g., longer hatchery rearing), the larger the ratio must be to 

reduce the effects of hatchery selection. 

 

1

 Terminology: NOR = Natural Origin Return, HOR = Hatchery Origin Return, NOB = Natural Origin fish 

included in hatchery Broodstock, and HOS = Hatchery Origin fish in the natural Spawning escapement. 
HSRG/WDFW/NWIFC Technical Discussion Paper #1: Integrated Hatchery Programs 

June 21, 2004 2 

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

Proportion natural origin fish in hatchery broodstock (pNOB)

Proportion hatchery fish on spawning 

grounds (pHOS)

1

9

4

2.33

1.5

Stronger Natural

Selective Forces

Figure 1. Proportionate effects of natural selective forces in integrated hatchery programs at 

equilibrium; values to the right indicate the ratio pNOB/(pHOS+pNOB); pNOB must be >0.1 to 

account for genetic drift. 

Operational Guidelines for Integrated Programs 

1. The targeted value of pNOB/(pHOS+pNOB) should be based upon the current status 

of the stock, the goals for the stock, and involves a benefit versus risk judgment. For 

any fixed pNOB, the smaller the pHOS, the stronger the selective forces for the 

natural environment (see Figure 1). 

2. The proportion of natural-origin fish in the broodstock must exceed the proportion of 

hatchery-origin fish on the spawning grounds (pNOB>pHOS) for the natural 

environment to drive adaptation, which is equivalent to pNOB/(pHOS+pNOB)>0.50. 

3. pNOB/(pHOS+pNOB) for integrated programs with stocks of moderate or high 

biological significance and viability (or goals to maintain or improve the biological 

significance and viability of the stock) should be greater than 0.7 (see Figure 1) to 

ensure high levels of natural dominance. 

4. pNOB should be a minimum of 10% to avoid divergence of the hatchery population 

from the natural component, even when pHOS is zero. 

5. A general rule of thumb is that the total number of adults (hatchery- and naturalorigin) used for broodstock cannot exceed the total number of natural-origin 

escapement. 

0.50

0.60

0.70

0.80

0.90
HSRG/WDFW/NWIFC Technical Discussion Paper #1: Integrated Hatchery Programs 

June 21, 2004 3 

6. Hatchery fish should be reared under conditions that deviate as little as possible from 

those experienced by the natural population component, to minimize the effects of 

selective forces in the hatchery: 

a) Rear in a hatchery environment that allows synchronization of adult maturation, 

incubation and emergence, and out-migration with natural populations. 

b) Use rearing protocols that produce juvenile fish similar to natural populations in 

growth rate and size, to reduce competition with and predation on natural stocks, 

and to maintain the age structure of the natural population. 

c) Rear fish at reduced densities in enriched environments, to produce a fish with 

cryptic coloration, territorial fidelity and behavior similar to naturally-produced 

fish. 

d) Release fish volitionally during the out-migration timing of the natural stock. 

7. The size of the program should take into account the quantity and quality of habitat 

available for juveniles and adult spawners, and the effect of the hatchery program on 

natural stocks. 

8. Use marks, tags or other methods to distinguish natural- and hatchery-origin fish 

among natural spawners, in hatchery broodstocks and in harvests. 

9. Take into consideration the potential selective impacts of harvest (for example, size 

selectivity) on the long-term viability of integrated programs. 

Implications/Constraints of Broodstock Management Guidelines for Integrated 

Hatchery Programs 

Broodstock management guidelines for an integrated 

hatchery program impose limitations on the size of that 

program. These limitations depend on the ability to control 

the mix of hatchery- and natural-origin fish both on the 

spawning grounds and in the hatchery. They also depend 

on factors affecting the number of natural spawners 

available for hatchery broodstock (i.e., the productivity of 

the natural environment and the harvest rate on natural 

fish). Identification of the options available to implement 

integrated programs (i.e., changing the ratio of pNOB to 

pHOS, and/or the size of the hatchery program) requires 

case-by-case analyses. 

Implementing an Integrated Hatchery Program

Currently, few hatchery programs are meeting the 

broodstock guidelines recently developed for programs 

where integration is a goal. Assuming that it has been determined that an integrated 

program is appropriate to meet resource goals, how should the transition occur? The 

answer depends in large part on the genetic make-up of the current hatchery and natural 

Supplementation is a term frequently 

used when referring to hatchery 

programs where the intent is for 

hatchery origin fish to spawn in the 

wild and make a contribution to 

harvest and/or conservation (e.g., 

RASP, 1991). The key question for 

supplementation programs is whether 

the hatchery fish spawning in the wild 

indeed confer a net benefit. The 

HSRG has concluded that this may be 

possible in some circumstances and 

that such programs should always be 

accompanied by comprehensive 

monitoring and evaluation efforts. 

Supplementation programs may be 

either integrated or segregated.
HSRG/WDFW/NWIFC Technical Discussion Paper #1: Integrated Hatchery Programs 

June 21, 2004 4 

population components. It also depends on a tolerance to risk that varies depending on 

the viability of, and goals for, the natural population. For example, in a recovery 

program, it may be necessary to rely on hatchery propagation to secure genetic resources, 

until the habitat is capable of supporting a fully integrated program. Initially, this type of 

program may have to be developed from one where the composite population is highly 

influenced by the hatchery environment, but where a detailed management plan has been 

developed to eventually have the natural environment dominate. Similarly, integrated 

harvest programs with goals to maintain or improve the biological significance of the 

stock should be operated to ensure that selective forces in the natural environment 

dominate. 

The tables below are intended to provide guidance in developing an action plan to 

implement an integrated program based on the initial condition (Scenarios 1-3). There 

may be circumstances where one or more elements of these approaches are not 

applicable.

Scenario 1: New Integrated Program

No hatchery program exists 

 Natural population has had little influence from hatchery fish

Recommended approach for initiating a new integrated 

program 

Considerations 

• Initiate hatchery program by collecting representative 

sample of natural fish.

• Collect a number of brood that allows for an effective 

population size of the composite population (natural plus 

hatchery) in excess of 500 fish. 

• If a long-term goal of the hatchery program is to provide a 

conservation benefit, or if the natural spawning of 

hatchery-origin fish will be difficult to control, then the 

effective population size of the hatchery component should 

also be greater than 500 fish.

• Incorporate a minimum of 10% NORs into hatchery 

broodstock each year. 

• Ensure that gene flow from the natural to the hatchery 

population is greater than gene flow from the hatchery to 

the natural population (pNOB > pHOS). 

• For stocks of moderate or high biological significance and 

viability (or goals to maintain or improve the biological 

significance and viability of the stock), 

pNOB/(pHOS+pNOB) should be greater than 0.7 . 

• Size program consistent with goals, the ability of the 

natural population to support hatchery broodstock 

requirements, and gene flow limitations to the natural 

population.

Likelihood of achieving natural adaptation: High 

likelihood of attaining stock goals (developing a 

program where the natural environment drives the 

adaptation of the composite hatchery and natural 

population), as long as broodstock collection is 

feasible and gene flow is maintained within 

recommended guidelines for the goals of the stock. 

Cost: Additional program cost compared to 

segregated programs, primarily for natural 

broodstock collection. 

Effect on Harvest: Changes in harvest contribution 

are dependent on productivity of the natural 

component of the population, as well as 

productivity of the hatchery component.
HSRG/WDFW/NWIFC Technical Discussion Paper #1: Integrated Hatchery Programs 

June 21, 2004 5 

Scenario 2: Transition from a segregated program to an integrated program

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had little influence from hatchery fish

Approach #1 - Not recommended because of 

low likelihood of attaining stock goals Considerations 

• Incorporate a minimum of 10% NORs into 

hatchery broodstock each year.

• Ensure that gene flow from the natural to the 

hatchery population is greater than gene flow 

from the hatchery to the natural population 

(pNOB > pHOS).

• Size program consistent with goals, the 

ability of the natural population to support 

hatchery broodstock requirements, and gene 

flow limitations to the natural population.

Likelihood of achieving natural adaptation: Low likelihood of attaining stock 

goals in the immediate future. Likelihood increases as additional NORs are 

incorporated into the hatchery population through time, or as the proportion of 

NORs in the hatchery broodstock is increased. Composite population is likely to 

have low to intermediate fitness in the natural environment. 

Cost: Increase in cost incurred for broodstock collection appears similar for all 

approaches. 

Effect on Harvest: Effect on harvest appears similar under all approaches other 

than Approach #2 in this and the next scenario, where the segregated harvest 

program is terminated or suspended to allow some level of adaptation of the 

hatchery stock. 

Approach #2 - Recommended approach if 

attaining harvest goal can be interrupted 

during transition to integrated program 

Considerations 

• Initiate a new hatchery program by 

collecting a representative sample of natural 

fish. 

• Collect a number of brood that allows for an 

effective population size of the composite 

population (natural plus hatchery) in excess 

of 500 fish. 

• If a long-term goal of the hatchery program 

is to provide a conservation benefit, or if the 

natural spawning of hatchery-origin fish will 

be difficult to control, then the effective 

population size of the hatchery component 

should also be greater than 500 fish. 

• Incorporate a minimum of 10% NORs into 

hatchery broodstock each year. 

• Ensure that gene flow from the natural 

population to the hatchery population is 

greater than gene flow from the hatchery to 

the natural population (pNOB > pHOS). 

• For stocks of moderate or high biological 

significance and viability (or goals to 

maintain or improve the biological 

significance and viability of the stock), 

pNOB/(pHOS+pNOB) should be greater 

than 0.70. 

• Size program consistent with goals and the 

ability of the natural population to support 

hatchery broodstock requirements and gene 

flow limitations to the natural population. 

• Terminate segregated harvest program.

Likelihood of achieving natural adaptation: High likelihood of attaining stock 

goals as long as broodstock collection is feasible and gene flow is maintained 

within recommended guidelines. 

Cost: Increase in cost incurred for broodstock collection appears similar for all 

approaches. 

Effect on Harvest: A loss of contribution to harvest would be expected between 

termination of the segregated program and achieving the final size of the new 

integrated program. 
HSRG/WDFW/NWIFC Technical Discussion Paper #1: Integrated Hatchery Programs 

June 21, 2004 6 

Scenario 2 (continued): Transition from a segregated program to an integrated program

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had little influence from hatchery fish

Approach #3 - Recommended approach if attaining harvest goal 

cannot be interrupted during transition to integrated program Considerations 

• Initiate new hatchery program by collecting representative sample 

of natural fish.

• Collect a number of brood that allows for an effective population 

size of the composite population (natural plus hatchery) to be in 

excess of 500 fish.

• If a long-term goal of the hatchery program is to provide a 

conservation benefit, or if the natural spawning of hatchery-origin 

fish will be difficult to control, then the effective population size of 

the hatchery component should also be greater than 500 fish. 

• Differentially mark and release offspring of old/new broodstock. 

Preferentially use returns that represent the NOS broodstock. Phase 

out use of old broodstock as new broodstock returns.

• Incorporate a minimum of 10% NORs into hatchery broodstock 

each year once new broodstock returns.

• Ensure that gene flow from the natural population to the hatchery 

population is greater than gene flow from the hatchery to the 

natural population (pNOB > pHOS).

• For stocks of moderate or high biological significance and viability 

(or goals to maintain or improve the biological significance and 

viability of the stock) pNOB/(pHOS+pNOB) should be greater than 

0.70 . 

• Size program consistent with goals and the ability of the natural 

population to support hatchery broodstock requirements and gene 

flow limitations to the natural population.

Likelihood of achieving natural adaptation: High 

likelihood of attaining stock goals, as long as 

broodstock collection is feasible and gene flow is 

maintained within recommended guidelines. 

Cost: Increase in cost incurred for broodstock 

collection appears similar for all approaches. An 

additional cost for differentially marking the two 

hatchery broodstocks would be incurred. Cost in terms 

of operational complexity is higher than all other 

approaches except the final approach, but should be 

no greater than rearing an additional species. 

Effect on Harvest: The loss of contribution to harvest 

in Scenario 2, Approach #2, above, could be avoided 

during transition with additional marking cost. 
HSRG/WDFW/NWIFC Technical Discussion Paper #1: Integrated Hatchery Programs 

June 21, 2004 7 

Scenario 3: Transition from an incompletely segregated program to an integrated program. (Most common scenario).

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had significant influence from hatchery fish

Approach #1 - Not recommended because of low 

likelihood of attaining stock goals Considerations 

• Incorporate a minimum of 10% NORs into 

hatchery broodstock each year.

• Ensure that gene flow from the natural 

population to the hatchery population is greater 

than gene flow from the hatchery to the natural 

population (pNOB > pHOS).

• Size program consistent with goals and the 

ability of the natural population to support 

hatchery broodstock requirements and gene flow 

limitations to the natural population

• Restrict natural spawning by HORs.

Likelihood of achieving natural adaptation: Lowest likelihood of all options 

in attaining stock goals in the immediate future since NORs incorporated into 

hatchery broodstock may themselves have suffered loss of productivity as a 

result of past hatchery influence. Likelihood of reaching stock goals increases 

as additional NORs are incorporated into the hatchery population through 

time or as proportion of NORs in hatchery broodstock is increased. 

Composite population is likely to have the lowest fitness in the natural 

environment of all the approaches. 

Cost: Increase in cost incurred for broodstock collection appears similar for 

all approaches. 

Effect on Harvest: Effect on harvest appears similar under all approaches 

other than Approach #2 in Scenarios 2 and 3. 

Approach #2 - Recommended approach if attaining harvest goal can be 

interrupted during transition to integrated program. Considerations: 

• Take steps to reduce the number of hatchery fish in the natural population to 

less than five percent of the natural population. (Reduce hatchery program, 

selective harvest to limit strays, weir, other measures to control straying)

• Allow a minimum of three to four generations to promote adaptation to the 

natural environment.

• Initiate a new hatchery program by collecting representative sample of 

natural fish.

• Collect a number of brood that allows for an effective population size of the 

composite population (natural plus hatchery) to be in excess of 500 fish.

• If a long-term goal of the hatchery program is to provide a conservation 

benefit, or if the natural spawning of hatchery-origin fish will be difficult to 

control, then the effective population size of the hatchery component should 

also be greater than 500 fish. 

• Incorporate a minimum of 10% NORs into hatchery broodstock each year.

• Ensure that gene flow from the natural population to the hatchery population 

is greater than gene flow from the hatchery to the natural population (pNOB 

> pHOS).

• For stocks of moderate or high biological significance and viability (or goals 

to maintain or improve the biological significance and viability of the stock) 

pNOB/(pHOS+pNOB) should be greater than 0.70.

• Size program consistent with goals and the ability of the natural population 

to support hatchery broodstock requirements and gene flow limitations to the 

natural population.

• Terminate segregated harvest program.

Likelihood of achieving natural adaptation: 

Intermediate likelihood of attaining stock goals 

because of the uncertainly of adaptation to the 

natural environment after three to four 

generations. The likelihood of meeting stock 

goals increases with the amount of time allowed 

before initiating new program and lower 

contribution of hatchery fish in the natural 

population. 

Cost: Increase in cost incurred for broodstock 

collection appears similar for all approaches. 

Effect on Harvest: Highest likelihood of loss of 

contribution to harvest of all the approaches since 

the segregated program would likely be reduced 

to allow adaptation of the natural stock and the 

segregated program would be terminated to 

initiate a new integrated program. 
HSRG/WDFW/NWIFC Technical Discussion Paper #1: Integrated Hatchery Programs 

June 21, 2004 8 

Scenario 3 (continued): Transition from an incompletely segregated program to an integrated program. (Most common 

scenario).

 Hatchery broodstock has had no systematic gene flow from the natural population 

 Natural spawning population has had significant influence from hatchery fish

Approach # 2 Plus Differential Marking - Recommended approach if attaining 

harvest goal cannot be interrupted during transition to integrated program Considerations 

• Take steps to reduce the number of hatchery fish in the natural population to less 

than five percent of the natural population (reduce hatchery program, selectively 

harvest to limit strays, use a weir or other measures to control straying).

• Allow a minimum of three to four generations to promote adaptation to the natural 

environment.

• Initiate a new hatchery program by collecting representative sample of natural fish.

• Collect a number of brood that allows for an effective population size of the 

composite population (natural plus hatchery) in excess of 500 fish.

• If a long-term goal of the hatchery program is to provide a conservation benefit, or if 

the natural spawning of hatchery-origin fish will be difficult to control, then the 

effective population size of the hatchery component should also be greater than 500 

fish.

• Differentially mark and release offspring of old/new broodstock. Preferentially use 

returns that represent the NOS broodstock. Phase out use of old broodstock as new 

broodstock returns.

• Incorporate a minimum of 10% NORs into hatchery broodstock each year once new 

broodstock returns.

• Ensure that gene flow from the natural to the hatchery population is greater than 

gene flow from the hatchery to the natural population (pNOB > pHOS).

• For stocks of moderate or high biological significance and viability (or goals to 

maintain or improve the biological significance and viability of the stock), 

pNOB/(pHOS+pNOB) should be greater than 0.70.

• Size program consistent with goals and the ability of the natural population to 

support hatchery broodstock requirements and gene flow limitations to the natural 

population.

Likelihood of achieving natural 

adaptation: Intermediate likelihood of 

attaining stock goals because of the 

uncertainly of adaptation to the natural 

environment after three to four generations. 

The likelihood of meeting stock goals 

increases with the amount of time allowed 

before initiating a new program and a 

lower contribution of hatchery fish in the 

natural population. 

Cost: Increase in cost incurred for 

broodstock collection appears similar for all 

approaches. An additional cost for 

differentially marking the two hatchery 

broodstocks would be incurred. Cost in 

terms of operational complexity is higher 

than all other approaches except Approach 

#4, but should be no greater than rearing an 

additional species. 

Effect on Harvest: Reduces loss of 

contribution to harvest during transition 

from the previous approach. 

References: 

Ford, M.J. 2002. Selection in captivity during supportive breeding may reduce fitness in 

the wild. Conservation Biology 16: 815-825. 

HSRG (Hatchery Scientific Review Group)–Lars Mobrand (chair), John Barr, Lee 

Blankenship, Don Campton, Trevor Evelyn, Tom Flagg, Conrad Mahnken, Robert 

Piper, Paul Seidel, Lisa Seeb and Bill Smoker. April 2004. Hatchery Reform: 

Principles and Recommendations of the HSRG. Long Live the Kings, 1305 Fourth 

Avenue, Suite 810, Seattle, WA 98101 (available from www.hatcheryreform.org). 

Mobrand, Lars. 1991. Regional Assessment of Supplementation Program (RASP). 

Project #1985-06200 (BPA Report DOE/BP-01830-11). Bonneville Power 

Administration, PO Box 3621, Portland, OR 97208. 

National Research Council Committee on Protection and Management of Pacific 

Northwest Anadromous Salmonids (NRC). 1996. Upstream: Salmon and Society in 

the Pacific Northwest, National Academy Press, Washington, DC. 

Williams, R. N., J. A. Lichatowich, P. R. Mundy, and M. Powell. 2003. Integrating 

artificial production with salmonid life history, genetic, and ecosystem diversity: a 

landscape perspective. Issue Paper for Trout Unlimited, West Coast Conservation 

Office, Portland. 
HSRG/WDFW/NWIFC Technical Discussion Paper #2: 

Segregated Hatchery Programs 

June 21, 2004 

Genetic and ecological interactions have been at the center of the debate over benefits 

and risks of hatchery programs (e.g., NRC 1995; HSRG 2004). The two options for 

managing these risks are either to minimize interaction through segregation (isolation) of 

the hatchery population from the natural population or to manage the hatchery population 

as an integral, benign component of a composite hatchery-natural population. All salmon 

and steelhead hatchery programs must be classified either as integrated or segregated by 

intent. These classifications lead directly to a series of genetic and ecological 

management guidelines for each of the two types of programs. How well programs meet 

this intent will vary; this variation provides an important measure for evaluating the 

biological risks posed by hatchery programs on natural populations. 

The purpose of this paper is to provide a definition of a segregated hatchery program, 

describe operational guidelines for implementation, and identify some of the implications 

and constraints imposed by the guidelines. 

Definition of a Segregated Hatchery Program 

The terms integrated and segregated describe the intended reproductive relationship of 

hatchery populations to naturally spawning populations. 

Formal Definition: A hatchery program is a Segregated Type if the intent is for the 

hatchery population to represent a distinct population that is reproductively isolated 

from naturally-spawning populations. 

Theoretical Premise for Segregated Programs 

Hatchery programs are classified as segregated if the hatchery population is propagated 

as a genetically discrete or segregated population relative to naturally spawning 

populations. The principal intent of a segregated program is to create a new, hatcheryadapted population to meet goals for harvest or other purposes (research, education, etc.). 

Hatchery broodstocks (and programs) are considered genetically segregated if the 

broodstock is maintained primarily or exclusively from adults returning back to the 

hatchery. As a consequence, little or no gene flow from a natural population to the 

hatchery broodstock is intended to occur in a segregated program. 

Natural spawning of fish from segregated programs may pose genetic and ecological 

risks to natural-spawning populations. The risks that segregated hatchery programs pose 

to natural populations depend on the status and goals for the natural populations, the 

extent to which hatchery-origin fish interact genetically and ecologically with naturalorigin fish, and on the amount of genetic and phenotypic divergence between the 

hatchery and natural populations. 
HSRG/WDFW/NWIFC Technical Discussion Paper #2: Segregated Hatchery Programs 

June 21, 2004 2

Operating Guidelines for Segregated Programs 

1. Each hatchery program should include a detailed genetic management plan for 

broodstock that outlines protocols, etc. 

2. Rear fish in a manner and/or at a location that minimizes potential straying and 

opportunities for natural spawning. 

3. Release fish in areas where opportunities to capture non-harvested adults are maximized, 

thus minimizing genetic risks to natural populations. 

4. Ensure adult production from segregated programs is commensurate with harvest 

opportunities. 

5. Take into consideration the potential selective impacts of harvest (for example, size 

selectivity) on the long-term viability of segregated programs. 

6. Ensure hatchery-origin adults constitute no more than five percent of the naturallyspawning population. 

7. Use marks, tags or other methods to distinguish natural- and hatchery-origin fish among 

natural spawners, in hatchery broodstocks and in harvests. 

8. Avoid unintentional inclusion of natural-origin adults in segregated broodstocks. 

9. Minimize the effects of predation and competition on naturally-spawning stocks when 

designing hatchery programs. 

Operational Considerations for Segregated Hatchery Programs 

Segregated programs, particularly those with only harvest goals, typically have few 

operational constraints. Segregated hatchery broodstocks may be bred selectively for 

particular traits (e.g., early run-timing), to facilitate ease of culture and/or to help achieve 

desired benefits (e.g., harvest). In general, segregated programs are managed in a way that 

maximizes productivity (i.e., recruits per spawner) or efficiency, irrespective of the ability of 

returning adults to reproduce naturally or confer any benefits to naturally spawning 

populations. Indeed, hatchery-origin fish from a genetically segregated program can impose 

unacceptable genetic and ecological risks to natural populations (Busack and Currens 1995). 

As a result, segregated programs often represent major trade-offs between minimizing 

biological risks to naturally spawning populations and maximizing efficiency and harvest 

benefits of the hatchery program. 

Many segregated hatchery programs in Puget Sound and coastal Washington have selectively 

bred adults, either purposefully or inadvertently, for “early” spawn or run timing, primarily 

by excluding late-returning adults from broodstocks. Many hatchery stocks of salmon and 

steelhead now return and spawn several weeks earlier than their natural-origin counterparts. 

Differences in return timing between natural- and hatchery-origin adults can be used as a 

management tool to focus fisheries on early-returning hatchery fish, while protecting latereturning natural fish. This approach can facilitate fisheries management from an agency 

perspective. 

Segregated programs can impose significant genetic risks to naturally spawning populations 

if non-harvested fish spawn naturally. Indeed, any natural spawning by fish from these 
HSRG/WDFW/NWIFC Technical Discussion Paper #2: Segregated Hatchery Programs 

June 21, 2004 3

broodstocks may be considered unacceptable, because of the potential genetic impacts on 

natural populations. Proponents of such “segregated” programs often argue that earlyreturning hatchery fish are mis-timed biologically to stream flows and water temperatures 

and, thus, fail to reproduce successfully even if they do spawn in nature. However, empirical 

and experimental evidence indicates that such early-returning hatchery fish do indeed 

reproduce successfully, albeit at a reduced rate relative to natural-origin fish (Chilcote et al. 

1986; Campton et al. 1991; Mackey et al. 2001). Although these hatchery-origin fish have a 

lower reproductive success relative to their natural-origin counterparts, their overall genetic 

and ecological risks can be substantial if hatchery-origin fish constitute a significant number 

of natural-origin spawners (Chilcote et al. 1986; Leider et al. 1990; Kostow et al., 2003). 

Clearly, the degree to which segregated hatchery programs are successful depends 

significantly on the degree to which genetic and ecological risks to natural populations can be 

minimized. Many segregated hatchery broodstocks also represent the genetic products of 

historical stock transfers among facilities or regions, thus further compounding the genetic 

and ecological risks that those programs may impose on naturally spawning populations. To 

minimize these risks, segregated hatchery programs need to be located in areas where 

virtually all returning adults can be harvested or recaptured, or where natural spawning or 

ecological interactions with natural-origin fish are considered minimal or inconsequential. 

Outplanting fish from segregated programs where effective adult recapture does not exist 

should be discontinued (see HSRG emerging issue paper on this topic). 

Implementing a Segregated Hatchery Program: 

Scenario 1: New Segregated Program 

No hatchery program exists 

Status of natural population in terms of past hatchery influence is not important

• Initiate the program with enough fish to provide a minimum effective population size of 500 fish. 

• Identify HORs and NORs; avoid unintentional inclusion of NORs in the broodstock

• Operate the program so that it does not create significant genetic or ecological interactions with natural populations 

(e.g., proper sizing, selective removal to limit strays, adult collection facilities or weir, long–term acclimation at point of

release, other measures to control straying).. 

• Ensure that the contribution of hatchery-origin fish spawning naturally does not exceed five percent of the natural 

spawning population. 

Scenario 2: Transition from a incompletely segregated or integrated program to a properly segregated program (Most 

common scenario for both incompletely segregated and incompletely integrated programs) 

Hatchery broodstock has had no systematic gene flow from the natural population 

Natural spawning population has had significant influence from hatchery fish 

• Identify HORs and NORs; avoid unintentional inclusion of NORs in the broodstock.

• Operate the program so that it does not create significant genetic or ecological interactions with natural populations 

(e.g., proper sizing, selective removal to limit strays, adult collection facilities or weir, long–term acclimation at point of

release, other measures to control straying).. 

• Ensure that the contribution of hatchery-origin fish spawning naturally does not exceed five percent of the natural 

spawning population.

Scenario 3: Transition from a well integrated program to a segregated program 

Hatchery broodstock has had systematic gene flow from the natural population 

Gene flow from the natural population to the hatchery population has been greater than gene flow from the 

hatchery to the natural population 
HSRG/WDFW/NWIFC Technical Discussion Paper #2: Segregated Hatchery Programs 

June 21, 2004 4

• Identify HORs and NORs; avoid unintentional inclusion of NORs in the broodstock. 

• Operate the program so that it does not create significant genetic or ecological interactions with natural populations 

(e.g., proper sizing, selective removal to limit strays, adult collection facilities or weir, long–term acclimation at point of

release, other measures to control straying).. 

• Ensure that the contribution of hatchery-origin fish spawning naturally does not exceed five percent of the natural 

spawning population 

References: 

Busack, C. A., and K. P. Currens. 1995. Genetic risks and hazards in hatchery 

operations: Fundamental concepts and issues. Pages 71-80 in H. L. Schramm , Jr. 

and R. G. Piper, editors. Uses and effects of cultured fishes in aquatic ecosystems. 

American Fisheries Society Symposium 15, Bethesda, MD. 

Campton, D. E., Allendorf, F. W., Behnke, R. J., Utter, F. M., Chilcote, M. W., Leider, S. 

A., and Loch, J. J. 1991. Reproductive success of hatchery and wild steelhead. 

Transactions of the American Fisheries Society 120: 816-827. 

Chilcote, M. W., S. A. Leider, and J. J. Loch. 1986. Differential reproductive success of 

hatchery and wild summer-run steelhead under natural conditions. Transactions of 

the American Fisheries Society 115: 726-735. 

HSRG (Hatchery Scientific Review Group)–Lars Mobrand (chair), John Barr, Lee 

Blankenship, Don Campton, Trevor Evelyn, Tom Flagg, Conrad Mahnken, Robert 

Piper, Paul Seidel, Lisa Seeb and Bill Smoker. April 2004. Hatchery Reform: 

Principles and Recommendations of the HSRG. Long Live the Kings, 1305 Fourth 

Avenue, Suite 810, Seattle, WA 98101 (available from www.hatcheryreform.org). 

Kostow, K. E., A. R. Marshall, and S. R. Phelps. 2003. Naturally spawning hatchery 

steelhead contribute to smolt production but experience low reproductive success. 

Transactions of the American Society 132:780-790. 

Leider, S. A., P. L. Hulett, J. J. Loch, and M. W. Chilcote. 1990. Electrophoretic 

comparison of the reproductive success of naturally spawning transplanted and wild 

steelhead trout through the returning adult stage. Aquaculture 88: 239-252.Mackey et 

al. 2001 

Mackey, G., J.E. McLean, T.P. Quinn. 2001. Comparisons of run timing, spatial 

distribution and length of wild and newly established hatchery populations of 

steelhead in Forks Creek, Washington. N. Am. J. Fish. Mgmt. 21:717-724. 

National Research Council Committee on Protection and Management of Pacific 

Northwest Anadromous Salmonids (NRC). 1996. Upstream: Salmon and Society in 

the Pacific Northwest, National Academy Press, Washington, DC. 
1

HSRG Technical Discussion Paper #3 

When Do You Start A Conservation Hatchery Program? 

March 7, 2005 

The potential use of hatcheries as a recovery tool for Pacific salmon has consistently raised the 

following questions: When is it appropriate to start a conservation hatchery program for a 

declining or imperiled stock? When does the risk of extinction, or negative genetic effects 

associated with small population size, exceed the risk of hatchery intervention? 

Several generalized guides have been published regarding the use of artificial propagation for 

stocks of Pacific salmon at risk (e.g., Hard et al. 1992, Brannon 1993, Brannon et al. 1998, Flagg 

and Nash 1999, ISAB 2003, Williams et al. 2003, Flagg et al. 2004). Four key population 

parameters can be used to assess the viability of salmon populations: abundance, growth rate, 

spatial structure, and diversity (McElhany et al. 2000). However, most current guidelines go 

little further than suggesting that the best time to intervene with a conservation program depends 

on the particular stock of fish, its level of depletion, the physical and management limitations of 

each individual hatchery action, and the biodiversity of the ecosystem. 

Biological significance 

A key factor in determining the need for a conservation action will be the biological significance 

of the stock. Biological significance is a function of the stock’s origin, inherent genetic diversity, 

biological attributes and uniqueness, local adaptation, and the genetic structure of the population 

relative to other conspecific populations. A population can be considered highly significant if it 

exhibits unique genetic and biological attributes that are not shared with other conspecific 

populations. These attributes may include unique life history, physiological, morphological, 

behavioral, and/or disease resistance characters, each determined in part by genetic factors. 

Genetic diversity 

Genetic diversity refers to the magnitude and distribution of genetic variation within and among 

individuals, as characterized by genetic components of phenotypic variance and population 

heterozygosities (Falconer and MacKay 1996). Genetic variation is important because it provides 

the foundation for responses to selection (natural or artificial) and local adaptations. Population 

viability in dynamic environments is directly related to genetic variation; that is, the fitness and 

productivity of a population in environments that vary temporally or spatially will be determined 

largely by the capacity of the population to adapt genetically (e.g., Falconer and MacKay 1996; 

Franklin 1980). Genetic diversity can be measured by estimating population and quantitative 

genetic parameters (i.e., allele frequencies at molecular loci and genetic components of 

phenotypic variance for life history traits). 
2

One of the most important parameters affecting genetic diversity is effective population size 

(Ne). Effective population size places an upper limit on the amount of genetic diversity that can 

be maintained in a population or species relative to its pedigree history and potential future 

losses due to genetic drift. Some general guidelines for maintaining minimum Ne in distinct 

populations have been proposed: 

• Ne > 50 to prevent inbreeding depression and a detectable decrease in viability or 

reproductive fitness of individuals in a population (Franklin 1980). 

• Ne > 500 to maintain constant genetic variance in a population resulting from a 

balance between loss of variance due to genetic drift and the increase in variance due 

spontaneous mutations (Franklin 1980; Soule 1980; Lande 1988) 

• Ne > 5,000 to maintain a constant variance for quasi-neutral genetic variation that can 

serve as a reservoir for future adaptations in response to natural selection and 

changing environmental conditions (Lande 1995). The rationale here is that Ne should 

be large enough to minimize genetic drift and the potential loss of “neutral” alleles 

that may confer fitness advantages under changing environmental conditions and new 

selection regimes. 

• The Ne > 5,000 rule applies primarily to an entire ESU or species over evolutionary 

time scales, whereas Ne > 50 applies primarily to closed, local populations over very 

short time scales (2-5 generations). However, the same basic principles apply to both 

local populations and entire species in both situations. For example, all individuals of 

a species with Ne < 50 are expected to show reduced viability due to inbreeding 

depression after a few generations. 

Imbalances among parameters affecting Ne can indicate needs for conservation intervention. For 

example, a detailed analysis of Ne in fluctuating populations may involve a distinction between 

the inbreeding effective number (NeI) and the variance effective number (NeV) (Crow and 

Denniston 1988; Simberloff 1988). The inbreeding effective size quantifies the increase in 

inbreeding – or the probability that two genes are identical by descent - over generations, while 

the variance effective size predicts the amount of genetic drift and the rate of loss of 

heterozygosity (Ryman et al. 1995). When population numbers are stable, NeI and NeV are nearly 

identical and constant over time, while in a rapidly declining population NeI may be much larger 

than NeV. 

Age class structure also affects effective population size. The effective population size of a 

population with overlapping generations is approximately the mean effective number of breeders 

per year, multiplied by the generation time, or average age of spawners, in years (Waples 1990). 

A complex age structure, with many overlapping generations tends to diminish the likelihood of 

a small population going extinct in a particular year in which an environmental disaster occurs. 
3

Population trends 

Viable salmon populations, whether natural or hatchery supplemented, exhibit a high intrinsic 

capacity for population growth. When abundance is reduced (e.g., due to environmental 

catastrophe or catastrophic harvest) the population can subsequently respond with a rapid 

increase in abundance, provided habitat of sufficient quantity and quality is available, ocean 

productivity is favorable, and the population has adequate genetic variation to respond 

demographically and maintain phenotypic resiliency. Extended periods of population depression 

are evidence either of diminished ecological productivity of habitat (or of the hatchery 

environment) or reduced genetic viability. Thus, trends of abundance and of variance of 

abundance over time can be indicators of population viability. More specifically, trends in 

productivity (adult progeny per parent - recruits/spawner) under stable environmental conditions 

are good indices of population viability. 

Salmon biologists may be required to determine the threshold population abundance at which 

hatchery propagation should be employed to reduce the demographic and genetic risks of 

extinction, including preventing losses of genetic diversity due to small population size. The 

threshold is not easy to define because several factors must be considered simultaneously. These 

factors include (a) the genetic effective size of the declining population, (b) the general trend or 

mean rate of decline per year over the past 2-5 generations, and (c) the magnitude and frequency 

of temporal, stochastic variations in abundance, including potential Allee effects (Dennis 2002). 

For example, a regression analysis of trend of abundance may predict extinction within 100 

years; however, if the inter-annual variance in abundance exceeds the mean rate of decline, then 

stochastic fluctuations are likely to result in either earlier extinction or substantial reductions in 

genetic diversity due to population bottlenecks. Reduction in genetic diversity could further 

reduce population resiliency and, thus, accelerate the rate of decline in an extinction vortex

(Tanaka 2000). 

Numerical Thresholds 

Here, we provide numerical threshold guidelines for initiating hatchery propagation of declining 

or imperiled populations of Pacific salmon and steelhead. The guidelines are simplistic because 

they only consider potential losses of genetic variation due to small effective population size. In 

practice, demographic factors related to the rate of decline and temporal variances in abundance 

would also be considered. Despite these limitations, the guidelines below are applicable to all 

situations where a reproductively-distinct, local population – or stock - of high biological 

significance may be imperiled. The rationale applied here is that some intervention may be 

desirable when a biologically unique population approaches a threshold level of abundance, 

below which declines in genetic diversity are expected due to reduced effective population sizes. 

Genetic models indicate that populations with genetic effective population sizes (Ne) greater than 

500 (Ne > 500) can maintain equilibrium levels of genetic diversity by minimizing losses due to 

genetic drift (Lande and Barrowclough 1987; Lande 1995). Consequently, a minimum threshold 

effective population size at which artificial propagation might first be considered would be: 

 Ne = 500 (1). 
4

For Pacific salmon and other semelparous species with overlapping generations, the genetic 

effective size of a population over a single generation equals the product of (a) the mean 

effective number of breeders per year ( Nb ) and (b) the generation time (g) or average age of 

spawners (Waples 2002): 

 Ne = Nb · g (2). 

Combining equations (1) and (2) yields the following population threshold, measured in terms of 

the effective number of breeders per year, at which hatchery propagation might be implemented 

as a conservation measure: 

 Nb = 500/g (3). 

For Chinook salmon (O. tshawytscha) or steelhead (O. mykiss), g is approximately 4 years. 

However, for pink salmon (O. gorbuscha), g = 1 because of their discrete 2-year life history; that 

is, the entire population spawns in a single year, every other year, and its generations do not 

overlap. 

For naturally spawning populations of Pacific salmon, the best available empirical data indicate 

that Nb, the effective number of breeders in a single year, is approximately one-tenth (0.10) to 

one-third (0.33) the observed number, or “census number” (Nc), of adults spawning naturally 

(Waples 2004). This difference between Nc and Nb results from the naturally high variance of 

reproductive success among individual fish: many adults produce no progeny, and some males 

may fertilize eggs from several females. If we assume that the variance of individual 

reproductive success among adults decreases as a compensatory mechanism for reduced 

population sizes and lower spawning densities (e.g., Ardren and Kapuscinski 2003), then we can 

assume that Nb is near the upper range of the estimated values, or approximately one-third the 

census number of naturally-spawning adults: 

 Nb = 0.33Nc (4). 

Combining equations (3) and (4) thus yields the following threshold at which hatchery 

propagation might be implemented as a conservation measure: 

 Nc =1500/g (5), 

where Nc is the mean, census number of spawning adults per year over one full generation (g). 

The threshold indicated by equation (5) varies among species depending on the generation time 

(average age at reproduction) of the population under consideration. For example, if chinook 

salmon have a generation time of four years, then hatchery propagation of a biologically 

significant population might be considered when the mean number of spawners per year - over a 

four-year period – approaches or declines below 375 adults/year (1500/4 = 375). 
5

Numerical effects of hatchery conservation on wild populations 

When considering the trapping and removal of natural-origin adults for conservation 

propagation, biologists and managers must also consider the effective number of breeders in the 

hatchery and the effective number of breeders remaining in the wild after adults are removed for 

artificial spawning. In this context, genetic viability and Nb for adult spawners in the hatchery 

need to follow the same genetic guidelines as those for natural populations (eq. 3). These 

guidelines for both the naturally-spawning and hatchery-spawned components allow the genetic 

effective population sizes of both components to each exceed desirable values (Ne > 500), thus 

circumventing potential Ryman-Laikre effects (Ryman and Laikre 1991; Ryman et al. 1995) if 

the hatchery program is highly successful. Moreover, this strategy reduces the risk of extinction 

equally between the two components in the event of catastrophic loss or extinction of either 

component. That is, a minimum effective population size may still be retained if either the 

hatchery or natural-origin component of the population (or gene pool) suffers a catastrophic loss. 

For adults spawning in a hatchery in a particular year, Nb in the hatchery will, most likely, be 

approximately equal to the actual number of adults spawned (NH) because mating and 

reproduction are controlled, and the variance of reproductive success among spawners can be 

similar to theoretical expectations for an “idealized” population (Campton 2004). Therefore, 

hatchery managers can protect the genetic viability of the hatchery portion of the population by 

keeping the number of adults trapped and spawned in the hatchery each year (NH) above the 

threshold: 

 NH > 500/g (6). 

Similarly, biologists can protect the viability of the population in the wild by ensuring that the 

number of adults remaining in the wild to spawn naturally (NW), after adults are removed for 

hatchery propagation, follows equations 3 and 5. These constraints collectively prescribe a series 

of minimum population-abundance thresholds at which hatchery propagation might 

appropriately be implemented as a conservation measure (Table 1). 

For a declining population of Chinook salmon, for example, hatchery propagation might first be 

considered when the mean census number of returning adults declines to near Nc = 500 adults per 

year. If a hatchery program is implemented, then a minimum of NH = 125 adults per year should 

be trapped and spawned artificially for four consecutive years, thus leaving a minimum of NW = 

375 adults each year to spawn naturally. At these minimum thresholds, the effective population 

size for each of the hatchery and naturally spawning components over a single generation would 

be approximately Ne = 500 (assuming no population bottleneck in a preceding generation). Thus, 

catastrophic loss of either component would still allow a minimum Ne to be retained. 

Multiple generations 

The objectives of a conservation hatchery program, as outlined here, are to: (1) provide a 

demographic increase in the total number of returning adults; (2) allow natural spawning by 

hatchery-origin adults with the goal of increasing natural reproduction and the total number of 

natural-origin adults returning in subsequent generations; and (3) maintain Ne > 500 to minimize 
6

potential losses of genetic variation due to small effective population sizes and genetic drift. At 

least two full generations are necessary to realize these objectives. Consequently, first-generation 

hatchery-origin fish would be returning and spawning in the wild when a second generation of 

hatchery propagation would be implemented. This latter situation raises the following question: 

What number and composition (% hatchery and % wild) of adults should the hatchery remove 

and spawn during the second generation of hatchery propagation? 

Our conclusions regarding this question are: (1) the total number of adults spawned artificially 

during the second generation should follow the same guidelines presented in Table 1; and (2) the 

percent composition of natural and hatchery-origin fish in the hatchery broodstock should be the 

same as the composition of the two groups among all returning adults. Thus, adult fish trapped 

for broodstock should be selected randomly among all returning fish with the goal of achieving 

the minimum broodstock sizes (NH) outlined in Table 1 for each species. This latter approach 

would result in the same spawner compositions for both the hatchery and natural environments. 

Such guidelines would automatically reduce the proportion of the total number of returning 

adults taken into the hatchery each year if the hatchery program was successfully meeting its 

objectives after one generation (i.e., NH/Nc in generation 2 would be less than the value of this 

ratio in the initial generation of hatchery propagation if the hatchery program was meeting its 

objectives). If the objectives of the hatchery program are met after two generations of 

propagation, then the program could be suspended or terminated, but with monitoring and 

evaluation (M&E) of adult returns continuing to assess overall extinction risks and the success of 

hatchery supplementation. 

For example, a near-term management strategy might “pulse” hatchery-produced fish into the 

population for two generations, followed by suspension of hatchery propagation for one to two 

generations to assess, via M&E, overall population responses and subsequent extinction risks. 

The hatchery program could be reinstituted at a later date, if necessary, until the causes of the 

original population declines were rectified. Alternatively, an integrated hatchery program could 

be developed with no immediate “sunset” clause if the factors responsible for the decline were 

expected to continue indefinitely (e.g., the presence of a hydropower facility). 

Overall, we believe the guidelines presented here provide a relatively simple, first-step approach 

for assessing the potential need for a conservation hatchery program when a population of high 

biological significance exhibits significant declines in abundance over at least one full 

generation. When the threshold levels of abundance outlined here are approached (Table 1), then 

demographic models of population viability could be invoked to predict extinction probabilities 

and mean times of persistence. However, the approach outlined here assumes that one goal of a 

conservation hatchery is to prevent significant losses of genetic variation before a population is 

at imminent risk of extinction. 

Literature cited 

Allendorf, F.W. 1993. Delay of adaptation to captive breeding by equalizing family size. 

Conservation Biology 7:416-417. 
7

Ardren, W.R., and A.R. Kapuscinski. 2003. Demographic and genetic estimates of effective 

population size (Ne) reveal genetic compensation in steelhead trout. Molecular Ecology 

12:35-49. 

Brannon, E. L. 1993. The perpetual oversight of hatchery programs. Fisheries Research (Amst.) 

18:19-27. 

Brannon, E., and six coauthors. 1998. Review of salmonid artificial production in the Columbia 

River Basin. Report 98-33, Northwest Power Planning Council. Portland, OR. 

Campton, D.E. 2004. Sperm competition in salmon hatcheries: the need to institutionalize 

genetically benign spawning protocols. Trans. Am. Fish. Soc. 133:1277-1289. 

Crow, J.F., and C. Denniston. 1988. Inbreeding and variance effective population numbers. 

Evolution 42:482-495. 

Dennis, B. 2002. Allee effects in stochastic populations. Oikos 96:389-401. 

Falconer, D. S. and T. D. F. MacKay. 1996. Introduction to Quantitative Genetics, 4th ed. 

Longman Press. London. 

Flagg, T.A. and C.E. Nash (editors). 1999. A conceptual framework for conservation hatchery 

strategies for Pacific salmonids. U.S. Dep. Commer., NOAA Tech. Memo. 

NMFS-NWFSC-38, 48 p. 

Flagg, T.A., R.N. Iwamoto, and C.V.W. Mahnken. 2004. Conservation hatchery protocols for 

Pacific salmon. Am. Fish. Soc. Symp. 44:603-619. 

Franklin, I. R. 1980. Evolutionary change in small populations. Pages 135-149 in M. E. Soule 

and B. A. Wilcox, editors. Conservation biology: An evolutionary-ecological perspective. 

Sinauer Assoc., Sunderland, MA. 

Hard,J.J., R.P. Jones, M.R. Delarm, and R.S. Waples. 1992. Pacific salmon and artificial 

propagation under the Endangered Species Act, NOAA Technical Memorandum NMFSNWFSC-2, Seattle. 

ISAB. 2003. Review of salmon and steelhead supplementation. Independent Scientific Advisory 

Board for the Northwest Power Planning Council, ISAB Review 2003-03, 229 p. 

Lande, R. 1995. Mutation and conservation. Conservation Biology 9:782-791. 

Lande, R. 1988. Genetics and demography in biological conservation. Science 241:1455-1460. 

Lande, R., and G.F. Barrowclough. 1987. Effective population size, genetic variation, and their 

use in population management. Pages 87-123. In: Soule, M.E. Viable populations for 

conservation. Cambridge University Press, Cambridge and New York. 

McElhany, P., M.H.Ruckelshaus, M.J. Ford, T.C. Wainwright, and E.P. Bjorkstdt. 2000. Viable 

salmon populations and the recovery of evolutionary significant units. NOAA Technical 

Memorandum NMFS-NWFSC-42, Seattle. 

Ryman, N., and L. Laikre. 1991. Effects of supportive breeding on the genetically effective 

population size. Conservation Biology 5:325-329. 

Ryman, N., P.E. Jorde, and L. Laikre. 1995. Supportive breeding and variance effective 

population size. Conservation Biology 9:1619-1628. 

Simberloff, D. 1988. The contribution of population and community biology to conservation 

science. Annual Review of Ecology and Systematics 19:473-511. 

Soule, M. E. 1980. Thresholds for survival: Maintaining fitness and evolutionary potential. Pages 

151-169 in M. E. Soule and B. A. Wilcox, editors. Conservation biology: An 

evolutionary-ecological perspective. Sinauer Assoc., Sunderland, MA. 

Tanaka, Y. 2000. Extinction of populations by inbreeding depression under stochastic 

environments. Population Ecology 42:55-62. 
8

Williams, R.N., J.A. Lichatowich, P.R. Mundy, and M.S. Powell. 2003. Integrating artificial 

propagation with salmonid life history, genetic, and ecosystem diversity: a landscape 

perspective, Issue Paper for Trout Unlimited, West Coast Conservation Office, Portland, 

4 September 2003, 83 p. 

Waples, R. S. 1990. Conservation genetics of Pacific salmon .III. Estimating effective population 

size. J. Hered. 81: 77-289. 

Waples, R.S. 2002. The effective size of fluctuating salmon populations. Genetics 161:783-791. 

Waples, R. S. 2004. Salmonid insights into effective population size. Pp. 295-314 in A. P. 

Hendry and S. C. Stearns, eds. Evolution illuminated: Salmon and their relatives. Oxford 

University Press, Oxford, UK.
9

 Table 1. Threshold spawner abundances below which a conservation hatchery program 

should be considered for a declining natural population. The implicit assumption here is 

that the mean census number of adults per year will continue decline below the threshold 

level in the absence of artificial propagation. Thresholds vary by species, depending on 

generation time and year class overlap. The threshold numbers shown below (Nc) are 

based on the general principle that the total effective number of breeders over one full 

generation should be at least 500 (Ne > 500) in each of the hatchery and wild 

components. NH is the number of adults required for the hatchery program. 

Number of Adults 

Species 

No. of 

years per 

generation 

(avg. age of 

spawners) 

(g) 

Threshold 

mean census 

number of 

adults/year 

(Nc) 

Hatchery 

(NH) 

Natural 

Environment 

(NW = Nc - NH) 

Resulting 

effective number 

of breeders per 

year in natural 

environment 

(Nb = 0.33NW) 

Chinook salmon 4 500 125 375 125 

Chum salmon 4 500 125 375 125 

Coho salmon 2.7 750 186 564 188 

Pink salmon 1 2000 500 1500 500 

Sockeye salmon 3.5 575 144 431 144 

Steelhead 4 500 125 375 125 
THE NEED

ABOUT THE PROJECT

HSRG

REFORM PRINCIPLES

REGIONAL REVIEWS

IMPLEMENTATION

PUBLICATIONS

CONTACT US

HSRG 

RECOMMENDATIONS 

HSRG RESEARCH GRANTS

CATEGORY A: SUSTAINABLE FISHERIES

Project Description Principal Investigators Year Funded

Development of Field Methods to Determine the Effects of 

Hatchery Release Methods on Residualism and 

Interactions Between Hatchery and Wild Juvenile 

Salmonids in Relation to Stream Carrying Capacity

Howard Fuss, WDFW; 

Stephen Riles, NOAA 

Fisheries

2000

Commercial Selective Harvest of Coho Salmon and 

Chinook Salmon on the Willapa River Using Tangle Nets 

and Gill Nets

Geraldine 

VanderHaegen, WDFW

2001

Impacts of Size Selective Gillnet Fisheries on Puget Sound 

Coho Salmon Populations

Curtis Knudsen, Steve 

Phelps and Craig 

Busack, WDFW

2001

Salmon Marine Trophic Demand-Distribution David Beauchamp, UW 2003

CATEGORY B: RECOVER AND CONSERVE NATURAL SPAWNING POPULATIONS

Project Description Principal Investigators Year Funded

Genetic Characterization of Lake Ozette Sockeye Salmon Ken Currens, NWIFC; 

Jim Shaklee, WDFW; 

Michael Crewson, Makah 

Tribe

2000

White River Acclimation Pond Evaluation Chuck Baranski, WDFW; 

Blake Smith, Puyallup 

Tribe; Richard Johnson, 

Muckleshoot Tribe

2001

Differences in Natural Production Between Hatchery and 

Wild Coho Salmon

Anne Marshall, WDFW, 

and Dr. Mike Ford, NOAA 

Fisheries

2005

Comparing the Success of Three Fish Cultural Strategies 

Implemented to Recover Snow Creek Coho Salmon 

Steve Schroder, WDFW 2001

Evaluation of Conservation Hatchery Rearing and Release 

Strategies for Steelhead Recovery in the Hamma Hamma 

River 

Barry Berejikian, NMFS 2004

CATEGORY C: IMPROVE QUALITY AND COST-EFFECTIVENESS OF HATCHERY PROGRAMS 
Project Description Principal Investigators Year Funded

Development of Engineered Streams for Salmon 

Production 

Ernest Brannon, UI 2001

Increase Post-Release Survival by Rearing Coho with 

NATURES Semi-Natural Raceway Habitat 

Desmond Maynard, 

NOAA Fisheries

2001

Using Semi-Natural Rearing Habitat to Improve SmoltAdult Survival of Chinook Salmon Geraldine 

VanderHaegen, WDFW; 

Bill St. Jean, Nisqually 

Tribe

2005

Development of BKD Vaccine Jed Varney, WDFW N/A

Nature vs. Nurture: Do Hatchery Practices Impair Brain 

Development and Compromise Fitness of Salmon?

Penny Swanson, NOAA 

Fisheries

2001

CATEGORY D: PROTECT GENETIC RESOURCES 

Project Description Principal Investigators Year Funded

Interactions between Wild and Hatchery Steelhead: 

Evaluating Key Assumptions 

Thomas Quinn, UW 2002

Residualism in Wild and Domesticated Broodstock 

Steelhead Trout (Oncorhynchus mykiss): growth 

modulation during juvenile rearing can reduce rates of 

residualism 

Cameron Sharpe, WDFW 2001

Olfactory Imprinting in Hatchery Salmon Andrew Dittman, NOAA 

Fisheries

N/A

CONTACT US | HOME
THE NEED

ABOUT THE PROJECT

HSRG

REFORM PRINCIPLES

REGIONAL REVIEWS

IMPLEMENTATION

PUBLICATIONS

CONTACT US

HSRG 

RECOMMENDATIONS 

Hatchery Scientific Review Group Meeting Summaries 

2004

February 2004 Meeting

April 2004 Meeting

May 2004 Meeting

June 2004 Meeting

July-September 2004 Meetings

October 2004 Meeting

November 2004 Meeting

December 2004 Meeting 

2003

January 2003 Meeting

February 2003 Meeting

March 2003 Meeting

April 2003 Meeting

May 2003 Meeting

June 2003 Meeting

July 2003 Meeting

August 2003 Meeting

September 2003 Meeting

October 2003 Meeting

November 2003 Meeting

December 2003 Meeting

2001

January 2001 Meeting

February 2001 Meeting

March 2001 Meeting

April 2001 Meeting

May 2001 Meeting

June 2001 Meeting

July 2001 Meeting

August 2001 Meeting

September 2001 Meeting

October 2001 Meeting

November 2001 Meeting

December 2001 Meeting

2000

March 2000 Meeting

April 2000 Meeting

May 2000 Meeting

June 2000 Meeting

July 2000 Meeting

August 2000 Meeting

September 2000 Meeting

October 2000 Meeting

December 2000 Meeting

2002

January 2002 Meeting

February 2002 Meeting

March 2002 Meeting

April 2002 Meeting

May 2002 Meeting

June 2002 Meeting

July 2002 Meeting

August 2002 Meeting

September 2002 Meeting

October 2002 Meeting

November 2002 Meeting

December 2002 Meeting

CONTACT US | HOME


INTRODUCTION

The Hatchery Reform Project

The Puget Sound and Coastal Washington Hatchery Reform Project (HRP) is a systematic, science-driven redesign of hatcheries to meet two new goals: 

1. Helping to recover and conserve naturally spawning salmonid populations. 

2. Supporting sustainable fisheries. 

The HRP was created by the U.S. Congress in 2000 with the support of Congressman

Norm Dicks (D-Wash), U.S. Senator Patty Murray (D-Wash), Washington Governor Gary

Locke and former U.S. Senator Slade Gorton.

This is the first independent scientific evaluation of hatchery programs against measurable goals, on a watershed scale, in the context of what the habitat can support and the

potential impact of the programs on every stock in the watershed.

Role of Hatcheries in Washington State

There are approximately 100 hatchery facilities in Puget Sound and coastal

Washington operated by the Washington State Department of Fish and Wildlife

(WDFW), Puget Sound and coastal Indian Tribes and Nations and the U.S. Fish and

Wildlife Service (USFWS). In operation for decades (some for over 100 years), these

hatcheries were built for differing purposes ranging from mitigation for lost habitat to

creating a fishery where none existed previously, and from meeting tribal trust responsibilities to helping to conserve genetic diversity and rebuild struggling populations.

Most hatcheries were built to produce fish for harvest, compensating for declines in

naturally spawning salmon populations. Hatcheries are very important to the North

Pacific sports and commercial fishing economy. They also play an important role in

meeting tribal treaty harvest obligations.

Hatcheries have generally been successful at fulfilling these purposes. However, they

have also been identified as one of the factors responsible for the depletion of naturally

spawning salmon stocks. Some facilities have created stresses for naturally spawning

fish, kept smolts from getting downstream and spawning fish from getting upstream and

lowered water quality. Physical and genetic interactions between naturally spawning and

hatchery fish may have weakened natural stocks. Hatchery management decisions have

often been piecemeal, not systemwide.

Hatchery Reform: A New Direction

Several Puget Sound and coastal salmon and steelhead stocks are listed or proposed

for listing under the federal Endangered Species Act (ESA). As part of a larger recovery

process, state, tribal and federal managers of Washington’s salmon and steelhead must

1
ensure their hatcheries do not present a risk to listed species. But the managers are

going beyond merely complying with ESA directives that hatcheries be operated to minimize risks to endangered fish. There is also an opportunity for hatcheries to provide

benefits to the recovery process, in addition to providing harvest, educational and cultural benefits. The managers have established a Hatchery Reform Coordinating Committee

(Coordinating Committee) as a vehicle for cooperative management on this reform effort.

The Northwest Indian Fisheries Commission (NWIFC), WDFW, USFWS, NOAA

Fisheries, Long Live the Kings (LLTK) and the Congressional Hatchery Science Advisory

Team are all represented on this committee.

The Hatchery Scientific Review Group

The Hatchery Scientific Review Group (HSRG) is the independent scientific panel established and funded by Congress to evaluate hatchery reform programs in Puget Sound

and coastal Washington. The objective of the HSRG is to assemble, organize and apply

the best available scientific information to provide guidance to policy makers who are

implementing hatchery reform.

The HSRG is composed of five independent scientists (selected from a pool of candidates nominated by the Past Presidents Council of the American Fisheries Society) and

four agency scientists designated by WDFW, NWIFC, NOAA Fisheries and USFWS. The

nine scientists serving on the HSRG have a broad range of experiences. Their scientific

disciplines range from biology, genetics, ecology, fisheries, fish culture, fish pathology,

and biometrics to other disciplines. Members include:

• John Barr, NWIFC (Vice Chair)

• Lee Blankenship, Northwest Marine Technology (Vice Chair)

• Donald Campton, PhD, USFWS

• Trevor Evelyn, PhD, retired, Department of Fisheries and Oceans Canada

• Conrad Mahnken, PhD, NMFS Manchester

• Lars Mobrand, PhD, Mobrand Biometrics (Chair)

• Lisa Seeb, PhD, Alaska Department of Fish & Game

• Paul Seidel, WDFW

• William Smoker, PhD, University of Alaska

The third party facilitator specified by Congress is LLTK, a private, nonprofit organization

whose mission is to restore wild salmon to the waters of the Pacific Northwest. LLTK’s

role includes providing facilitation and project management to the HSRG and the

Coordinating Committee, and helping the managers communicate hatchery reform

progress to Congress, state legislators, stakeholder groups and the public. LLTK

retained Gordon, Thomas, Honeywell to serve on the facilitation team.

Applying a Scientific Approach to Hatchery Management

In the HRP’s first year, the HSRG developed a number of tools to assist with the reviews

and for the managers’ use. These tools have been essential to the project’s methodical

2
and scientific review of hatchery programs. They include 1) a scientific framework that

underlies and informs the group’s tools, processes and recommendations; 2) a process

that assesses benefits and risks associated with specific actions and choices in hatchery

management; 3) hatchery operational guidelines consistent with the scientific framework;

4) a research program to fill information gaps (to date, the HSRG has funded four

rounds of research on marine environments, hatchery and rearing environments, physiology and disease, and ecological and genetic interactions between hatchery and wild

salmonids); and 5) monitoring and evaluation criteria for determining the success of

hatchery programs and for gathering data for research and adaptive management.

Early in the process, the HSRG and Coordinating Committee agreed that it is important

to evaluate hatchery programs in the context of the watersheds in which they operate

and the goals set forth by the managers. For this reason, they divided Puget Sound and

the coast into ten regions, providing an opportunity to make region-by-region recommendations based on 1) regional management goals for conservation, harvest and other purposes; 2) stock status (biological significance and population viability); 3) habitat status

(current and future); and 4) the particulars of each hatchery program.

This document summarizes area-wide and specific recommendations developed by the

HSRG upon reviewing the first six regions during 2001 and 2002. Recommendations on

the remaining four regions will be added after they are reviewed in 2003. 

3
AREA-WIDE RECOMMENDATIONS

This section describes reform measures applicable to the entire Puget Sound and

coastal Washington area, and wherever hatcheries are used as tools to help meet harvest, conservation or other goals for the fish resource. The HSRG has concluded that

three general principals should guide hatchery reform: 1) Goals, 2) Scientific

Defensibility, and 3) Informed Decision Making. 

1. GOALS

The HSRG has observed that goals for the fish resource are not always explicitly communicated and/or fully understood by the managers and operators of hatchery programs.

It is not uncommon for the direct hatchery output (i.e., numbers or pounds of juveniles

released) to be cited as the goal by which the program’s success is measured. 

Goals for the resource should be expressed in terms of values to the community (harvest, conservation, education, research, employment, recreation, etc.), and once they

are, hatcheries can serve as a tool to help meet those goals. Harvest goals include production of salmon as a commercial food commodity, and the provision of fish for recreational opportunities and ceremonial and subsistence purposes. Conservation goals

include endangered species protection and recovery, environmental aesthetics, maintenance of cultural values and traditions, etc.

Hatcheries are by their very nature a compromise, a balancing of benefits and risks to

the target stock, other stocks and the environment affected by the hatchery program.

The use of a hatchery program is appropriate when the balance of benefits and risks is

more favorable than that associated with other strategies for meeting similar goals.

Thus, in addition to the goals for the stock targeted by the hatchery program, the regional context (the status of and goals for the habitat and other stocks) affects the appropriate role of the hatchery program. 

The HSRG has developed the following recommendations to help ensure a comprehensive goal setting process:

Take a Regional Approach to Managing Hatchery Programs

The HSRG and the managers have agreed that evaluating hatchery programs in the

context of the regions and watersheds in which they operate and the goals set for them

by the managers is vital to the success of the process. This same regional approach will

be essential to the implementation of hatchery reform.

Measure Success in Terms of Contribution to Harvest, Conservation and Other Goals

In the past, hatchery programs too often have been evaluated on the basis of the number of fish released. More appropriate measures of success include fish quality, harvest

opportunity and adults returning to reproduce and sustain the stock. In the future, hatcheries may also be evaluated on the basis of their socio-economic benefits and their contribution to the ecosystem as a whole.

4
Size Hatchery Programs Consistent with Stock Goals

Fisheries managers should determine the proper size (number of fish released) of a

hatchery program based on their goals for the stock. The determining factors will differ

depending on whether the program is a conservation, integrated harvest or segregated

harvest program.

Have Clear Goals for Educational Programs

The educational programs conducted at, or supported by, hatchery facilities are valuable

for educating the public on the biology of salmon, importance of maintaining healthy

salmon habitat and sustainable fisheries. It is incumbent upon the fisheries managers to

ensure that specific goals, and methods for determining if those goals are being met,

are developed for these programs and understood by participants.

2. SCIENTIFIC DEFENSIBILITY

Once the goals for the resource have been established (see above), a scientific rationale for designing, building and/or operating each hatchery and hatchery program must

be spelled out as working hypotheses. These hypotheses should explain why and how

the hatchery program expects to produce its desired outcomes and should include performance indicators for measuring success. Documentation should include citations

from the scientific literature and models that take into account the various factors (e.g.,

predation assumptions, cumulative effects, etc.).

This approach will establish actions within hatcheries and hatchery programs as experiments, designed so that uncertainties can be resolved through observation and evaluation. The HSRG has developed the following recommendations to help achieve scientific defensibility for hatcheries and hatchery programs.

Operate Hatcheries within the Context of Their Ecosystems

The benefits and risks of hatcheries can only be evaluated in a complete manner in the

context of their ecosystems. The current and future status of these ecosystems, including the status of naturally spawning stocks and the environment, will determine the

potential for success and the limitations on any hatchery program.

Operate Hatchery Programs as either Integrated or Segregated Relative to

Naturally Spawning Populations

Hatchery programs can be classified as either integrated (if the goal is to manage the

broodstock as an artificially propagated component of a naturally spawning population)

or segregated (if the goal is to maintain a hatchery broodstock that is genetically discrete from naturally spawning populations). Every hatchery program must be identified

as either integrated or segregated, with operational procedures designed to achieve the

specific goals for one of those two types of programs. In this context, “intermediate” programs cannot exist without potentially posing unacceptable risks to natural populations.

5
Emphasize Quality, Not Quantity, in Fish Releases

It is important that some measure of the quality, rather than simply the quantity, of fish

released from hatcheries be made and evaluated in a regional context. 

Develop a System of Wild Steelhead Management Zones

The HSRG recommends an entirely new approach to managing steelhead. The managers should develop a system of “wild steelhead management zones” for each region

in Puget Sound and coastal Washington, where streams are not planted with hatchery

fish and are instead managed for native stocks. Harvest for steelhead within these

zones may be compatible with this approach, but no hatchery-produced steelhead would

be introduced.

Use In-Basin Rearing and Locally-Adapted Broodstocks

Some hatchery programs, for lack of adequate facilities and/or proper escapement management, require the importation and movement of eggs and juveniles into and out of

the region. The managers should use in-basin rearing and locally-adapted broodstocks.

Take Eggs throughout the Natural Period of Adult Return

Certain life history traits can be lost in hatchery stocks (for example, the failure to

spread hatchery egg take over the natural period of adult return can result in a shift in

spawn timing). To assure long-term sustainability, the managers should adopt and implement policies that conserve or recover natural life history traits.

Develop Spawning Protocols to Maximize Effective Population Size

The mating of hatchery fish should strive to achieve two principal objectives: 1) maximize the genetic effective number of breeders; and 2) ensure that every selected adult

has an equal opportunity to produce progeny. This is particularly critical in conservation

programs, where populations are small or have experienced significant declines.

Take into Account both Freshwater and Marine Carrying Capacity in Sizing

Hatchery Programs

There seems to be reduced capacity to support hatchery and naturally spawning

salmonids over the past decade in certain regions of Puget Sound and the coast.

Because of the scientific uncertainty involved, hatchery production should not be

increased until managers have a better understanding of the factors controlling survival.

Closure of certain unproductive hatcheries and reduced production at other hatcheries

may benefit the quality and survival of both naturally spawning and hatchery fish.

Reduce Risks Associated with Outplanting and Net Pen Releases

Releasing smolts in streams geographically removed from a hatchery or adult collection

facility is commonly called outplanting. Similarly, saltwater net pens are used to acclimate and release salmon smolts in marine areas where a targeted marine fishery on

returning adults is desired. A common feature of these programs is the release of fish

where no facilities exist to trap returning adults that escape target fisheries. This may

pose significant genetic risks by promoting straying to freshwater areas where interbreeding with naturally spawning populations is undesirable. The HSRG recommends

reducing the number and/or size of outplanting and net pen programs and has outlined

specific steps the managers can take to reduce risks in those that remain.

6
3. INFORMED DECISION MAKING

Assuming that goals for the resource have been established (see #1 above), and the

scientific rationale has been developed for how a hatchery and/or hatchery program will

help achieve this goal (see #2 above), the HSRG further recommends that the managers’ decision making processes must be responsive to new information. 

Indicators and standards must be identified so that monitoring activities will focus on

key uncertainties and effective evaluation of monitoring results can occur. Results of

the monitoring and evaluation (M&E) must then be brought forward to the decision

making process in a clear and concise way so needed changes can be implemented.

This responsive process should be structured to allow for innovation and experimentation so hatchery programs may be responsive to new goals and new concepts in

culture practice.

The HSRG has developed the following recommendations to help implement information

responsive decision-making:

Incorporate Flexibility into Hatchery Design and Operation

Facilities should be designed and operated in such a way that they are able to respond

relatively easily to changes in harvest and conservation goals and priorities, ocean carrying capacity, stock status, freshwater habitat conditions and the myriad other factors

that will alter current policies and programs. Programs must also be able to respond to

uncertainty and risk.

Evaluate Hatchery Programs Regularly to Ensure Accountability for Success

Hatchery reform will require expanded M&E, with some level of commonality and standardization across Puget Sound and coastal Washington. Each region of Puget Sound

and the coast will need to develop its own M&E program consistent with the goals and

programs of that region. 

7
REGIONAL REVIEWS

This section provides examples of the recommendations developed by the HSRG upon

reviewing the first six regions during 2001 and 2002. These reviews were conducted via

in-region meetings and supported by a collaborative information gathering and sharing

process among the management agencies and the scientists. The reviews included a

consideration of each hatchery program’s effects on all hatchery and naturally spawning

salmonid stocks in the region. 

Regions to be reviewed

2001

• Eastern Straits

• South Puget Sound 

• Stillaguamish/Snohomish Rivers 

2002

• Skagit River Basin 

• Nooksack/Samish Rivers 

• Central Puget Sound 

2003

• Hood Canal

• Willapa Bay 

• Grays Harbor 

• North Coast 

1. Eastern Strait of Juan de Fuca

This region includes the eastern portion of the Strait of Juan de Fuca, from Point Wilson

to the Hoko River. Twelve hatchery programs were reviewed in this region, with 60 specific reforms recommended (see February 2002 HSRG Recommendations Report).

There are major restoration efforts being planned in this region’s two large watersheds

(dam removal/watershed restoration on the Elwha River, habitat restoration at the mouth

of the Dungeness River). Historically, the Elwha River boasted one of the most magnificent and genetically distinct runs of chinook on the Pacific coast. Remnants still return,

bumping their noses against the base of the first dam. What happens to an endangered

run of chinook when a dam is removed and a hundred years’ sediment cascades downstream? The hatcheries on this river system will play a central role in protecting and

restoring this run until the habitat is ready to support them again. Federal, state and tribal managers in this region must determine how best to do this. The regional review

process has helped them answer questions about how long the fish should be reared in

captivity and when and where their progeny should be released to re-establish a naturally spawning population.

8
2. South Puget Sound

This region includes the portion of Puget Sound south of the Tacoma Narrows. Sixteen

hatchery programs were reviewed in this region, with 64 specific reforms recommended

(see February 2002 HSRG Recommendations Report).

With the exception of the Nisqually River and Delta—where ambitious habitat restoration

efforts are underway—habitat in the South Sound region is less likely to be the focus of

large-scale restoration activities in the coming years than habitat in the Eastern Straits.

The managers designated this region a harvest management zone as part of their postBoldt Decision efforts to provide adequate fishing opportunities for the Puyallup,

Nisqually and Squaxin Island tribes, all of which have “usual and accustomed” fishing

areas here. It includes several old Washington Department of Wildlife trout facilities not

suited to salmon production and therefore has been managed based on a series of interbasin stock transfers. At its height, this region was releasing up to ten million smolts per

year (around ten percent of the total releases in Puget Sound and coastal Washington).

Despite increased production, returns have declined. The scientists strongly recommend

an analysis of the carrying capacity of the Sound and that production be capped or

decreased in this region until more certainty is established.

3. Stillaguamish/Snohomish Rivers

This region includes the watersheds contained by the Stillaguamish and Snohomish

rivers and Tulalip Bay. Sixteen hatchery programs were reviewed in this region, with 94

specific reforms recommended (see February 2002 HSRG Recommendations Report).

Habitat in the Stillaguamish River system has been heavily altered and compromised by

land use activities such as logging, diking, housing development and dairy farming.

Population growth could result in a watershed once rural in character becoming urbanized. The Skykomish features relatively undisturbed habitat. While the Snoqualmie is

wild-like above North Bend, in rural, eastern King County it has been affected by agriculture and development. When the Skykomish and Snoqualmie join and form the

Snohomish, the effects of development are even clearer. The Tulalip Tribes operate a

successful terminal harvest program in Tulalip Bay, meaning that all returning fish are

targeted by the Tribes and non-Indian sports fishers. The HSRG emphasized the importance of determining whether a significant number of these fish are straying to other

regional streams and presenting risks to naturally spawning salmon. Another distinguishing characteristic of this region is its popular steelhead sport fishery. Unfortunately,

steelhead in Washington state have been subject to decades of indiscriminate stock

transfers without proper consideration of genetic or ecological concerns. Accordingly,

this region is one where the HSRG’s “wild steelhead management zones” concept (see

Area-Wide Recommendations above) was a particular focus of the recommendations.

4. Skagit River Basin

This region includes the watersheds contained by the Skagit River Basin (including the

Skagit, Baker, Sauk and Suiattle rivers) and Whidbey Island. Eleven hatchery programs

9
were reviewed in this region, with 48 specific reforms recommended (see March 2003

HSRG Recommendations Report).

The Skagit River Basin is the largest watershed in Puget Sound and is home to all six

species of anadromous salmonids. A significant amount of natural habitat is still available in this region, though it has been affected by hydropower and other land uses.

The Skagit Basin is an important region for the recovery of Puget Sound salmon

stocks. Strong spring, summer and fall chinook runs existed in the past and there is

still a fair amount of this diversity left. However, there are conservation concerns for

several stocks, including chinook, coho and steelhead. The region has a number of

hatchery programs serving as indicator stocks for the US/Canada Treaty and other

processes. These are important to fisheries management, but not central to recovery.

Natural production goals are key for all species in this region. The HSRG recommended the managers size these indicator programs to meet indicator stock needs,

but not above that level. The group also noted Baker Lake sockeye as an example of

a hatchery program that is meeting its conservation goal by maintaining a stock that

would otherwise go extinct.

5. Nooksack/Samish Rivers

This region includes the watersheds contained by the Nooksack and Samish rivers and

the San Juan Islands. Nineteen hatchery programs were reviewed in this region, with 89

specific reforms recommended (see March 2003 HSRG Recommendations Report).

The Nooksack/Samish region reminded the HSRG of the Stillaguamish/Snohomish

region, in that its habitat has been heavily altered and compromised by natural resource

land use activities. Because of this, natural production has been severely impaired.

Spring chinook stocks, in particular, are dependent on hatchery programs for recovery.

The region also reminded the HSRG of the South Puget Sound region, in that management goals have emphasized hatchery production for harvest, especially on chinook and

coho. This region was in the past the center of Puget Sound chinook harvest, but both

hatchery production and harvest have been reduced over the last decade or so. The

HSRG recommended the managers ensure their hatchery programs are consistent with

conservation goals, in particular those for spring chinook. The group pointed out the

importance of making sure recovery programs do not produce numbers of fish that

exceed the capacity of the limited habitat into which they are released and to which they

return. If this occurs, a program might be rebuilding one stock, while at the same time

producing strays that compete with natural stocks in other streams.

6. Central Puget Sound

This region includes the central portion of Puget Sound, including the Puyallup River,

Green River, Lake Washington and East Kitsap watershed. Thirty-one hatchery programs were reviewed in this region, with 149 specific reforms recommended (see March

2003 HSRG Recommendations Report).

10
Central Puget Sound is the largest region the HSRG has reviewed, both in terms of the

number of programs reviewed and the number of recommendations provided. It is also

where the largest concentration of the human population lives in Puget Sound and

coastal Washington, putting particular focus on issues surrounding how salmon and people coexist. The HSRG reviewed four sub-regions within Central Puget Sound and found

that each had its own distinct character. 

The Puyallup River sub-region has been affected by land use and hydropower and is

home to White River chinook, the last remaining spring chinook stock in South and

Central Puget Sound. White River chinook owes its recent recovery to a successful

hatchery intervention. The HSRG said this program has been successful enough that it

is time to begin locally-adapting the stock, moving away from out-of-basin rearing. 

The East Kitsap sub-region features smaller, shorter streams and is only now beginning

to confront the rapid population growth and corresponding pressure on habitat that much

of Central Puget Sound has already experienced. Consistent with its short streams,

hatchery programs in this sub-region have emphasized chum production. Though the

harvest benefits derived from these programs are not always large, the HSRG saw them

as good examples of how hatcheries can be used for environmental education, in that

they make extensive use of volunteers from the general public, many drawn from the

new arrivals who need to learn about protecting salmon stocks and their habitat. 

Goals other than conservation and harvest (i.e., education and research) are featured

at hatchery facilities in the Lake Washington sub-region, such as Issaquah Hatchery

and the University of Washington. Another major effort in this sub-region is the conservation and harvest hatchery program directed on Lake Washington sockeye. The

HSRG provided a number of recommendations for allowing fish from this program to

more closely emulate the natural life history pattern of sockeye in the Cedar River

and Lake Washington.

The Green River sub-region has more than a century’s history of hatchery and natural

production existing side-by-side on a chinook stock that has remained relatively healthy.

The region also features several net pen programs, which acclimate and release smolts

in marine areas where a targeted fishery of returning adults is desired. Accordingly, this

region is one where the HSRG’s recommendations about reducing straying risks from

outplanting and net pen programs (see Area-Wide Recommendations above) were a

particular focus.

11
CONCLUSION

It is important to note that the HSRG’s recommendations are based upon current goals

and the best scientific information available at the time the reviews were conducted. In

keeping with the tenets of adaptive management, it will be necessary to review and

adapt these recommendations as new scientific information arises and/or goals change.

The managers have asked the HSRG to assist them as they design the mechanisms

necessary to implement the recommendations and adaptively manage hatchery programs in the future. 

The report also focuses primarily on issues that need to be addressed and recommends

changes that need to be made. It should not be read as a complete review listing every

positive attribute alongside those that need to be changed. The HSRG has been very

impressed by the diligence—and frequently the ingenuity —with which the state and tribal staffs carry out their programs, and with their dedication to the resource. 

The full recommendations and all other Hatchery Reform Project-related publications

(including the HSRG’s review tools and a description of the process used to apply them)

are available on the project’s web site (www.lltk.org/hatcheryreform.html) or by contacting Long Live the Kings at (206) 382-9555.

12

HATCHERY REFORM PROJECT

Quote Page

“The Hatchery Reform Project is the first time anyone has taken a big-picture, 

systematic look at the Puget Sound and coastal hatcheries. Only a comprehensive plan 

like the Hatchery Reform Project can balance all of the related, complex interests, such 

as tribal treaty rights, sport fishing and conservation.”

––Representative Norm Dicks (D-Wash.)

“The Hatchery Reform Project is a model for natural resource management––

integrating science and policy-making in a meaningful way. This is especially important 

for salmon recovery, and it moves us toward more coordinated and sophisticated 

management of hatcheries, harvest and habitat.” 

––Washington Governor Gary Locke

“Recovery will only be successful if the best available science is used to determine 

existing conditions and guide priorities for action. Science can also help us monitor the 

results of our efforts over time and provide insight for adapting our approach.”

––Washington State Salmon Recovery Funding Board Chairman William Ruckleshaus

“It is critical that the findings of the Hatchery Scientific Review Group are adopted by 

the co-managers and appropriate federal agencies.”

—Washington State Department of Fish and Wildlife Director Jeff Koenings

“By moving ahead with these reforms, the states and tribes will not only go beyond the 

Endangered Species Act’s requirements to minimize hatchery impacts, they intend to 

help us bring back the wild salmon.”

––Senator Patty Murray (D-Wash.)
“This report shows that we can help, not hinder, the dual goals of recovering natural 

fish stocks and sustaining fisheries. As one of the earliest sponsors of this research, I 

could not be more proud.”

—Former U.S. Senator Slade Gorton 

“With the Hatchery Reform Project, the co-managers are turning traditional hatchery 

management on its ear. This is a comprehensive, scientific, and systematic rethinking of 

how to redesign and manage the largest hatchery system in the world to achieve the 

twin goals of salmon recovery and sustainable fisheries. The co-managers are to be 

commended for their commitment to the process.”

—Long Live the Kings Executive Director Barbara Cairns

“The Hatchery Reform Project boasts peer-reviewed science, strong partnerships, local 

solutions backed by federal dollars. This blueprint for reform will be central to our 

successful recovery of threatened salmon in the Pacific Northwest.”

—Representative Jennifer Dunn (R-Wash.)

“These reforms are based on a solid, scientific framework that was reviewed by more 

than 200 people, including scientists, decision makers, environmentalists, sport and 

commercial fishers, and other stakeholders. The Hatchery Scientific Review Group has 

conducted monthly, three-day meetings for two years, spending thousands of hours to 

create a solid, scientific foundation for this new approach to hatcheries in 

Washington state.”

––Hatchery Scientific Review Group Chairman Lars Mobrand

“We are confident that by working together we can achieve our goal of returning wild 

salmon stocks to abundance. Reforming hatchery practices is another step on the road 

to wild salmon recovery.” 

––Northwest Indian Fisheries Commission Chairman Billy Frank, Jr.

“This combination of clear goals, independent science and collaborative policy-making 

is the model for hatchery management of the future.” 

––U.S. Fish and Wildlife Service Regional Director Anne Badgley
“The Hatchery Reform Project is an excellent example of how we must use science to 

guide policy decisions in our effort to recover and preserve Northwest salmon.” 

––National Marine Fisheries Service Regional Director Bob Lohn
FOR IMMEDIATE RELEASE Contact: Barbara J. Cairns

February 19, 2002 Executive Director

Long Live the Kings

(206) 382-9555, ext. 23

Hatchery Reform Measures to Help Restore 

Washington’s Salmon, Support Sustainable Fisheries

SEATTLE, WA––After two years of evaluation, an independent team of scientists 

working on the Hatchery Reform Project is releasing a groundbreaking report 

containing both area wide and site-specific recommended reforms that will change the 

way hatcheries are managed in the Puget Sound and coastal Washington.

The Hatchery Reform Project is a systematic and scientific redesign of Washington’s 

Puget Sound and coastal salmon hatcheries, guided by new goals: supporting 

sustainable fisheries and helping to restore threatened stocks. 

Washington State Department of Fish and Wildlife Director Jeff Koenings and 

Northwest Indian Fisheries Chairman Billy Frank, Jr. were joined by Governor Gary 

Locke, Senator Patty Murray (D-Wash.) and Representative Norm Dicks (D-Wash.) for 

today’s announcement of the reform measures. 

“The Hatchery Reform Project is the first time anyone has taken a big-picture, systemic 

look at the Puget Sound and coastal hatcheries. Only a comprehensive plan like the 

Hatchery Reform Project can balance all of the related, complex interests, such as tribal 

treaty rights, sport fishing and conservation,” said Representative Dicks.

Governor Locke added, “The Hatchery Reform Project is a model for natural resource 

management––integrating science and policy-making in a meaningful way. This is 

especially important for salmon recovery, and it moves us toward more coordinated 

and sophisticated management of hatcheries, harvest and habitat.” 

A nine-member Hatchery Scientific Review Group (HSRG) recommended that hatchery 

managers change the way they measure the success of a hatchery program, from 

looking at the number of salmon released to focusing on the program’s contribution to 

conservation, harvest or other goals. 

“These reforms are based on a solid, scientific framework that was reviewed by more 

than 200 people, including scientists, decision makers, environmentalists, sport and 

commercial fishers, and other stakeholders,” said HSRG Chairman Lars Mobrand.

-MoreIn addition, the HSRG is recommending the following measures:
• Evaluating hatchery programs in the context of the watersheds in which they 

operate and the goals set for them by the managers, and taking this same regional 

approach to implementing reforms.

• Measuring success by the number of healthy adult salmon returning to spawn.

• Creating flexibility in hatchery design and operation so managers can respond 

quickly to changing circumstances and goals.

• Developing an integrated, region wide monitoring and evaluation system.

• Creating “wild steelhead management zones.”

• Using only in-basin rearing and locally adapted broodstocks at hatcheries to reduce 

risks and increase hatchery stock productivity.

• Conserving and recovering life-history traits of the hatchery stocks to ensure longterm sustainability.

• Capping hatchery production until there is a better understanding of which factors 

affect salmon survival.

The Hatchery Reform Project was recommended in 1999 when a group of leading 

scientists reported that systematic hatchery changes can have a major positive impact 

on the recovery of wild salmon in just a few years and at a relatively small cost. 

Adopted by Congress in 2000, the project has received bipartisan support from state 

and congressional leaders including Murray, Dicks, Representative Jennifer Dunn (RWash.) and former U.S. Senator Slade Gorton. 

“By moving ahead with these reforms, the states and tribes will not only go beyond the 

Endangered Species Act’s requirements to minimize hatchery impacts, they intend to 

help us bring back the wild salmon,” said Senator Murray.

Congress also assigned Long Live the Kings, a private, nonprofit wild salmon 

restoration organization, to manage the project.

“We are confident that by working together we can achieve our goal of returning wild 

salmon stocks to abundance. Reforming hatchery practices is another step on the road 

to wild salmon recovery,” said Northwest Indian Fisheries Commission Chairman Billy 

Frank, Jr.

The reform measures in the report released today are based on the review of three of ten 

regions in Puget Sound and coastal Washington. The regions reviewed include the 

Eastern Straits, South Sound and the Stillaguamish/Snohomish Rivers. The HSRG will 

evaluate and release recommendations for the final seven regions in 2002 and 2003.

Copies of the HSRG report, press materials, maps of the reviewed regions and other 

project publications are available at www.longlivethekings.org.

For B-roll film, call Aimee Bruneau at (206) 382-9555 Ext. 21.
Hatchery Scientific Review Group 

Policies and Procedures 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

I. Purpose 

The Hatchery Scientific Review Group (Scientific Group) was established by Congress in FY 

2000 to ensure that hatchery reform programs in Puget Sound and Coastal Washington be 

scientifically founded and evaluated; that independent scientists interact with agency and tribal 

scientists to provide direction and operational guidelines; and that the system as a whole be 

evaluated for compliance with scientific recommendations. The goal of hatchery reform is to 

ensure that hatchery programs in Puget Sound and Coastal Washington are managed and 

operated in order to meet one or both of the purposes for hatcheries: 1) helping recover and 

conserve naturally spawning populations and 2) supporting sustainable fisheries. The objective 

of the Scientific Group is to assemble, organize and apply the best available scientific 

information to provide guidance to policy makers who are implementing hatchery reform. 

II. Scope of Scientific Group Activities 

A. Objectives 

Based on an agreed-upon scientific framework and criteria for decision-making, the 

Scientific Group will: 

1. Develop and maintain a scientific framework to provide a basis for 

strategic planning for hatchery reform. 

2. Work with tribal, federal and state agencies to review hatchery 

management plans, policies and program implementation for consistency 

with the scientific framework. 

3. Make recommendations for reform of the hatchery system. 

4. Identify information needs and recommend further research.

5. Develop a monitoring and evaluation system to verify that hatchery reform 

is occurring. 

6. Communicate with agencies, the scientific community, interested parties 

and the public. 

7. Submit a written report annually to the agencies, tribes and Congress, 

evaluating progress toward meeting goals, with any disagreements clearly 

and evenly presented.

B. Relationship to State and Federal Agencies and Tribes 

The Scientific Group shall establish regular communication with the agencies and tribes 

that manage hatchery programs, and with agencies having regulatory review of hatchery 

programs, in Puget Sound and Coastal Washington. The initial method of achieving such 

communication will be through the Hatchery Reform Coordinating Committee, other 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

meetings and via written communications. The Scientific Group will work with the 

fisheries managers to develop work plans and products that provide for timely scientific 

direction and review of current and future hatchery operations. Questions and issues for 

consideration by the Scientific Group should be submitted to the Scientific Group 

Coordinator, as described in section IV.A. 

III. Membership 

A. Appointment Procedures 

As directed by Congressional legislation, the Scientific Group is composed of five 

independent scientists and four agency scientists. The independent scientists were 

initially selected by the Congressional Hatchery Science Advisory Team from a pool of 

candidates nominated by the Past Presidents Council of the American Fisheries Society 

(AFS). The agency scientists include one each designated by the Washington State 

Department of Fish and Wildlife, the Northwest Indian Fisheries Commission, the 

National Marine Fisheries Service, and the US Fish and Wildlife Service. In the future, 

when an independent scientist steps down, a replacement will be selected by the 

Scientific Group from a list of three nominees provided by the AFS Past Presidents 

Council. When an agency scientist steps down, a replacement will be selected by that 

agency, following consultation with the Scientific Group. If an independent scientist is 

interested in serving an additional term, that person may be reappointed by vote of the 

Scientific Group. If an agency scientist is interested in serving an additional term, that 

person may be reappointed by the agency, following consultation with the Scientific 

Group. If an agency scientist wishes to have an alternate member, the alternate will be 

selected by that agency, following consultation with the Scientific Group. 

B. Criteria 

The following specific criteria should be considered in selecting members: 

1. High achievement in a relevant scientific discipline, which may include 

biology, genetics, ecology, fisheries, fish culture, fish pathology, 

biometrics or other appropriate disciplines. 

2. A strong record of scientific accomplishment documented by contribution

to the peer-reviewed literature or other evidence of creative scientific 

accomplishment. 

3. High standards of scientific integrity, independence and objectivity. 

4. Ability to forge creative solutions to complex problems. 

5. Interest in and ability to work effectively in an interdisciplinary setting. 

6. Each of the agency scientists should have technical skills in relevant 

fields, such as biology or fish genetics, and some understanding of agency 

hatchery processes; administrative status within the agency is not relevant. 

7. Like the independent scientists, the agency scientists are responsible for 

evaluating scientific merits and are not to represent agency policies. 

2 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

C. Length of Appointments 

Appointment to the Scientific Group will normally be three years. Terms will be 

staggered to preserve continuity and institutional memory. Appointments can be renewed 

using the normal appointment procedures outlined above. 

D. Staff

1. The Scientific Group may contract for staff or consider alternative 

arrangements. 

2. The Chair will appoint a staff coordinator, to support the Scientific Group 

in its work. The coordinator will work closely with the Chair in 

establishing and executing Scientific Group agendas and work plans. 

3. The staff will assist the Chair and the Scientific Group in contacts with 

other organizations and committees in the region. The staff will act as a 

resource to the Scientific Group and should be familiar with the policies 

and scientific issues that are likely to come before the Scientific Group. 

E. Outside Expertise 

It may be necessary to secure the services of outside experts to provide assistance 

on specific activities. Such appointments can be made by the Scientific Group 

Chair, as allowed by budget limitations. Temporary appointees meet the same

criteria as regular members (section III.B) and are subject to the same rules 

regarding bias and conflict of interest as regular members (section IV.F). 

IV. Procedures

A. Agenda 

Questions or issues to be considered for inclusion on the Scientific Group agenda should 

be submitted to the Scientific Group coordinator. The coordinator will bring these to the 

Chair, who will consider the scientific aspects of the questions or issues and whether they 

fit within Scientific Group work plans and priorities. The Chair and the Scientific Group 

coordinator will develop a draft agenda for each meeting, for consideration by and 

approval of the group. 

B. Meetings 

The Scientific Group will meet on a regular basis. Much of the work of the Scientific 

Group will be conducted between meetings by members and task teams or committees, 

responding to assignments from the Chair or the Scientific Group as a whole. Meetings 

will provide the opportunity to report back, discuss work and formulate Scientific Group 

positions and recommendations. Members are expected to place a high priority on 

attendance and participation in Scientific Group meetings. Members may bring relevant 

staff to informational sessions on the Scientific Group agenda, but should coordinate this 

3 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

attendance in advance with the Scientific Group Chair and coordinator. Scientific Group 

discussion and decision-making sessions are to be attended by Scientific Group members 

and support staff only. 

Meetings are normally to be held at a location in western Washington at intervals 

appropriate to the requirements of Scientific Group business. Summaries of meetings will 

be prepared by support staff and reviewed by the Chair and will include a summary of 

decisions and actions, work assignments and schedules. Scientific Group members may 

be compensated for time and travel. 

C. Confidentiality of Scientific Group Deliberations 

The Scientific Group is subject to the following confidentiality standards: 

1. In order to encourage individual members to express their views freely 

and to encourage a full and complete scientific debate on issues, 

deliberations of the Scientific Group are to be considered confidential and

privileged communications. To protect the confidentiality of the 

deliberative process, Scientific Group members and staff are asked to 

refrain from disclosing the contents of Scientific Group meetings and draft 

reports. Decisions, actions and descriptions of issues under review by the 

Scientific Group may be communicated. If a member is unsure about what 

is appropriate to communicate on any issue, that member should consult 

the Chair. 

2. In addressing any individual funding proposal submitted to the Scientific 

Group, a summary of the Scientific Group evaluation may be provided to 

the author of the proposal, provided the summary preserves the anonymity 

of Scientific Group members who performed the evaluation. 

3. Any reports prepared by the Scientific Group should provide a full 

explanation of the rationale for Scientific Group decisions, in order to 

provide the public with an understanding of why those decisions were 

made. 

D. Work Plan

The Chair of the Scientific Group will work with the Scientific Group coordinator to 

prepare short-term and long-term work plans to accomplish the purposes of the Scientific 

Group. Frequency of meetings will be determined by the work plan. 

E. Communication 

1. The Chair of the Scientific Group will normally act as spokesperson, 

unless another member is designated by the Chair to speak on specific 

topics or at specific times. The Scientific Group will normally respond to

questions or issues in writing. Public statements by the Chair or designated 

spokesperson should reflect Scientific Group decisions and positions. 

4 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

2. The Scientific Group coordinator will act as the point of contact for 

inquiries and requests to the Scientific Group. The coordinator will ensure 

that these communications are promptly conveyed to the Chair. 

3. Within the Scientific Group, a standard procedure for communication of 

documents and messages (including electronic communication) will be

established to maximize work efficiency. 

4. Procedures will be established for communicating with relevant agencies

and tribes and for providing Scientific Group reports and testimony to 

Congress. 

F. Bias and Conflict of Interest 

For the efforts of the Scientific Group to be influential and credible, the Scientific Group 

must be perceived to be free of any significant conflict of interest, not compromised by 

bias and untainted by allegations of scientific misconduct. The Scientific Group will deal 

with a broad range of issues concerning hatchery reform efforts. For this reason, there is 

ample opportunity for potential conflicts to arise for members on specific topics. It is 

imperative that the members of the Scientific Group are aware of the potential for conflict 

and are especially aware of the dangers of a perception of conflict. The Scientific Group 

will define bias and conflict as follows: 

1. Bias—Bias relates to views stated or positions taken that arise not from

scientific analysis, but from the close identification or association with the 

positions or perspectives of a particular group. 

2. Conflict of Interest—Conflict of interest means any financial or other 

interest which would benefit the individual and which conflicts with the 

service of an individual because it could impair the individual’s objectivity 

or create an unfair competitive advantage for any person or organization. 

3. Bias and Conflict of Interest Procedures 

a. Members of the Scientific Group are expected to take the 

responsibility for ensuring that real or perceived biases or conflicts 

of interest on their part are identified prior to taking part in any 

project. Members are expected to excuse themselves from work on 

any topic on which they perceive a real or potential conflict or 

bias. 

b. Each member of the Scientific Group will submit to the Scientific 

Group Coordinator and Chair relevant information regarding 

financial interests, research support, agency or group affiliation, 

public statements and positions, and other circumstances or 

information. 

c. Relevant disclosure information should include connections 

between the individual and work relating to the Scientific Group. 

d. Information submitted will be considered confidential. 

e. The Chair will take this information into account in making 

assignments on specific tasks. Members are also expected to 

5 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

announce any potential conflict or bias relating to particular 

assignments. 

f. In the event there remains any substantial question on the existence 

of a conflict of interest, it is preferred that the member involved 

request to be excused, in order to protect the Scientific Group from

any appearance of conflict or bias. Unresolved questions will be 

decided by a vote of the Scientific Group (see section IV.H. for 

voting procedures). 

G. Organization 

1. Officers 

a. Elections—Officers of the Scientific Group will be elected by the 

members. Election of officers should occur at least 30 days prior to 

the expiration of the previous officer’s term. 

b. Officers and Terms—Officers of the Scientific Group shall consist 

of the Chair and one or more Vice Chairs, who will serve one-year

terms. Officers can stand for reelection. 

c. Duties of Chair—The Chair is the executive officer of the 

Scientific Group. The Chair acts as the spokesperson of the group 

and designates another member to serve as an alternate 

spokesperson when the Chair is not available. The Chair works 

with Scientific Group support staff to arrange the time and place 

for meetings, produce meeting summaries and ensure summaries 

and other documents are forwarded to the membership. The Chair 

ensures that meeting business is conducted in a timely and efficient 

manner and that each member has the opportunity to contribute 

and be heard. The Chair of the Scientific Group is to be selected by 

Scientific Group members from the independent scientists chosen 

from the AFS nominations. The Chair should have experience in 

dealing effectively with complex, controversial, scientific issues. 

d. Duties of the Vice Chair(s)—The Vice Chair(s)’ role shall be to 

assist the Chair in implementing the Scientific Group work plan 

and other activities of the Scientific Group, as assigned by the 

Chair. 

2. Committees, Task Groups and Assignments 

The Chair may designate members of the Scientific Group to perform

assignments and to form committees and/or task teams to address specific topics. 

Each committee or task team should have a designated lead responsible for 

overseeing completion of the task. Committees may include experts from outside 

the Scientific Group. Such appointments can be made by the Chair. 

H. Decision-Making 

Decisions of the Scientific Group will normally be made by consensus. The Chair will 

clearly explain the proposed decision to the group and check for consensus. If there is any 

6 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

question or doubt about whether consensus has been achieved on an issue, any Scientific 

Group member can request that a motion be made on the subject, according to Robert’s 

Rules of Order, in which case, after discussion, a majority vote will decide the issue. 

I. Publications

1. Goals 

a. Encourage peer-reviewed publication of scientific work of the 

Scientific Group. This work may be derived from the HSRG’s 

Scientific Framework for Artificial Propagation of Salmon and 

Steelhead, regional reviews, issue papers, internal discussion, or other 

scientific products. 

b. Establish an open process for development of publications that: 

i. Extends the Scientific Group’s consensus-based decision-making 

process to publications. 

ii. Encourages discussion during the early stages of development of a 

paper of the following: 

1. Scope of the proposed publication. 

2. Objective of the proposed publication. 

3. Intended audience and appropriate journal for the proposed 

publication. 

c. Identify and deal equitably with the question of authors and author 

order for the proposed publication. 

2. Protocol and Process—These publication policies apply only to papers or 

ideas that have been discussed or developed in Scientific Group meetings 

or as part of a Scientific Group project or review. All decisions involved in 

applying these policies will be made according to the Scientific Group’s 

decisions- making policies, as described earlier in this document. 

a. Proposals for publication should be submitted to the Chair for initial 

review and scheduling as an agenda item for the next meeting. 

Proposals should be brief, but describe the particulars of how the 

proposed publication addresses the goals identified above. Group 

discussion will likely dictate the future course of action on most 

proposals. If a jointly-authored publication is approved by the 

Scientific Group, a task team will be established to bring the 

publication to an internal review stage, and to finalize it for 

submission. 

b. Type of paper—In general, there will be three types of papers 

proposed: 

i. HSRG Paper—Authorship to include all current Scientific Group 

members. Former members may be included at the discretion of 

the Scientific Group or the Chair. 

ii. HSRG Subset Paper—A paper that is authored by several, but not 

all, Scientific Group members. Members of the facilitation team or 

agency science teams may be included at the discretion of the 

Scientific Group or the Chair. 

7 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

iii. Proprietary Paper—A paper authored by one or a few members of 

the Scientific Group (and possibly other, non-HSRG authors) that, 

while based on a core of work conducted under a Scientific Group 

project; evolves beyond that core work of the Scientific Group 

project. 

c. Author Order 

i. HSRG Paper—Authorship on group papers will be Chair first, then 

alphabetical order, unless special circumstances on a particular 

paper suggest that another approach would be more appropriate 

and agreement can be reached on author order. Alternative 

approaches include strict alphabetical order of Scientific Group 

members, and Scientific Group members listed by order of 

contribution to paper. 

ii. HSRG Subset Paper—Authorship for these papers should be 

determined in order of the relative contribution of the various 

authors. Care should be taken to ensure that Scientific Group 

members not listed as authors on the paper are comfortable with 

the proposed publication and the author list. Obviously, members 

that make a material contribution to the manuscript should be 

included as authors. 

iii. Proprietary Papers—Sometimes there will be little distinction 

between this type of paper and the HSRG Subset Paper described 

above. In general, proprietary papers would be ones where the core 

or genesis for the paper occurs in the process of a Scientific Group 

assignment; however, development of the idea into a manuscript 

for publication goes well beyond the work conducted within the 

Scientific Group assignment and may or may not involve other 

Scientific Group members. Authorship for these papers should be 

determined in order of the relative contributions of the various 

authors to the manuscript. 

d. Publication Costs—Publication costs for Scientific Group papers and 

Scientific Group subset papers will be covered by the Scientific 

Group. Publication costs for proprietary papers will be at the discretion 

of the Scientific Group or the Chair. 

e. Replication—It is the practice of the Scientific Group to make its 

scientific tools and regional review processes publicly available, as 

models that can be adopted for similar challenges elsewhere. The 

Scientific Group requests that it be cited appropriately as the source of 

these tools and processes. The Scientific Group further requests that 

where tools and processes are modified for other applications, it be 

made clear that these adaptations differ from the original products of 

the Scientific Group. 

J. Soliciting, Reviewing and Deciding on Grant Requests 

8 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

The US Congress has directed the Scientific Group to oversee a competitive grant 

program funding scientific research projects that support the goals of hatchery reform in 

Puget Sound and Coastal Washington. The Scientific Group has established the following 

procedures for administering this grant program:

1. The Washington State Interagency Commission for Outdoor Recreation 

(IAC) shall be the administrative agency for the grant program. 

2. The steps involved in the grant program each fiscal year could include: 

a. A Request for Pre-Proposals will be issued by the Scientific 

Group. 

b. Pre-Proposals received will be reviewed and evaluated by the 

Scientific Group. Applicants with pre-proposals selected for 

further consideration will be asked to prepare final proposals. 

c. Final proposals will be reviewed, evaluated and accepted or 

rejected by the Scientific Group. 

d. Applicants will be informed by the Scientific Group whether their 

proposal was accepted. 

e. Funds will be disbursed by IAC to accepted research proposals. 

f. Progress reports and final reports will be provided to the Scientific 

Group by funded researchers. 

3. Proposals will be judged—using a standardized evaluation system— based 

on scientific merit, the qualifications of the investigators, ability to provide

quantifiable results and the potential to achieve results applicable to 

hatchery reform goals. Preference will also be given to projects that show 

collaboration with multiple researchers between sectors and agencies of

the salmon restoration community and commitment of other resources to 

the project (matching funds; non-federal and/or federal). 

4. The Scientific Group will use its Scientific Framework for Artificial 

Propagation of Salmon and Steelhead to identify research needs. 

Innovative research in other areas of Hatchery Reform will also be 

considered. 

5. Multiple-year projects are encouraged, but funds will only be awarded on

a year-to-year basis. Successful grants from the previous year must submit

pre-proposals to be considered for a second year of funding. 

6. Although the Scientific Group respects and understands the need for 

protecting the intellectual property contained in research proposals, 

Washington state law requires that materials submitted in response to this

grant announcement shall become the property of the IAC and shall be 

deemed public records. 

7. Applications approved for funding will be required to sign a Project 

Agreement that incorporates the full proposal, negotiated parameters and 

any required federal terms and conditions as appropriate. 

References 

The Reform of Salmon and Steelhead Hatcheries in Puget Sound and Coastal Washington to 

Recover Natural Stocks While Providing Fisheries, Gorton Science Advisory Team, May 7, 1999. 

9 
Hatchery Scientific Review Group Policies and Procedures, 

Adopted April 14, 2000; Revised February 13, 2002 and December 10, 2003 

Washington State Hatchery Reform Language, FY 2000 Consolidated Appropriations Act, US 

Fish and Wildlife Service, Resource Management, Page H12365 

Washington State Hatchery Reform Language, FY 2001 Department of the Interior 

Appropriations Act, House of Representatives, 106 914, Conference Report to Accompany HR 

4578, September 29, 2000. 

Scientific Framework for Artificial Propagation of Salmon and Steelhead, Hatchery Scientific 

Review Group, December 2000. 

Hatchery Reform Recommendations, Hatchery Scientific Review Group, February 2002. 

Scientific Framework and Hatchery Review Program, Hatchery Scientific Review Group, March 

2002. 

10