NOAA Technical Memorandum NMFS-NWFSC-117

Fish Culture Technology 

and Practices for 

Captive Broodstock Rearing 

of ESA-listed Salmon Stocks

April 2012

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Northwest Fisheries Science Center
NOAA Technical Memorandum

NMFS-NWFSC Series

The Northwest Fisheries Science Center of the National 

Marine Fisheries Service, NOAA, uses the NOAA Technical 

Memorandum NMFS-NWFSC series to issue scientific and 

technical publications. Manuscripts have been peer reviewed 

and edited. Documents published in this series may be cited 

in the scientific and technical literature.

The NMFS-NWFSC Technical Memorandum series of the 

Northwest Fisheries Science Center continues the NMFSF/NWC series established in 1970 by the Northwest & 

Alaska Fisheries Science Center, which has since been split 

into the Northwest Fisheries Science Center and the Alaska 

Fisheries Science Center. The NMFS-AFSC Technical 

Memorandum series is now used by the Alaska Fisheries 

Science Center.

Reference throughout this document to trade names does not 

imply endorsement by the National Marine Fisheries Service, 

NOAA.

This document should be referenced as follows:

Maynard, D.J., T.A. Flagg, W.C. McAuley, D.A. Frost, 

B. Kluver, M.R. Wastel, J.E. Colt, and W.W. Dickhoff. 

2012. Fish culture technology and practices for captive 

broodstock rearing of ESA-listed salmon stocks. U.S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-117, 65 p.
NOAA Technical Memorandum NMFS-NWFSC-117

Fish Culture Technology 

and Practices for 

Captive Broodstock Rearing 

of ESA-listed Salmon Stocks

Desmond J. Maynard, Thomas A. Flagg, W. Carlin McAuley, 

Deborah A. Frost, Bryon Kluver, Mike R. Wastel, John E. Colt, 

and Walton W. Dickhoff

Northwest Fisheries Science Center

Resource Enhancement and Utilization Technologies Division

2725 Montlake Boulevard East

Seattle, Washington 98112

April 2012

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
Most NOAA Technical Memorandums

NMFS-NWFSC are available at the 

Northwest Fisheries Science Center

Web site, http://www.nwfsc.noaa.gov

Copies are also available from the

National Technical Information Service

5285 Port Royal Road

Springfield, VA 22161

Phone orders: 1-800-553-6847

E-mail orders: orders@ntis.fedworld.gov

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iii

Table of Contents

List of Figures...............................................................................................................................................v

List of Tables..............................................................................................................................................vii

Executive Summary.....................................................................................................................................ix

Introduction...................................................................................................................................................1

Broodstock Histories.....................................................................................................................................3

ESA-listed Endangered Snake River Sockeye Salmon ..........................................................................3

ESA-listed Threatened Snake River Spring/summer Chinook Salmon .................................................4

Broodstock Coordination........................................................................................................................6

Fish Culture Facilities...................................................................................................................................7

Facilities Selection .................................................................................................................................7

Seawater Facilities..................................................................................................................................9

Freshwater Facilities.............................................................................................................................11

Fish Culture Practices.................................................................................................................................15

Biosecurity Protocols ...........................................................................................................................15

Rearing Densities .................................................................................................................................17

Loading Densities.................................................................................................................................17

Turnover Rates.....................................................................................................................................19

Tank and Raceway Cover.....................................................................................................................19

Feed ......................................................................................................................................................19

Spawning Procedures...........................................................................................................................20

Egg Incubation .....................................................................................................................................22

Egg and Fish Transportation.......................................................................................................................24

Snake River Sockeye Salmon...............................................................................................................24

Snake River Chinook Salmon ..............................................................................................................26

Program Production ....................................................................................................................................27

Snake River Sockeye Salmon...............................................................................................................27

Snake River Spring/summer Chinook Salmon.....................................................................................27

Biological Metrics of NMFS Captive Reared Fish.....................................................................................33

Snake River Sockeye Salmon Culture..................................................................................................33
iv

Chinook Salmon Culture ......................................................................................................................39

Adult Fish Transportation.....................................................................................................................47

Insights and Recommendations ..................................................................................................................50

References...................................................................................................................................................53

Appendix A: Transport Details for Intersite Fish Transfers .......................................................................59
v

List of Figures

Figure 1. Diagram of the path that fish follow in NMFS’s Snake River sockeye salmon captive 

broodstock and rearing operations................................................................................................................4

Figure 2. Flow diagram illustrating ODFW’s approach of coupling captive broodstock technology 

with conventional hatchery production to restore Grande Ronde spring Chinook salmon ..........................5

Figure 3. IDFG’s captive rearing approach to Salmon River spring/summer Chinook salmon 

rebuilding......................................................................................................................................................5

Figure 4. Smolt-to-adult rearing tanks in main ESA seawater rearing building at MRS...........................10

Figure 5. Fry-to-presmolt rearing room at BCH........................................................................................12

Figure 6. Smolt-to-adult rearing tanks at BCH..........................................................................................12

Figure 7. Raceways inside greenhouse type building used for final freshwater maturation of 

sockeye salmon ...........................................................................................................................................13

Figure 8. Incubation buckets in aluminum troughs at BCH.......................................................................13

Figure 9. Illustrations of isolation egg incubator system and its individual components..........................14

Figure 10. Growth rate projection for Redfish Lake sockeye salmon reared in 10°C freshwater 

at BCH ........................................................................................................................................................20

Figure 11. NMFS annual production of prespawning sockeye salmon adults for release in 

Stanley Basin lakes.....................................................................................................................................28

Figure 12. NMFS sockeye salmon eyed egg production available for recovery actions...........................28

Figure 13. Number of eggs NMFS retained each year for incorporation into its captive 

broodstock program ....................................................................................................................................29

Figure 14. Number of eggs NMFS retained for incorporation into adult release production ....................29

Figure 15. Number of eggs and juvenile fish IDFG supplied each broodyear for incorporation 

into NMFS captive broodstock and rearing programs................................................................................30

Figure 16. Number of Salmon River spring/summer Chinook salmon adults produced from each 

broodyear for stock rebuilding activities in Idaho ......................................................................................30

Figure 17. Number of Grande Ronde River spring/summer Chinook salmon produced from each 

broodyear for stock rebuilding activities in Oregon ...................................................................................31

Figure 18. Number of Salmon River spring/summer Chinook salmon smolts transferred to MRS 

from Idaho...................................................................................................................................................31

Figure 19. Number of Grande Ronde River spring/summer Chinook salmon smolts transferred 

to MRS from Oregon ..................................................................................................................................32

Figure 20. Average survival from green egg to eyed egg stage of Redfish Lake sockeye salmon 

by spawn year at NWFSC facilities, 1994–2008 ........................................................................................33

Figure 21. Average survival by broodyear from eyed egg stage to mature adult for Redfish Lake 

sockeye salmon captive broodstock reared at NWFSC facilities................................................................34
vi

Figure 22. Percent by broodyear of Redfish Lake sockeye salmon males in the captive 

broodstock program maturing as 2-, 3-, and 4-year-old adults...................................................................35

Figure 23. Percent of broodyear 1991–2004 female Redfish Lake sockeye salmon reared in 

freshwater at NWFSC facilities maturing as 2-, 3-, and 4-year-old fish.....................................................36

Figure 24. Average fork length for mature 3- and 4-year-old female Redfish Lake sockeye salmon 

spawned at NWFSC freshwater facilities, 2003–2007 ...............................................................................36

Figure 25. Average fecundity of 3-year-old female Redfish Lake sockeye salmon captive 

broodstock females spawned at NWFSC facilities, 1994–2008 .................................................................37

Figure 26. Average fecundity of 4-year-old female Redfish Lake sockeye salmon captive 

broodstock females spawned at NWFSC facilities, 1994–2008 .................................................................38

Figure 27. Average number of eggs produced per gram of 3-year-old spawning Redfish Lake 

sockeye salmon captive broodstock, 1996–2008........................................................................................38

Figure 28. Average green egg weight by spawn year for 3-year-old spawning Redfish Lake 

sockeye salmon captive broodstock, 2003–2008........................................................................................39

Figure 29. Average eyed egg weight for 3-year-old spawning Redfish Lake sockeye salmon 

captive broodstock, broodyear 1991–2008 .................................................................................................40

Figure 30. Average eyed egg weight for 4-year-old spawning Redfish Lake sockeye salmon 

captive broodstock, 1993–2008 ..................................................................................................................40

Figure 31. Percent survival by broodyear for West Fork Yankee Fork stock of Salmon River 

spring/summer Chinook salmon at MRS....................................................................................................41

Figure 32. Percent survival by broodyear for Lemhi River stock of Salmon River spring/summer 

Chinook salmon at MRS.............................................................................................................................42

Figure 33. Percent survival by broodyear for East Fork stock Salmon River spring/summer 

Chinook salmon at MRS.............................................................................................................................42

Figure 34. Percent survival by broodyear for Lostine River stock of Grande Ronde River 

spring/summer Chinook salmon at MRS....................................................................................................43

Figure 35. Percent survival by broodyear for Catherine Creek stock of Grande Ronde River 

spring/summer Chinook salmon at MRS....................................................................................................43

Figure 36. Percent survival by broodyear for Grande Ronde River stock of Grande Ronde River 

spring/summer Chinook salmon at MRS....................................................................................................44

Figure 37. Average fork length of prespawning 3- and 4-year-old adult Salmon River and 

Grande Ronde River spring/summer Chinook salmon at MRS..................................................................45

Figure 38. Average weight of prespawning 3- and 4-year-old adult Salmon River and Grande 

Ronde River spring/summer Chinook salmon at MRS...............................................................................45

Figure 39. Percent of Salmon River stocks of Snake River spring/summer Chinook salmon 

reared at MRS maturing as 2-, 3-, 4-, 5-, and 6-year-old fish.....................................................................46

Figure 40. Percent of Grande Ronde River stocks of Snake River spring/summer Chinook salmon 

reared at MRS maturing as 2-, 3-, 4-, 5-, and 6-year-old fish.....................................................................46
vii

List of Tables

Table 1. NMFS biosecurity protocols for facilities operation....................................................................16

Table 2. Summary of adult fish transfer success from MRS facilities to Oregon and Idaho.....................48

Table A-1. Transport details for intersite fish transfers.............................................................................60

Table A-2. Transport details for intersite fish transfers, Salmon River spring Chinook salmon...............63

Table A-3. Transport details for intersite fish transfers, Snake River (Redfish Lake) sockeye salmon ....65
viii
ix

Executive Summary

The goals of captive broodstock programs for Pacific salmon listed under the U.S. 

Endangered Species Act (ESA) include 1) rescuing small extant populations on the verge of 

extinction and 2) increasing population size in captivity so that sufficient numbers of individuals 

can be returned to their native habitat in attempts to rebuild natural populations to self-sustaining 

levels. Captive broodstock programs are a form of artificial propagation where salmon are 

reared through all or most of their life protected from predation and other forms of natural 

mortality. Theoretically, captive broodstock programs could increase the number of fish 

surviving to maturation by more than two orders of magnitude over survival in nature. However, 

at the start of these programs, full term survival to spawning adults was problematic and research 

and technological development was needed to reach the programs’ potential. The National 

Marine Fisheries Service’s (NMFS) Northwest Fisheries Science Center (NWFSC) captive 

broodstock programs for Redfish Lake sockeye salmon (Oncorhynchus nerka) and 

spring/summer Chinook salmon (O. tshawytscha) have been in operation for almost 20 years 

with notable success and a great deal learned. This report describes the facilities, fish culture 

practices, production, and biological metrics of these programs.

In 1991 Snake River sockeye salmon were listed as endangered under the ESA. That 

same year, NMFS and the Idaho Department of Fish and Game (IDFG) initiated a Bonneville 

Power Administration–funded cooperative captive broodstock for those sockeye salmon. After 

listing, the majority of the remaining anadromous population was taken into captivity for a gene

rescue program. NMFS and IDFG maintained parallel captive broodstocks for this critically 

endangered evolutionarily significant unit. The dual broodstocks in separate federal and state 

facilities comprise a hedge against catastrophic loss of important components of the gene pool. 

This technical memorandum describes only the NMFS portion of the total broodstock effort. 

NWFSC provides full life cycle culture of Snake River sockeye salmon that includes freshwater 

and marine rearing, spawning, and egg incubation. Our cooperative program has successfully 

maintained fish in safety net captive broodstocks for more than five generations and is now 

providing a substantial number of juveniles to Idaho for reintroduction into their natural 

environment. The successful reintroduction effort has resulted in the return of several thousand 

sea-run adult sockeye salmon to Idaho’s Stanley Basin.

Snake River spring/summer Chinook salmon were listed as threatened under the ESA in 

1992. Subsequently in the mid-1990s, captive broodstock safety nets were initiated for three 

Idaho Salmon River and three Oregon Grande Ronde River populations. Oregon cooperators 

choose a traditional captive breeding approach for their Grand Ronde River stocks in which fish 

are reared to maturity at the NWFSC Manchester Research Station (MRS), Manchester, 

Washington, then transferred to the Oregon Department of Fish and Wildlife (ODFW) for 

spawning and rearing of offspring in conventional hatcheries for release as smolts that migrate to 

sea and return as sea-run adults. IDFG adopted a captive rearing approach for the Salmon River 

stocks in which fish are reared to adult in captivity, then returned to Idaho for release into their 
x

natal streams for natural spawning. The NWFSC role for both captive broodstock programs was 

to provide seawater rearing during the marine phase of their life cycle.

NWFSC has freshwater and seawater facilities, enabling it to accommodate a range of 

environmental needs of anadromous fish over the course of their life cycle. NWFSC’s Burley 

Creek Hatchery (BCH) is used for freshwater final maturation of prespawning adults, spawning, 

incubation, and fry-to-smolt rearing. Marine rearing during the smolt-to-prespawning-adult 

stages of the life cycle is conducted at MRS. BCH has pathogen-free ground water to minimize 

development of fish disease and facilitate fish transfer between fish health management zones. 

Seawater at MRS is filtered to five microns and disinfected with ultraviolet (UV) radiation. At 

both facilities, effluent water is treated with either ozone or UV radiation to eliminate potential 

pathogen transfer. Primary and secondary backup generators are employed at both facilities to 

ensure a constant delivery of power to pumps and tertiary backup oxygen is available to maintain 

fish during electrical maintenance and in the rare event of complete electrical failure. The fish 

are protected from predation and vandalism at both facilities by rearing in secure buildings. 

Artificial lighting in fish rearing areas follows a natural photoperiod for proper entrainment of 

natural circadian and seasonal rhythms, and slowly ramps up at dawn and down at dusk to avoid 

startle responses. Marine rearing at MRS is done in circular tanks ranging from 4.1 to 6.1 m 

diameter and freshwater rearing and final maturation occur in circular tanks ranging from 1.5 to 

3.7 m and in 5.8 m long raceways at BCH.

NWFSC has adopted a suite of fish culture practices for its captive broodstocks that 

ensures excellent fish health, maximizes survival, minimizes the risk of inbreeding, and 

maximizes safety net population genetic diversity. These practices begin with stringent 

biosecurity protocols designed to prevent the spread of disease from local fish to the ESA stocks 

and among various ESA stocks. Stress is minimized by handling fish with extreme care such as 

minimizing de-watering of fish during transport and processing. Fish health is monitored daily 

and mortalities are examined for cause of death and to control any pathogen outbreaks early in 

their development. Additional proactive fish health measures include vaccination against Vibrio 

anguillarum before transfer to seawater and giving prophylactic and therapeutic erythromycin 

and azithromycin treatments as deemed prudent.

Stress is minimized by holding rearing densities below 8 kg/m3 (0.5 lbs/ft3

) for immature 

fish and below 15 kg/m3 (1.0 lbs/ft3) when fish near maturity. Except for nonfeeding adults held 

in oxygen-supplemented water, loading densities are kept below 0.84 kg/L/min (7 lbs/gal/min) to 

ensure that the rearing environment does not induce stress that may lead to disease outbreaks.

Maturing and immature fish are identified and sorted each spring using ultrasound 

imaging to assess gonadal development. Maturing spring/summer Chinook salmon are 

transferred to their state of origin, where they are spawned artificially or released into the wild 

for natural spawning. Maturing sockeye salmon are transferred from seawater at MRS to 

freshwater at BCH in June and July. In September several hundred of the maturing sockeye 

salmon in fresh water are transported to Redfish Lake Idaho to spawn naturally. NWFSC retains 

approximately 300 maturing sockeye salmon each year for spawning at BCH.

For the Redfish Lake sockeye salmon program, standard spawning protocols are used to 

identify ripe females, strip gametes, and fertilize eggs. Gonadotropin-releasing hormone analog 
xi

implanting of almost all males is required to synchronize final maturation with females. All 

males and females are sampled for bacterial and viral pathogens at spawning. Fertilization 

crosses are conducted following an inbreeding-avoidance matrix using allele sharing coefficients 

developed by IDFG. Each female is mated with two males and when possible every male is 

mated with two females to reduce the loss of unique genes held by individuals of either sex. 

Fertilized egg incubation follows standard salmon culture protocols. Each full sibling lot is held 

in an individual down-well bucket incubator to minimize potential pathogen transfer.

NWFSC has transferred eyed eggs, smolts, and prespawning adults to facilities in 

Washington, Oregon, and Idaho. Through 2008, NWFSC has supplied 2,210 maturing adults 

and 1,922,700 eyed eggs to Idaho’s Redfish Lake sockeye salmon program. As of July 2008, 

NMFS has reared 3,523 prespawning Chinook salmon that were delivered to Idaho for 

reintroduction to the Salmon River watershed and provided 4,031 adult Chinook salmon to 

ODFW. Eyed eggs are shipped in plastic mesh tubes wrapped in moist towels held in insulated 

containers. Eyed egg shipments are via air to Idaho and truck to Oregon. Prespawning Chinook 

salmon are transferred by truck from seawater at MRS to freshwater in Idaho and Oregon. 

Transport water consists of 25% seawater and 75% freshwater with fish density less than 0.06 

kg/L (0.5 lbs/gal). Transport survival of captive broodstock fish has been excellent. There has 

been no mortality during 12 years of adult sockeye salmon transfer from NMFS facilities to 

Redfish Lake and of adult Chinook salmon transfer to ODFW’s Bonneville Fish Hatchery. 

There was no mortality for 5 years of transfer of adult Chinook salmon to IDFG’s Eagle Fish 

Hatchery.

Survival of sockeye salmon and Chinook salmon in the captive programs was 

substantially higher than expected in nature. Survival of sockeye salmon from the green-to-eyed 

stage at NMFS facilities averaged 62.2% between years 1994 and 2008. The average survival of 

sockeye salmon captive broodstock during the longer eyed-egg-to-mature-adult period was 

61.7%. Overall green-egg-to-adult survival was 38.4%, which is at least two orders of 

magnitude higher than the estimated 0.3% or less survival expected for a relatively stable 

population in nature. The overall average survival of Chinook salmon (broodyears 1994–2003) 

was 58.8% for Salmon River stocks and 67.9% for the Grand Ronde River stocks.

The fish culture technologies described in this report have successfully maintained ESAlisted sockeye salmon and Chinook salmon stocks in safety net programs. The programs have 

maintained significant genetic diversity of the founding populations and generated large numbers 

of fish for use in restoration. Key factors leading to the success of safety net programs include 

pathogen-free water, onshore tanks, fully enclosed buildings, and rigorous biosecurity protocols. 

Rearing sockeye and Chinook salmon at low densities in large tanks is critical for high fish 

survival. Use of mating strategies designed to reduce loss of unique genetic traits and minimize 

inbreeding helps maintain genetic diversity. Maintenance of duplicate genetic groups in 

geographically separate facilities greatly reduces the potential for catastrophic loss of stocks. 

Rigorous fish transportation measures have led to excellent fish survival in moving fish among 

facilities. The technologies and standards developed for full life cycle captive salmon rearing 

have provided a valuable tool for rebuilding ESA-listed populations of Pacific salmon.
xii
Introduction

This technical memorandum documents the current fish culture practices, technologies, 

and results that the National Marine Fisheries Service’s (NMFS) Northwest Fisheries Science 

Center (NWFSC) utilizes for captive broodstock efforts for selected stocks of Pacific salmon 

(Oncorhynchus spp.) of the Columbia River basin listed under the U.S. Endangered Species Act 

(ESA). Since the early 1990s, NWFSC has been involved with three major captive broodstock 

efforts for Columbia River basin stocks: 1) ESA-listed endangered Snake River sockeye salmon 

(O. nerka), 2) three stocks of ESA-listed threatened Snake River spring/summer Chinook salmon 

(O. tshawytscha) from the Salmon River basin in Idaho, and 3) three stocks of ESA-listed 

threatened Snake River spring/summer Chinook salmon from the Grande Ronde basin in 

Oregon. Each of these efforts is partnered with the local, state, and tribal agencies involved with 

recovery planning and implementation actions for the individual stocks.

Captive broodstock programs are a form of artificial propagation. However, they differ 

from traditional hatchery programs in one important respect: fish are cultured in captivity for 

their entire life cycle (Flagg and Mahnken 1995). The high fecundity of Pacific salmon, coupled 

with their potentially high survival in protective culture, affords an opportunity for captive 

broodstocks to aid restoration efforts (Flagg et al. 1995a, Schiewe et al. 1997). The high egg-tosmolt survival offered by the protective culture environment is used to rapidly increase the 

number of spawning adults above that which would occur if they had been released to the 

environment and gone to sea. Most captive broodstock programs follow a breeding approach 

where captive maturing fish are spawned, offspring incubated, and egg-to-smolt stages released 

into native watersheds. A captive rearing approach is also sometimes utilized where maturing 

adults are released back into their natal streams to spawn naturally. All forms of captive 

broodstock programs can be viewed as gene rescue efforts to preserve and maintain the genetics 

of populations at risk of extinction or, if adequate source stock is available, at levels to 

supplement natural salmon populations.

At the initiation of the NWFSC programs, captive broodstock rearing of Pacific salmon 

was considered an evolving technology, without well-defined standards (Flagg and Mahnken 

1995). Full-term rearing to adult was considered problematic: high mortality rates and low egg 

viability were common in previously attempted programs. Egg-to-adult survival rates generally 

ranged well below 30%, viability of eggs to the eyed stage from captive-reared brood was 

commonly only 30–60% compared to viabilities of more than 80% for the eggs from wild 

cohorts, and the size of captive-reared adults was generally smaller than that of wild fish (Flagg 

et al. 1995a).

During the evolution of NWFSC participation in the current captive broodstock 

programs, a number of engineering advances have occurred in available equipment and 

considerable research and development have been conducted on captive broodstock technologies 

(Swanson et al. 1996, Berejikian 2000, 2002, 2004, Berejikian and Nash 2001, 2003). 

Specialized captive broodstock rearing facilities were developed and refined. Additionally, 
2

guidelines have been proposed covering when to implement and how to conduct a captive 

broodstock action (Pollard and Flagg 2004). The overall success of captive broodstock rearing 

has improved dramatically; egg-to-adult survival now routinely ranges 50–80%, egg viability has 

improved greatly to more than 75%, and size and body conformation of fish is often equivalent 

to the wild progenitors.

In this document, we describe the development and use of these captive broodstock 

technologies at NWFSC facilities and provide our current set of facility and culture guidelines on 

the health and well-being of captive broodstock fish. Although the information presented is 

specific to fish reared at NWFSC facilities, we believe the results can be generalized to 

expectations for other facilities following similar guidelines. Additional details on NMFS

culture protocols and facilities are available in a series of annual reports to the Bonneville Power 

Administration (BPA) (Flagg 1993, Flagg and McAuley 1994, Flagg et al. 1996, 2001, Frost et 

al. 2003a, 2003b, 2005b, 2006, 2008a, 2008b, Maynard et al. 2003a, 2003b, 2005, 2006, 2007, 

2009a, 2009b, 2009c).
3

Broodstock Histories

ESA-listed Endangered Snake River Sockeye Salmon

Snake River sockeye salmon were listed as endangered under the ESA in 1991 (Waples et 

al. 1991). The last known remnants of the stock return to Redfish Lake in the Sawtooth Valley 

of Idaho. Only minimal numbers of fish (0–8 per year) had returned to Redfish Lake in the years 

preceding the listing and the probability of extinction was high. On the basis of critically low 

population numbers, aggressive gene rescue actions were initiated during the year of ESA listing 

to stem extinction risks for Snake River sockeye salmon. These measures included taking a 

majority of the remaining population into captivity and initiating actions in the freshwater 

rearing habitat to promote survival of reintroduced fish (Flagg et al. 1995a, 2004). Participants 

included NMFS, Idaho Department of Fish and Game (IDFG), Shoshone-Bannock Tribes of 

Idaho, University of Idaho, and BPA.

At project initiation, it was recognized that the effective population size for establishment 

of the captive broodstock was likely to be extremely small. During the 1990s, a total of 16 wild 

fish (0–8 per year) returned to Redfish Lake. IDFG captured all returning fish and placed them 

in a captive broodstock program as a gene rescue effort (Flagg et al. 1995b). In addition, 

approximately 900 smolts and 25 residual sockeye salmon were captured for captive broodstock 

rearing in 1991–1993. To reduce the risk of catastrophic loss, the fish have been maintained at 

NWFSC and IDFG facilities. The program currently has fish that have been in captive 

broodstock culture for multiple generations. Core lineages are tracked by IDFG and mated so as 

to maintain genetic diversity (Kozfkay et al. 2008). On an annual basis, IDFG ships groups of 

approximately 450–1,000 eyed eggs to NWFSC for its portion of the captive broodstock 

program. The program has had success during the gene rescue phase and is currently 

transitioning to include a large supplementation effort (see Flagg et al. 2004, Hebdon et al. 2004, 

Peterson et al. 2008, Kozfkay et al. 2008).

The NMFS portion of the work includes captive broodstock and captive rearing as 

illustrated in Figure 1. The rearing of each year-class typically begins with the receipt of eyed 

eggs shipped from IDFG’s Eagle Fish Hatchery (EFH), Eagle, Idaho, to NWFSC’s Burley Creek 

Hatchery (BCH), Burley, Washington, in early winter. The eggs are then incubated until fry 

swimup, at which time they are ponded and reared in freshwater circular tanks until they reach 

the smolt stage. Some of the smolts are retained in freshwater whereas others are sent to 

NWFSC’s Manchester Research Station (MRS), Manchester, Washington, for seawater rearing. 

The fish are maintained in culture until they begin to show signs of maturation. In most years, 

slightly more than one-half of the maturing fish are returned to Redfish Lake, where they are 

allowed to spawn volitionally in a captive rearing program. The remainder of the fish are 

spawned at BCH with the resulting eggs shipped to restocking programs when they reach the 

eyed stage. Historically the majority of stocked eggs have gone into egg box programs. The 

remainder are shipped to production hatcheries where the fish are grown for restocking as 

summer fry (discontinued), autumn presmolts, and spring smolts.
4 

Start with 1,000 eyed eggs received from IDFG EFH

Incubate 1,000 eggs

Pond 990 swimup fry

Rear fry in culture to produce 700 prespawning adults

Release 400 prespawning adults 

into Redfish Lake and allow to 

spawn naturally

Artificially spawn 300 adults

Produce 187,500 fertilized eggs for outplanting

Produce 127,875 eyed eggs for outplanting

Select 1,000 for next 

generation captive 

program if needed

Plant 56,785 in egg 

boxes in Stanley Basin 

lakes for natural rearing

Transfer 70,000 to production hatchery 

for growout

40,000 fall presmolt 

release

30,000 spring smolt 

release

Figure 1. Diagram of the path that fish follow in NMFS’s Snake River sockeye salmon captive 

broodstock and rearing operations. Numbers reflect typical survivals among life stages.

ESA-listed Threatened Snake River 

Spring/summer Chinook Salmon

Snake River Chinook salmon were listed as threatened under the ESA in 1992 (Mathews 

and Waples 1991). In spring 1995, NMFS, IDFG, U.S. Fish and Wildlife Service, Oregon 

Department of Fish and Wildlife (ODFW), Confederated Tribes of the Umatilla Indian 

Reservation, and Nez Perce Tribe initiated captive broodstocks as part of conservation efforts for 

ESA-listed stocks of Snake River spring/summer Chinook salmon. Two approaches were 

identified: a conventional captive broodstock approach (Flagg and Mahnken 1995) and a less 

conventional captive rearing approach (Berejikian et al. 2004). ODFW choose the traditional 

captive breeding approach, where maturing fish are spawned and the offspring incubated, reared 

to the smolt stage, then released into their native watersheds (Figure 2). IDFG adopted a captive 

rearing approach where maturing adults are released back into their natal streams to spawn 

naturally (Figure 3). Both approaches shared the same goal of maintaining Snake River Chinook 

salmon metapopulation structure by preventing year-class failures and local extinctions. 
5 

Source parr from stream

Rear parr at Wallowa Fish Hatchery to smolt stage

Transfer smolts to MRS and BFH for smolt to adult rearing

Rear smolts until they show the first signs of maturation

Transfer maturing adults to BFH for final maturation

Artificially spawn adults at BFH

Produce eyed eggs for production rearing

Incubate eggs and rear juveniles to smolt stage at Lookingglass Fish Hatchery

Transfer and release smolts from acclimation ponds on natal river

Figure 2. Flow diagram illustrating ODFW’s approach of coupling captive broodstock technology with 

conventional hatchery production to restore Grande Ronde spring Chinook salmon. MRS = 

Manchester Research Station, BFH = Bonneville Fish Hatchery. 

Figure 3. IDFG’s captive rearing approach to Salmon River spring/summer Chinook salmon rebuilding. 

EFH = Eagle Fish Hatchery.

Start with 300 eyed eggs sourced from Salmon River redds

Incubate 300 eyed eggs at EFH

Pond 297 swimup fry at EFH

Rear fry in culture to produce 290 smolts

Transfer 290 smolts to MRS for seawater rearing adults

Rear smolts to prespawning stage ready for freshwater reentry

Return 203 prespawning adults to natal spawning area

Allow 203 surviving mature adults to spawn naturally
6

The Oregon captive broodstock program focused on three stocks (upper Grande Ronde 

River, Catherine Creek, and Lostine River) captured as juveniles from the Grande Ronde River 

basin. Idaho’s Snake River captive broodstock program included three stocks (Lemhi River, 

East Fork Salmon River, and West Fork Yankee Fork) captured as eyed eggs or juveniles from 

the Salmon River basin (Hoffnagle et al. 2003, Venditti et al. 2002). After collection, the fish or 

eyed eggs were transported to the IDFG EFH or the ODFW Lookingglass Fish Hatchery, Elgin, 

Oregon, for freshwater rearing until they reached the smolt stage. Most smolts from the IDFG 

program (about 150 stock) and one-third to one-half of the smolts from the ODFW program

(about 450 stock) were transferred to the NWFSC marine rearing facilities at MRS. The fish

were reared in seawater until they began to show signs of maturity. They were then transferred 

back to freshwater facilities in Idaho and Oregon for final maturation. The mature fish in the 

IDFG captive rearing program were released into enclosed stream sections in Salmon River 

streams to spawn naturally. ODFW artificially spawned the mature fish in its captive broodstock 

program at its Bonneville Fish Hatchery (BFH), Cascade Locks, Oregon, to produce juveniles for 

smolt releases in its Grande Ronde Basin supplementation program. ODFW, IDFG, and NMFS

investigators are comparing the relative success of the two reintroduction strategies and the 

effect of freshwater versus seawater rearing.

Broodstock Coordination

The Redfish Lake sockeye salmon captive broodstock program is overseen by the BPAchaired Stanley Basin Sockeye Technical Oversight Committee. The captive rearing program 

for Snake River spring Chinook salmon and the Grand Ronde Basin spring Chinook salmon 

captive broodstock program are overseen by the BPA-chaired Chinook Salmon Captive 

Propagation Technical Oversight Committee and the Oregon Technical Oversight Team, 

respectively. All three groups contain representatives of state, federal, tribal, and private groups 

involved in the conservation of the respective ESA-listed stocks. Members meet regularly to 

review program activities and provide overall recommendation for collection, rearing, and 

release strategies.
7

Fish Culture Facilities

Facilities Selection

At the initiation of the first of the NWFSC captive broodstocks for ESA-listed Columbia 

River basin fish (Redfish Lake sockeye, 1991), little was known regarding methods to ensure 

survival of fish to adulthood in captive culture. Most past attempts at captive broodstock culture 

of Pacific salmon indicated that full-term culture in pathogen-free freshwater generally resulted 

in much higher survival to spawning and much higher percentages of viable gametes than culture 

in seawater (Mahnken and Flagg 1995). Therefore, full-term freshwater rearing in pathogen-free 

water was chosen for initiation of this sockeye endangered species rearing program (Flagg et al. 

1995a, Schiewe et al. 1997).

Nonetheless, anadromy with smolt-to-adult rearing in seawater is the normal life history 

for sockeye and other Pacific salmon. Anadromous spring/summer Chinook and sockeye salmon 

spawn in freshwater, spend 1 to 2 years rearing in streams and rivers, then migrate to sea as 

smolts where they spend the majority (2–4 years) of their life (Burgner 1991, Healey 1991). 

When they begin to mature, adults migrate back to their natal streams, rivers, or lakes to spawn. 

Salmon are thought to migrate to the sea because it provides better feeding and growing 

conditions, even though it imposes greater predation risk. Thus potential survival reductions are 

offset by females producing more eggs and males developing enhanced sexual capabilities (e.g., 

size and milt volume) compared to population members that remain in freshwater. In addition, 

anadromous populations, with a portion of their members at sea each year, have an increased 

chance of survival when natural catastrophes (volcanic ash falls, drought years, etc.) eliminate all 

freshwater residents.

Anadromy is the key life history characteristic of Pacific salmon that enabled them to 

colonize the vast vacant areas west of the Continental Divide after glacial recession. The 

importance of seawater rearing during the marine phase of the salmon life cycle is recognized 

and called for by the NMFS Interim Standards for the Use of Captive Broodstocks to eliminate 

possible selection against anadromous traits that might occur with full-term freshwater rearing 

(Pollard and Flagg 2004). Therefore, tests were initiated using a non-ESA-listed stock to 

compare freshwater versus seawater culture to adulthood for sockeye salmon and to establish the 

facilities criteria for the Redfish program (Flagg et al. 1996). At the initiation of these studies in 

1992, it appeared probable that many past husbandry problems in seawater were related to 

culture in net pens exposed to near surface environmental conditions. Several environmental 

factors critical to survival (e.g., temperature, salinity, toxic plankton blooms) are more variable at 

the surface than in the deeper marine waters preferred by most salmonids. In addition, fish held 

in net pens are at risk of escape, natural catastrophes, disease transmission, and predation from 

marine mammals and birds.

Studies were carried out in seawater at the NMFS MRS and in freshwater at a MRS

satellite facility located at the University of Washington’s Big Beef Creek (BBC) Fisheries 
8

Research Station near Seabeck, Washington. Studies comparing seawater and freshwater rearing 

were conducted with two year-classes (1990 and 1991 brood) of Lake Wenatchee sockeye 

salmon. Three replicates of approximately 300 yearling smolts were placed in each of the 

following environments: 1) 4.1 m diameter circular fiberglass tanks supplied with fresh well 

water at 10°C at BBC (freshwater tank [FWT] treatment); 2) 4.1 m diameter circular fiberglass 

tanks supplied with pumped, filtered, and ultraviolet (UV) radiation–sterilized seawater at MRS

(saltwater tank [SWT] treatment); and 3) 4.9 m square seawater net pens at MRS (saltwater pen 

[SWP] treatment). Water depth in each rearing environment was adjusted to provide 

approximately 12 m3 of fish rearing space per container.

As described in Flagg et al. (1998), for the entire 2-year study sockeye salmon reared in 

the freshwater tanks had generally higher survival and growth rate compared to the seawater 

groups. Although for the 1990 brood Lake Wenatchee sockeye salmon, there was no significant 

difference in survival to adult (32% FWT, 35% SWT, and 26% SWP, P > 0.05), survival to 

spawning for the 1991 brood averaged 88% for FWT, 61% for SWT, and 22% for SWP, (P < 

0.02). The high mortality in all groups of the 1990 brood was attributed to severe infections of 

Renibacterium salmoninarum, the causative agent of bacterial kidney disease (BKD). For the 

1991 brood, BKD was noted as a severe problem only in fish reared in net pens. For both 

broodyears, growth differences (P < 0.05) were noted, with the treatments ranked FWT > SWT 

(69.5% of FWT weight) > SWP (65.9% of FWT weight) for the 1990 brood and FWT > SWT 

(70.8% of FWT weight) = SWP (78.0% of FWT weight) for the 1991 brood. There were no 

significant differences (P > 0.10) in eyed egg survival for the 1990 brood Lake Wenatchee 

sockeye salmon (50% FWT, 42% SWT, 45% SWP). Significant differences (P < 0.001) in eyed

egg survival were noted for 1991 brood spawners between the FWT and SWT and SWP 

treatments (67% FWT, 43% SWT, 40% SWP).

The test data indicated that culture in seawater net pens was a poor choice for sockeye 

salmon and probably most other captive broodstock programs. Full-term culture to adult in 

freshwater appeared to provide lowest disease incidence and highest viability. The study 

indicated that if seawater rearing was deemed necessary to preserve anadromy, then rearing in 

filtered and sterilized seawater appeared to be the best choice for captive broodstock programs 

(Flagg et al. 1998). Therefore, with BPA support, appropriate facilities were constructed at MRS

to rear Redfish Lake sockeye salmon captive broodstocks in freshwater and seawater protective 

culture conditions. This document describes the facilities in their current state.

Over the duration of the project, changes have been made at the facilities as the programs 

evolved. For example, the seawater portion of the facilities was expanded with the onset of the 

Chinook salmon captive broodstocks in the mid-1990s. Likewise, the freshwater rearing facility 

was physically relocated from the University of Washington BBC facility to the MRS BCH. 

However, the basic design elements and functions have remained the same (For specifics of 

facilities status during various stages of development, see BPA Web-based annual reports for the 

NMFS Redfish Lake sockeye salmon and Snake River Chinook salmon captive broodstock 

programs, online at www.efw.bpa.gov/IntegratedFWP/technicalreports.aspx.).
9

Seawater Facilities

MRS is located near Manchester, Washington, on Clam Bay, a small bay adjoining the 

central basin of western Puget Sound. A major advantage of the site is its excellent seawater 

quality. Clam Bay is a major tidal mixing zone between Sinclair and Dyes inlets to the west and 

waters of central Puget Sound to the east. Annual seawater temperature at the site normally 

ranges 7–15°C and salinity ranges 26–29 ppt. The high quality seawater environment, combined 

with a 250 m pier made available to the station by the U.S. Environmental Protection Agency 

Region X Laboratory, make MRS an excellent site for the culture of anadromous salmonids 

during their marine life history phase.

A constant source of processed seawater ensures successful captive rearing survival. A 

60 hp centrifugal pump supplies approximately 5,000 L/min (1,250 gal/min) of seawater through 

a 700 m pipeline from the east end of the pier to the station’s land-based facilities. The system is 

outfitted with a backup 50 hp pump in case of primary pump failure. The pumps are attached to 

a floating platform that remains at a constant level above the water surface with rising and falling 

tides. This floating platform is equipped with a 1.1 m × 2.3 m × 1.7 m deep sump located 

beneath the pumps. The sump is fitted with a 0.6 m diameter and 3.7 m long snorkel intake that 

draws in seawater 4.9 m below the surface. The intake is equipped with 1.9 cm × 3.2 cm 

diamond mesh screen to prevent larger objects being sucked into the pump wet end. An alarm 

system monitors the pumps and electrical supply and is tied into an automatic dialer system 

linked to cellular telephones. Redundant emergency generators (330 KW each) are 

automatically serially activated in the event of a power failure.

The seawater supplied to the station is processed to prevent naturally occurring bacterial 

pathogens and parasites from entering the rearing tanks. Primary filtering consists of six 1.9 m2

deep bed fiberglass sand filters. The filters use either number 20 grade sand or number 25 glass 

micro beads as filter media. The sand filters remove all materials greater than 20 microns in 

diameter, and a portion of smaller materials. Immediately after leaving the sand filters, the 

seawater enters 2 filter systems, which contain a total of 148 cartridge filters ensuring removal of

all particles larger than 5 microns. To control for pathogens, the seawater next passes through 

stainless steel UV chambers where it is irradiated with a UV dosage of 55,000 to 90,000 

microwatts per second per cm2. After UV filtration, the seawater goes directly to rearing tanks. 

Sensors monitor water flow and pressure through the seawater filtration system.

Land-based seawater captive broodstock rearing is conducted in two secure buildings 

with 1,280 m2 and 400 m2 of floor space for fish rearing tanks. The 1,280 m

2 facility houses 

twenty 6.1 m diameter circular fiberglass tanks (Figure 4). The 400 m

2 seawater laboratory 

contains six 4.1 m diameter circular fiberglass tanks. Water depth in the 6.1 m diameter tanks is 

generally maintained around 1.5 m and in the 4.1 m tanks near 0.9 m. Before entering fish 

rearing tanks, the processed seawater passes through packed column degassers which are filled 

with plastic bio-rings that break up the water, boosting dissolved oxygen (DO) levels and 

allowing off-gassing of excess nitrogen, which can be present in pumped water situations. Water 

leaving the packed columns can either go directly to individual tanks within the captive 

broodstock rearing building or a portion of the seawater can be diverted through chillers. 

Seawater lines that have been inactive are thoroughly flushed for 24 hours before being used to 

supply water to culture tanks. This practice eliminates harmful metabolites that can develop in 
10

Figure 4. Smolt-to-adult rearing tanks in the main ESA seawater rearing building at MRS.

the lines when they are inactive. Summer water temperature in Clam Bay can reach 15°C, which 

can be detrimental to maturing salmonids. Generally, two 35-ton chillers with titanium plate 

heat exchangers are brought online in summer to ensure that water remains below 13°C. In 

addition, each tank is directly supplied with oxygen to maintain life support in the event of an 

interruption in water flow.

Effluent seawater from rearing tanks is treated before it is returned to Puget Sound. MRS

complies with Washington State Department of Fish and Wildlife (WDFW) quarantine 

certification standards by depurating all effluent from the captive broodstock rearing areas by 

ozone treatment. The ozone treatment system consists of four parts, 1) a below ground 3-

chamber 25,000 gallon concrete depuration tank, 2) a recirculation pump system to move water 

from the depuration tank through the ozone building where the water is injected with ozone gas, 

3) an air-cooled 6-module ozone generator capable of producing 360 g/hr of ozone, and 4) an 

ozone destruct system to control ozone off-gassing.

Adopting lighting controls that avoid light shock reactions and maintain fish on a natural 

photoperiod promote good physiological condition and the entrainment of natural circadian 

rhythms (see Heinen 1998 for review). Captive broodstock buildings at MRS are equipped with 

an automated Lutron system (Lutron Electronics Co. Inc., Coopersburg, Pennsylvania) that 

slowly (over 20 minutes) ramps up incandescent lights at dawn and down at dusk to avoid light 

shock reactions. All rearing areas have been equipped with either windows or transparent panels 

to provide some natural light. A series of light readings (four inside and four outside) were taken 

at midday on 15 June 2010 to compare light levels inside and outside of building 13. The mean 

light level outside building 13 was 28,775 ±1,242 SD lux and was more than 3 orders of 

magnitude higher than the 47 ±5 SD lux recorded inside building 13. Interior or exterior lights 

that might inadvertently light rearing and incubation areas are turned off at dusk and not turned 

on until dawn to ensure natural photoperiod entrainment. Security measures to protect fish and 

property include water flow, fire, and intruder alarms. Alarms are monitored through a security 
11

system linked to pagers and cellular telephones. A backup generator automatically activates 

during power failures.

Freshwater Facilities

Freshwater rearing is conducted at the MRS BCH satellite facility near Burley, 

Washington (≈21 km from Manchester). The facility includes two buildings and a portable 

greenhouse for fish rearing. A 613 m2 building contains nine 3.7 m postsmolt to adult rearing 

tanks and ten 1.5 m diameter swimup fry to presmolt rearing tanks (Figure 5 and Figure 6). A 

256 m

2 building contains four 5.8 m × 1.2 m × 1.2 m tall grey raceways for maturing adult fish 

and four 3.7 m grey circular tanks for rearing postsmolt to adult fish. The 189 m

2 portable 

greenhouse building contains ten 5.8 m × 1.2 m × 1.2 m tall grey raceways for holding maturing 

salmon under near natural light levels (Figure 7). The water depth is maintained at 1.0 m in the 

3.7 m tanks, 0.5 m in the 1.5 m tanks, and 0.8 m in the 5.8 m raceways. Each raceway is

supplied with hatchery well water and supplemental oxygen and is covered one-quarter to onethird of its length with a dark tarp to provide shelter for the fish to seek refuge. A separate 

incubation room accommodates aluminum troughs with approximately 300 Novotny et al. (1985) 

type downwell incubators for isolated egg incubation (Figure 8 and Figure 9).

The hatchery is supplied with approximately 2,000 L/min of high quality 10°C well water 

pumped from two wells. Two additional wells are on site to allow well cycling and provide 

backup. Before distribution to the rearing tanks, the water flows through a packed column 

degassing tower that removes excess nitrogen from the pumped water and raises DO levels to a 

prefish baseline of about 10.3 ppm (about 90% saturation). Water supplied to incubation and fry 

rearing can be diverted through a chiller to decrease the water temperature to 5°C to regulate the 

fish developmental rate. A bulk liquid oxygen tank supplies oxygen through air stones to the 

rearing tanks for supplementation and for life support in the event of water flow disruption. 

Effluent from the hatchery is depurated through a settling basin and UV irradiation system, per 

WDFW quarantine requirements. Entry to BCH is limited by a 2.2 m chain link fence topped 

with barbed wire.

Low levels of natural lighting and photoperiod are maintained in the rearing areas by 

screened windows. Measurements made between 9 April and 21 April 2009 indicated area 

lighting ranged from 32 to 129 lux during daylight hours. The fish rearing areas at BCH are 

equipped with an automated Lutron fluorescent light system and a sunlight tracking timer 

(Suntracker, Paragon Technologies, Two Rivers, Wisconsin) that slowly (over 10 minutes) 

ramps lights up at dawn and down at dusk. Interior or outside lights that might inadvertently 

light rearing and incubation areas are turned off at dusk and not turned on until dawn to ensure 

natural photoperiod entrainment. Security measures to protect fish and property include water 

flow, fire, and intruder alarms. Alarms are monitored through a security system linked to 

cellular telephones. A backup generator automatically activates during power failures.
12

Figure 5. Fry-to-presmolt rearing room at BCH.

Figure 6. Smolt-to-adult rearing tanks at BCH.
13

Figure 7. Raceways inside the greenhouse type building used for final freshwater maturation 

of sockeye salmon.

Figure 8. Incubation buckets in aluminum troughs at BCH.
14

Figure 9. Illustrations of the isolation egg incubator system and its individual components.
15

Fish Culture Practices

Captive broodstock fish are reared at BCH and MRS using standard fish culture practices 

and approved therapeutics (for a general overview of methods, see Leitritz and Lewis 1976, 

Piper et al. 1982, FRED 1983, McDaniel et al. 1994, Schreck et al. 1995, Pennell and Barton 

1996). Fish culture practices conform to the husbandry requirements detailed in ESA Section 10 

Propagation Application for Permit 1148 for NMFS rearing of ESA-listed Snake River sockeye 

salmon. This permit specifies the number of fish that can be reared and released. It requires the 

use of prudent fish culture practices that maximize survival and minimize the risk of artificial 

selection in the hatchery environment. These include maintaining fish in water to the maximum 

extent possible during handling, providing adequate water replenishment in holding units, and 

not handling fish when water temperatures exceed 20°C. The permit specifies that NWFSC must 

conduct coordinated planning under the Stanley Basin Sockeye Technical Oversight Committee

and that fish taken into the program be selected to represent the entire genetic spectrum of the 

founding population.

Biosecurity Protocols

Biosecurity practices are in place to prevent the spread of diseases from local fish to the 

ESA stocks and from one stock to another within the ESA program (Table 1). Housing fish 

within a fully enclosed building and rearing them on treated water is essential to ensure that 

pathogens from wild fish do not reach the ESA captive broodstocks. For the seawater system, an 

insight developed over the course of operations was to ensure a direct linkage (both on or both 

off) between the pumps and the UV treatment to ensure that untreated water was not pumped 

into ESA tanks. In recent years, we prohibited the holding of salmonids in facility net pens 

located near the intake pumps to reduce potential salmonid pathogens from entering the water 

supply.

Biosecure culture practices form the basic approach to prevent pathogens from being 

spread from one cultured stock to another. Separate brushes and nets are provided for each pool; 

staff use a new pair of disposable gloves per pool when brushing pools or removing mortalities. 

All equipment is disinfected in 100 ppm iodophore for a minimum of 30 minutes before being 

moved to a new pool. Disinfection includes crowder screens, nets, transfer tubes, anesthetic 

tank, tables, weighing pan, scale, passive integrated transponder (PIT) tag reader equipment,

waders, and rain gear. Personnel are expected to change rain gear as they move between pools to 

provide proper disinfection time. Shower curtains are placed around anesthetic tanks during fish 

sampling and transfer to prevent splashed water from reaching adjacent pools. Adjacent pools 

may be temporarily covered with disinfected plastic when there is a risk of cross-contamination. 

After fish handling, the floor is sprayed with an iodophore disinfectant.

In general, the fish are handled with extreme care and kept in water to the maximum 

extent possible during transport and processing procedures. This includes the use of a waterfilled fish transfer tube for moving fish between buildings at BCH. The 3.7 m diameter rearing 
16

Table 1. NMFS biosecurity protocols for facilities operation. These procedures are performed on a 

continuous basis throughout the program.

• Maintain stocks in fully enclosed buildings.

• For seawater systems, filter incoming water to 5 microns then treat with 55,000–90,000 

microwatts/sec of UV radiation. Do not culture salmonids in net pens near pump intake.

• For freshwater systems, use well (ground) water supplies.

• Maintain rearing densities below 8 kg/m3 and loading densities below 0.84 kg/L/min.

• Provide chilled water (below 12°C) during summer high water temperatures.

• Provide backup power supply for pumps and disinfection system tied together to ensure seawater 

does not flow to tanks unless UV system treatment system is active.

• Maintain zoned rearing areas for individual stock groupings (e.g., Idaho sockeye vs. Chinook 

salmon).

• Use foot baths with 100 ppm iodophore at all building access points and between individual zoned 

areas.

• Use separate crowder screens for each stock grouping (e.g., Idaho sockeye vs. Chinook salmon).

• Use separate waders and raingear for each stock grouping (e.g., Idaho sockeye vs. Chinook 

salmon).

• Use separate brushes and nets for each pool.

• Use a new pair of disposable gloves per pool when brushing pool or picking mortalities.

• Iodophore disinfect rearing pools (100 ppm for 30 min).

• Iodophore disinfect all sampling equipment between pools (100 ppm for 10 min), including:

o Crowder screens

o Nets and hauling boots

o Anesthetic tank

o Table

o Weighting pan, scale, and table

o PIT tag reader equipment

o Rain gear—it will be changed between pools to increase disinfection time in iodophore.

• Place shower curtain around anesthetic tanks during sampling to control splash contamination.

• Spray down floor areas and working surfaces with idiophore after fish handling.

tanks are constructed to hold at least 15 cm of water when the external standpipes are removed. 

This minimized the chance of fish being accidentally dewatered during tank draining or flushing. 

As experience has taught us, this safety device that prevents complete dewatering of the tank 

must be removed to allow 100% drawdown when tanks are disinfected to ensure all disinfectant 

is flushed from the tank. Low levels of natural and artificial lighting and natural photoperiod are 

maintained in the rearing areas by screened windows and a sunlight-tracking timer on the rearing 

area lighting system.

Fish health is monitored in several ways. Fish are observed daily for feeding response, 

external condition, and behavior as initial indicators of developing problems. Indicators include 

signs of lethargy, erratic swimming, side swimming, flashing, unusual respiratory activity, body 

surface abnormalities, and unusual coloration. Dead or morbid fish are removed immediately, 

bagged, PIT tags read, and submitted for pathology screening. A fish pathologist performs 

necropsies to determine cause of death. Infectious disease screening includes collection of 

kidney tissue, which is subjected to enzyme-linked immunosorbent assay (ELISA) to determine 
17

BKD infection. Virology screening is performed on the kidney samples using a Chinook salmon 

epithelial cell tissue culture–based assay in order to detect infectious hematopoietic necrosis 

virus (IHNV) and viral hemorrhagic septicemia virus (VHSV). Any tissue culture monolayer 

showing signs of cytopathic effects is then subjected to polymerase chain reaction–based 

identification of the virus species. Samples from other overt lesions are also cultured on a 

variety of laboratory medium and subjected to microbial analysis.

Other common bacterial pathogens that may be encountered include furunculosis 

(Aeromonas salmonicida), vibriosis (Vibrio anguillarum), and members of the Flavobacterium 

genus. Typically, when a treatable pathogen is either detected or suspected, the NMFS fish 

pathologist prescribes appropriate prophylactic and therapeutic drugs (e.g., oxytetracycline or 

erythromycin). Azithromycin (an erythromycin derivative) is also used to treat BKD in R. 

salmoninarum–infected populations. Medication is either mixed with feed or injected, with 

dosage based on fish weight. Prior to transfer to seawater, fish in the adult release group receive 

an injection of the V. anguillarum bacteria vaccine. In addition, maturing fish are injected with 

erythromycin as a prophylactic approximately 1 month prior to spawning. The injection is 

administered interperitoneally at the base of the ventral fins at a dose of 20 or 30 mg/kg of fish 

wet weight. Ovarian fluid and milt from spawning adults are also screened with the BKDELISA and for IHNV and VHSV.

Rearing Densities

At our ESA captive broodstock culture facilities, rearing density is maintained less than 8 

kg/m3 (0.5 lb/ft3) for most of the juvenile-to-adult period. This value is on the low end of the 4.8 

to 32.0 kg/m3 (0.3 to 2.0 lb/ft3

) maximum allowable range Senn et al. (1984) established for 

production hatcheries. Senn et al. (1984) production hatchery criteria cover fish ranging in size 

from 0.38 to 64.4 g and allow rearing density to increase as fish grow within this size range. 

Given the increased postrelease survival derived from rearing juvenile production fish at lower 

densities (see Maynard et al. 1995 for review), it was determined that setting the rearing density 

for immature ESA-listed fish in a safety net conservation program at or below the lowest values 

used in typical production programs would be the conservative approach. Therefore, we set the 

immature rearing density criteria at 8 kg/m3 (0.5 lb/ft3

).

As the fish approach maturity, rearing density is allowed to increase to 15 kg/m3 (1 

lb/ft3). This increase in allowable holding density results from the lower metabolic wastes 

associated with maturing fish that are no longer feeding. As with juveniles, a conservative 

approach is taken, with the established value being about one-half to two-thirds of the accepted 

30 kg/m3 (1.9 lb/ft3

) and 24 kg/m3 (1.5 lb/ft3) density established for the respective holding of 

ocean-returned spring Chinook and sockeye salmon adults in flow through raceways and 

rectangular ponds at production hatcheries (Senn et al. 1984).

Loading Densities

Based on practical experience and published literature, loading densities for ESA captive 

broodstocks should not exceed 0.84 kg/L/min (7 lb/gal/min), except for nonfeeding maturing 

adults with oxygen supplementation. In practice, loading densities at BCH in freshwater tanks 

ranged from 0.24 kg/L/min (2 lb/gal/min) to 0.84 kg/L/min (7 lb/gal/min) for active feeding fish, 
18

while raceway loading densities at BCH reached a maximum of 1.85 kg/L/min (15.4 lb/gal/min) 

with nonfeeding maturing adults and supplemental oxygen. Seawater loading densities reached a 

maximum of 1.08 kg/L/min (9 lb/gal/min).

Loading density targets were derived based on the following literature review. Based 

solely on the theoretical oxygen requirements, loading densities for large salmon (0.5–5 kg, 1–10 

lb) in seawater should be set in the 0.84 to 1.44 kg/L/min (7–12 lb/gal/min) range according to

Liao (1971). However, the presence of metabolic wastes, decaying food, and the control of 

pathogenic organisms lead most authorities to recommend lower loading densities. Piper et al. 

(1982) recommend that enhancement facilities rearing Chinook salmon for smolt release should 

be maintained at loading densities in the 0.14 to 1.56 kg/L/min (1.2–13 lb/gal/min) range. These 

loading density values were derived from Wedemeyer and Wood (1974) and vary with fish size 

and water temperature. Wedemeyer and Wood’s loading density recommendations for the 

largest (15 fish/lb) size category they considered are 0.66 kg/L/min (5.5 lb/gal/min) at 17.2°C

(63°F) and 1.56 kg/L/min (13 lb/gal/min) at 3.3°C (38°F).

Senn et al. (1984) also consulted Wedemeyer and Wood (1974) for generating their 

loading density recommendations. However, Senn et al. (1984) modified the recommendations 

so that they can be applied to larger juveniles. Senn et al. (1984) recommend that loading 

density not exceed 0.72 kg/L/min (7.2 lb/gal/min) for Chinook salmon that are 75.6 g (6 fish/lb) 

at 14.4°C (58°F).

Loading density recommendations for Chinook salmon reared in enhancement facilities 

are also provided in Pennell and McClean (1996), who established flow needs based on fish size, 

water temperature, feed rate, and fish quality. Their A level recommendations for fish to be 

released as ocean-ranched smolts range from a low of 0.20 kg/L/min (1.67 lb/gal/min) for 20 g 

fish being fed 2.23% body weight per day at 15°C up to 1.16 kg/L/min (9.68 lb/gal/min) for 20 g 

fish that are not being fed and being held at 10°C. These numbers are lower than those presented 

in Piper et al. (1982). Piper et al. (1982), Senn et al. (1984), and Pennell and McClean (1996) 

loading density recommendations should be reduced in seawater because oxygen content at any 

given temperature is lower in seawater than in freshwater.

Wood (1979) observed that significant water quality problems develop when Chinook 

salmon are reared in loading densities above 0.48 kg/L/min (4 lb/gal/min). Wood (1979) 

observed bacterial gill disease infections in Chinook salmon reared in ponds when loading 

densities exceed 0.48 kg/L/min (4 lb/gal/min). Bacterial gill disease infections were observed at 

loading rates of 0.60 to 0.72 kg/L/min (5−6 lb/gal/min) in standard raceways when fish were at a 

size of 90 to 110 fish/lb (5.0−4.1 g). Wood (1979) suggested that larger fish were more tolerant 

of higher loading rates and avoided developing bacterial gill disease. Piper et al. (1982) noted 

that parasite infections become uncontrollable when loading density in steelhead (Oncorhynchus 

mykiss) ponds exceeded 0.84−0.96 kg/L/min (7−8 lb/gal/min).

A general relationship exists between water flow, feeding rate, and sanitary conditions in 

fish rearing vessels. Prolonged feeding rates in excess of 0.019 kg/day/L/min (0.150 

lb/day/gal/min) of inflow can lead to the outbreak of bacterial gill disease in juvenile Chinook 

salmon in freshwater (Fowler 1989). The relationship between feed and flow limits the rate at 

which fish can be grown when water flow is limited.
19

Several loading density recommendations have been made for holding nonfeeding adult 

salmon that have returned from the sea and are maturing in freshwater. Pepper (1984) 

recommended 2.5 L/min/kg (0.30 gal/min/lb) as a satisfactory flow rate for holding nonfeeding 

Atlantic salmon (Salmo salar) brood. Unspecified lower loading densities were recommended 

for aquaculture brood that are feeding. Senn et al. (1984) recommended 1.80 kg/L/min (15 

lb/gal/min) for nonfeeding adult Pacific salmon being held for maturation. Schreck et al. (1995) 

recommended that returning ocean-ranched Pacific salmon brood be held at 1 kg for every 3.8 

L/min of flow, which is equivalent to 0.26 kg/L/min (2.2 lb/gal/min).

Based on this review, it seems prudent to rear ESA captive broodstocks at loading 

densities no greater than 0.84 kg/L/min (7 lb/gal/min). Although lower loading rates are 

preferred, it is recognized that they may limit captive broodstock production and significantly 

increase operational costs.

Turnover Rates

The most rapid turnover rate for the 6.1 m diameter circular tanks at MRS is 0.38 

times/hour and 0.80 times/hour for the 4.1 m diameter circular tanks. At BCH the quickest 

turnover rate is 0.53 times/hour for the 3.7 m diameter circular tanks, 1.17 times/hour for the 

raceways, and 2.46 times/hour for the 1.5 m diameter circular tanks. When the tanks are lightly 

loaded, the turnover rate can be as low as one-third of these values. WDFW (1996) recommends 

turnover rates be greater than 1.0 for rearing ponds and large raceways and greater than 2.0 for 

standard raceways. In most cases, water availability and the drain design of our circular tanks 

precludes our meeting these standards. The adoption of the above lower rearing and loading 

density standards helps compensate for these reduced turnover rates.

Tank and Raceway Cover

All tanks and raceways used for sockeye captive broodstock rearing are completely 

covered with a taut 2.5 × 2.5 cm or smaller mesh nylon netting to prevent fish from escaping. 

The energy absorbing properties of the nylon mesh minimizes injuries that might occur to fish 

when they leap against it. In addition to the mesh covering, one-half of each tank is covered with 

solid black fabric that provides a shaded area for fish to take refuge. Raceways are one-fourth to 

one-third covered with dark plastic tarps.

Feed

Fish at BCH are reared on commercial feeds produced by Bio-Oregon or Skretting 

(Vancouver, British Columbia). Beginning at swimup at BCH, fry are fed a semimoist starter 

mash. As they grow, the fish are transitioned through standard pelleted semimoist or dry grower 

feeds and progressed through brood ration sizes (6 mm, 9 mm). Fish reared at MRS receive 

Skretting commercial feed in dry pellet sizes appropriate for fish size, dispensed by disk and belt 

automatic feeders. The pellet size utilized follows the feed manufacturer’s recommendations, 

based on current guidelines for commercial aquaculture and guidance provided in Fowler (1989). 

However, pellet size is adjusted from the recommendation to ensure that the smallest fish in the 

population are able to feed. Daily ration ranges from 5.6% body weight per day for swimup fry 
20

to 0.4% for adults, depending on fish size and water temperature (Iwama 1996). The fish are 

grown according to the profile described in Figure 10, which is based on periodic sample weights 

of past broodyears. In order to determine adherence to the growth profiles, the fish are sampled 

one to three times per year to assess weight and length.

Feeding swimup fry is initiated with ad libitum hand feeding in 1.8 m diameter circular 

tanks. After the fish are transferred to 3.7 m diameter circular tanks, their diet is either hand fed 

or rationed by belt feeders. Prior to loading the feeders, a portion of the day’s ration is broadcast 

over the surface to observe the fish’s feeding response. Feeding frequency varies with day 

length, feeder type, and fish size, as suggested by Fowler (1989).

Spawning Procedures

All Chinook salmon captive broodstock are transferred to states of origin as prespawning 

adults. Therefore, only Redfish Lake sockeye salmon spawn at NMFS facilities. The peak 

spawning period for Redfish Lake sockeye salmon is October to mid-November. As fish 

approach maturation (age-3 and age-4), feeding is reduced by one-half through May and 

discontinued in June to coincide with the time when ocean run sockeye typically begin entering 

the Columbia River. Ultrasonic examinations in June, July, and August allow estimates of sex 

and maturity by detecting gonad development. The ultrasound determinations aid in early 

Figure 10. Growth rate projection for Redfish Lake sockeye salmon reared in 10°C freshwater at BCH. 

Growth profile based on historical data for sockeye reared in freshwater by NMFS.

y = 0.5194x2 – 9.3253x + 25.363

R2 = 0.9591

0

500

1,000

1,500

2,000

2,500

3,000

3,500

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44

Average wt (g)

Months post-ponding
21

separation of maturing from nonmaturing fish to prevent feed deprivation for an extended period 

in nonmaturing fish. Maturing adults for release in Idaho are transferred from seawater at MRS 

to freshwater at BCH in June and early July for final freshwater maturation. In September, 

maturing adult fish are transported from BCH to Idaho’s Stanley Basin where they are released 

for volitional spawning.

Gamete crosses are structured to maintain genetic diversity. Eggs from each female are 

divided into two lots. Each lot is paired with a different male to decrease the risk of all eggs of 

one female being crossed with an infertile male. Currently, an inbreeding avoidance matrix 

using allele-sharing coefficients guides breeding decisions within the sockeye salmon captive 

broodstock program. The matrix, produced by IDFG geneticists,1 is a listing of preferential 

mates based on the proportion of shared alleles at 14 microsatellite loci. The lower the matrix 

number, the better the cross because the individuals share fewer alleles in common. The use of 

an inbreeding avoidance matrix minimizes losses of genetic diversity that might occur in a 

random mating system.

During the captive broodstock spawning season, mature salmon are anesthetized (a 50 

g/L stock solution of tricaine methanesulfonate [MS-222] is added to a handling tank to produce 

a final anesthetic environment of approximately 26 mg/L) and females are checked for ripeness 

on a weekly basis, or more frequently as the fish mature. In most years at the onset of the 

spawning season, males may have had low milt volumes when live spawned, and sometimes the 

milt lacked sufficient motility. Hormone implants consisting of 100 to 150 μg gonadotropin 

releasing hormone analog (GnRHa) pellets supplied by the Center for Marine Biotechnology

(University of Maryland, Baltimore) are injected into the dorsal musculature of many of the 

males to expedite spermiation to coordinate spawning timing between males and females 

(Swanson 1995). The GnRHa implants subsequently increase the volume of milt produced. The 

implants also aid in ensuring the availability of a sufficient number of spermiating males to pair 

with ovulating females at the outset of spawning for desirable matrix crosses containing fewer 

shared alleles. At the end of the spawning season, a few late ripening females may also be 

implanted to ensure that their eggs reach the eyed stage in time to be transported and placed in 

the Stanley Basin lakes before ice-over.

Female fish that are ready to spawn, as determined by egg expression and ventral softness 

(FRED 1983), are anesthetized, killed, and their PIT tag, fork length, and weight recorded. The 

females are bled for 3 to 5 minutes by severing the caudal peduncle to the depth of the caudal 

blood vessels. The bleeding procedure limits the amount of blood that might accumulate with 

the eggs and interfere with fertilization. Females are then abdominally incised with a sterile 

spawning knife. The free flowing eggs are then gently stripped and collected into a preweighed 

4 L zipper-locking plastic bag. The eggs from each female are weighed, divided into two lots, 

and held on an insulating layer of plastic placed over ice in a cooler until they are fertilized. All 

spawned fish are analyzed for common bacterial and viral pathogens by analysis of tissue and 

fluid samples that are collected from the kidney, spleen, and pyloric caeca of each fish and 

ovarian fluid from each female. The samples are placed on ice until they can be transported to 

the fish health facility at the NWFSC’s Montlake Laboratory in Seattle, Washington.

 

1 C. Kozfkay, Idaho Dept. Fish and Game, Eagle, ID. Pers. commun., September 2006.
22

All available males (producing motile milt) are used at least once in spawning, and many 

are used twice. Males are selected based on their ripeness and ranking on the spawning matrix. 

Males are live-spawned by ventral compression, and the milt collected into preweighed 4 ml 

Whirl-Pak bags (Nasco, Fort Atkinson, Wisconsin). The milt is weighed and a spermatocrit 

sample extracted with a standard hematocrit tube. Milt motility is then qualitatively assessed 

using a microscope (40×) and classified as very good (near 100% motility) good (80% motility), 

fair (about 50% motility), poor (less than 20% motility), or no good (0% motility). To ensure 

consistency, the qualitative milt analyses are typically performed by the same individual. There 

is no statistically detectable (P > 0.05) difference in viability of milt classified as very good, 

good, or fair. Therefore, the use of fair motility milt, while held to a minimum, occurs when a 

better alternative is not available or to allow an individual male his only opportunity to 

contribute genetic material. On the day they are collected, bags of milt are inflated with oxygen, 

sealed, and chilled until used. Once spawning is completed for the season, all males are killed 

and tissue samples are collected for health analysis.

Eggs are fertilized following dry method procedures (Piper et al. 1982). A measured 

amount of milt (0.5 to 5 ml) from an individual male is transferred by a sterile pipette into the 

plastic bag containing one egg lot. The eggs and milt are mixed for 1 full minute by gently 

palpating the bag. Enough water is added to just cover the eggs and activate the sperm, and the 

eggs are lightly agitated to distribute the activated milt. The bags are left undisturbed for 

approximately 5 minutes for fertilization to take place. The eggs are water hardened in a 1 ppm 

free iodine solution (buffered to obtain a pH of 6.5–7.0) for 20 minutes, then poured from the 

bags into downflow containers for isolated incubation.

Egg Incubation

Individual lots of eggs are placed into isolation containers in the incubation troughs at 

BCH and covered with heavy black plastic to eliminate light. Beginning two days after 

fertilization, the eggs are treated with a formalin drip into the hatchery head tank at 1,668 ppm 

for 15 minutes on alternating days for control of Saprolegnia spp. (water mold). The eggs are 

left undisturbed during the sensitive period beginning 48 hours after fertilization until they reach 

the eyed stage (30 days at 10°C). Eyed eggs are shocked and dead or unfertilized eggs are 

removed and counted or weighed to determine eyed egg viability rates. The eggs are then 

packed into plastic mesh tubes (AquaSeed Corp., Seattle, Washington), packaged, and shipped to 

IDFG for outplanting (see below).

Captive broodstock eggs that are received from IDFG and the subsequent sac fry are

periodically checked for mortalities. Early growth is regulated by temperature to bring 

emergence timing into closer synchrony with the wild sockeye salmon, reducing the need for 

limiting post-ponding feeding. In 2002 the incubation water temperature was chilled from the 

ambient 10°C to 7.5°C to more closely equate the temperature units of the individual groups of 

eggs. Beginning in 2003 the water temperature was chilled to 5°C to align the egg and fry 

development with that of their wild counterparts in the Stanley Basin lakes. At swimup stage, 

when the yolk sac is completely absorbed and the fish are off the bottom of the bucket, the inner 

flow-through containers with the swimup fry are moved from the incubation stacks and 

suspended in floating foam rings in blue plastic 1.8 m diameter tanks (Figure 5). To assure that 

fry are feeding and thriving, they remain in the containers or are transferred to larger flow-
23

through suspended containers until they reach approximately 0.7 g, at which time they are 

released from the containers into the tank. The water temperature is normally increased to 10°C 

(ambient well water temperature) on or around April 1.

The fish are reared in the 1.8 m diameter tanks until they are tagged with individually 

identifying PIT tags (Prentice et al. 1990) and combined into the 3.7 m diameter rearing pools 

(Figure 6). At tagging or within a few months after tagging, a tissue sample is taken from the 

adipose fin for DNA analysis by IDFG to construct a spawning matrix for when the fish mature. 

Adult release fish are also DNA sampled for comparison with outmigrating smolt offspring and 

adults returning to Stanley Basin lakes.
24

Egg and Fish Transportation

Several types of egg and fish transfers are conducted for ESA-listed sockeye and

Chinook salmon captive broodstocks at the MRS seawater rearing facility and BCH freshwater 

satellite.

1. For ESA-listed endangered Redfish Lake sockeye salmon, 1) small egg lots of

approximately 400–500 eggs each are transferred to BCH by IDFG to establish rearing 

lineages (Baker et al. 2005, 2006a, 2006b, 2007), 2) smolt-to-adult stages are transferred 

within and between facilities, 3) approximately 400–500 prespawning adults are 

transferred to Idaho annually for release into Redfish Lake habitats to spawn naturally 

(Flagg et al. 2004), and 4) approximately 150,000–200,000 eyed eggs are transferred to 

IDFG annually for use in recovery efforts (Flagg et al. 2004).

2. For ESA-listed threatened Snake River spring/summer Chinook salmon from the Salmon 

River basin in Idaho, 1) groups of approximately 150 smolts from select lineages are 

usually transferred to the MRS seawater facilities and 2) all prespawning adults are 

transported to Idaho for release to natal streams to spawn naturally.

3. For ESA-listed threatened Snake River spring/summer Chinook from the Grande Ronde 

Basin in Oregon, 1) groups of up to 450 smolts from select lineages are usually 

transferred to the MRS seawater facilities and 2) all prespawning adults are transported to 

ODFW’s BFH, where they are spawned by ODFW personnel and the eggs used for 

recovery efforts.

Transfer protocols for each species and life history stage are similar, but differ in travel time and 

destination environment.

Snake River Sockeye Salmon

All smolt transfers from BCH to MRS are made by NMFS. Protocols for transferring and 

receiving smolts revolve around the transition from freshwater to seawater. Smolts are generally 

taken off feed several days prior to transfer. Transfer takes place in 100% freshwater. On arrival 

at MRS, smolts (≈100 g average weight) are netted a few at a time out of the transfer tank and 

into the receiving pool. The pool is filled with freshwater with oxygen aeration to saturation 

level. Small aquarium powerhead-type submersible pumps are used to create a small current to 

circulate the water. The temperature difference between transfer water and receiving water 

should be within 2°C. Generally the freshwater at MRS is warmer than the transport water, so 

ice is added to bring the temperature differential within specifications. After all smolts are 

unloaded, a low flow of seawater is added (≈7 gal/min) to the pool and the smolts are slowly 

transitioned to full strength seawater (29 ppt) over approximately 12 hours. Feeding is initiated 

as soon as the fish exhibit a feed response, usually within 2 days of transfer.

The intersite transportation of adult fish is done by IDFG and NMFS (Appendix A). 

IDFG and NMFS use standard fish hauling trucks and equipment. All transportation conducted 
25

by NMFS is done in a manner that emphasizes fish health and safety. Transfer protocols for 

adults involve transition from seawater back to freshwater. All transportation occurs in (265–

7,950 L) insulated transfer tanks and the temperature is not allowed to rise more than 3°C. The 

transport tanks are supplied with a continuous oxygen supply that maintains DO at full 

saturation. The oxygen reservoir, two K cylinders (≈4,500 L), contain at least twice the oxygen 

needed to make the entire trip. Oxygen is metered in at a rate of 0.25–0.50 L/min and the 

oxygen level is maintained at 10–20 mg/L. Temperature and oxygen levels are checked at 

departure and every 2–3 hours during transport. Fish transport densities are kept at or below 

0.06 kg/L (0.5 lb/gal). Transport temperature is typically approximately 10°C. Additionally, 

drivers are equipped with cell phones and have backup personnel ready to respond in event of 

equipment failure.

Seawater-reared adults (≈3 kg average weight) are transferred to two different locations 

between June and September. In June adult fish are sorted for maturity at MRS. Fish are taken 

off feed 2 weeks prior to sorting. Adults are sorted for maturity and transferred back to 

freshwater (BCH) on the same day. Fish are lightly crowded in the pool, anaesthetized, length 

measured, weighed, examined for reproductive status (using ultrasound), and loaded directly into 

the transfer tank. Water in the transfer tank is 25% seawater and 75% freshwater. When loading 

density is reached, typically 1–2 hours, the fish are then trucked (0.5 hour trip) to BCH. 

Transition from seawater to freshwater occurs during the transfer with the adults being unloaded 

directly into 100% freshwater. Total transition time from seawater to freshwater is 

approximately 2 hours. Approximately 1 month after the first transfer of maturing adults, the 

remaining fish at MRS are re-sorted for maturity to ensure that all maturing adults are transferred 

back to freshwater.

Maturing adults are held in freshwater at BCH until early September. Typically the day 

after Labor Day the fish are loaded into IDFG and NMFS transport tanks and transferred from 

BCH to Redfish Lake near Stanley, where they are released into the lake for volitional spawning. 

Loading is done with the fish being netted directly out of the raceways and into the transfer 

tanks. The fish are transported in 100% freshwater at 10°C for approximately 10 hours to 

IDFG’s EFH near Boise, Idaho. On arrival, approximately half of the transfer water is 

exchanged with fresh well water at the hatchery. After approximately 1 hour of water exchange, 

the fish are then trucked another 3 hours to Redfish Lake where they are released. If necessary, 

water is again exchanged to achieve temperature acclimation. Liberation is done via discharge 

tube from the IDFG truck and via dip net from the NMFS truck. Total transport time from BCH

to Redfish Lake is approximately 14 hours.

Eggs from sockeye salmon spawned at BCH to be shipped to Idaho are placed in openmesh perforated plastic AquaSeed egg tubes (27.7 cm long × 6.4 cm diameter) at approximately 

2,500 eggs per tube. Each packed tube is wrapped in wet paper toweling to contain moisture and 

placed in a small shipping container (cooler). A small amount of ice is placed in a top layer of 

toweling to keep the eggs cool and moist during shipment. Shipment to Boise is by common 

carrier flight of approximately 2 hours. At Boise, the eggs are picked up at the airport by IDFG 

personnel and transferred to the IDFG EFH (Baker et al. 2005, 2006a, 2006b, 2007).
26

Snake River Chinook Salmon

Transport of all smolts to MRS is conducted by ODFW and IDFG (Baker et al. 2005, 

2006a, 2006b, 2007, Hoffnagle et al. 2003). Protocols for transferring and receiving Chinook 

smolts are virtually identical to the protocols used for sockeye (see Snake River Sockeye Salmon 

subsection above).

The majority of intersite transportation of adult fish is done by ODFW and IDFG with 

assistance from NMFS (Appendix A). All three agencies use standard fish hauling trucks and 

equipment. Transfer protocols for Chinook salmon adults from MRS (seawater) back to ODFW 

and IDFG facilities (freshwater) is also virtually identical to the protocols used for sockeye 

adults (see Snake River Sockeye Salmon subsection above).

Adult fish are taken off feed a minimum of 1 week prior to transfer. Adults being 

transferred from MRS back to Oregon and Idaho are transferred in 25% seawater and 75% 

freshwater. Transition from seawater to freshwater occurs during the transfer, with the adults 

being unloaded directly into 100% freshwater. Depending on the destination, this transfer 

acclimation time can be as short as 4 hours or as long as 22 hours.

Adults (≈2 kg average weight) from the Oregon captive brood program are sorted for 

maturity and transferred back to freshwater (BFH) on the same day in late April and again in late 

May. Fish are lightly crowded in the pool, anaesthetized, and measured for metrics and 

reproductive status (using ultrasound). Maturing fish are injected with erythromycin (40 mg/kg) 

and loaded directly into the transfer tank. When loading density is reached, typically 1–2 hours, 

the fish are then trucked to BFH. Total transition time from seawater to freshwater is 

approximately 5 hours. Adults from subsequent pools are sorted and held overnight for transfer 

the next day. Transfer protocols are the same with the exception that the fish are loaded into the 

transfer tank without anesthesia.

Adults (≈2.5 kg average weight) from the Idaho captive brood program are sorted for 

maturity 1 to 5 weeks prior to transfer back to freshwater in Idaho. The procedure is the same as 

for the Oregon program. Fish are lightly crowded, anaesthetized, measured for metrics and 

reproductive status, and returned to a holding pool for later transfer.
27

Program Production

Snake River Sockeye Salmon

The main goal of the NMFS component of the Redfish Lake sockeye salmon captive 

broodstock program is to supply maturing adults and eyed eggs to Idaho’s Stanley Basin. This 

production and the numbers of gametes and juvenile fish received to generate this production are 

described in Figure 11 through Figure 15.

The first transfer of maturing adults began in 1996. From 1996 through 2008, 11 

transfers were made for a total program production of 2,210 maturing adults (Figure 11). 

Transfers of eyed eggs to Idaho began in 1994. From 1994 to 2008, 14 transfers totaling 

1,922,700 eyed eggs were made (Figure 12).

In addition to producing eyed eggs for Idaho, the program supplies eyed eggs for 

continuation of the NMFS portion of the program. A total of 3,277 eyed eggs were retained for 

the years 1996–2008, with 814 used in the captive broodstock program (Figure 13) and 2,463 

used in the adult release program (Figure 14). The NMFS program receives eyed eggs from 

Idaho to support the program. The number of eyed eggs received from Idaho is shown in Figure

15.

Snake River Spring/summer Chinook Salmon

The main goal of the MRS Chinook salmon marine rearing program is to receive smolts 

from the Snake River basin, rear these fish in seawater when they would naturally be at sea, then 

supply prespawning adults to Idaho and Oregon (Figure 16 through Figure 19). As of July 2008, 

a total of 3,523 prespawning adults have been returned to Idaho for release back into their natal 

streams for natural spawning (Figure 16). By the same date, a total of 4,031 prespawning adults 

had been returned to Oregon for that state’s stock rebuilding actions (Figure 17). The number of 

smolts brought onto the station for each of these broodyears is shown in Figure 18 and Figure 19.
28

Figure 11. NMFS annual production of prespawning sockeye salmon adults for release 

in Stanley Basin lakes.

0

50,000

100,000

150,000

200,000

250,000

300,000

350,000

400,000

450,000

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of eyed eggs

Figure 12. NMFS sockeye salmon eyed egg production available for recovery actions.

0

50

100

150

200

250

300

350

400

450

500

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of prespawning adults
29

0

50

100

150

200

250

300

350

400

450

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of eyed eggs

Figure 13. Number of eggs NMFS retained each year for incorporation into its captive 

broodstock program.

0

100

200

300

400

500

600

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of eyed eggs

Figure 14. Number of eggs NMFS retained for incorporation into adult release production.
30

0

500

1,000

1,500

2,000

2,500

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of propagules

Figure 15. Number of eggs and juvenile fish IDFG supplied each broodyear for incorporation into NMFS

captive broodstock and rearing programs.

0

100

200

300

400

500

600

700

800

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004* 2005*

Number of adults

 

Total production through July 2008 = 3,523 adults

Figure 16. Number of Salmon River spring/summer Chinook salmon adults produced from each 

broodyear for stock rebuilding activities in Idaho. Asterisk (*) indicates maturation of broodyear 

not yet complete.
31

0

100

200

300

400

500

600

700

800

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004* 2005*

Number of adults

 

Total production through July 2008 =4,031 adults

Figure 17. Number of Grande Ronde River spring/summer Chinook salmon produced from each 

broodyear for stock rebuilding activities in Oregon. Asterisk (*) indicates maturation of 

broodyear not yet complete.

0

100

200

300

400

500

600

700

800

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of smolts

Figure 18. Number of Salmon River spring/summer Chinook salmon smolts transferred to MRS

from Idaho.
32

0

100

200

300

400

500

600

700

800

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of propagules

Figure 19. Number of Grande Ronde River spring/summer Chinook salmon smolts transferred to MRS

from Oregon.
33 

Biological Metrics of NMFS Captive Reared Fish

Snake River Sockeye Salmon Culture 

The survival of sockeye salmon at NMFS facilities covers two conjoining, but distinct, 

portions of the entire life cycle. The earliest portion of the life cycle, from green egg 

(unfertilized) to the eyed stage, is the product of the fish that personnel spawn and incubate to the 

eyed stage at NMFS facilities. When these fish reach the eyed stage, they are shipped to other 

facilities for outgrowing or stocking. The remainder of the life cycle—from eyed egg to mature 

adult—represents NMFS’s success in rearing eyed eggs received from IDFG’s EFH. Although 

NMFS has sourced fish for the adult release program from spawned eggs, these fish are released 

into Redfish Lake for volitional spawning before they complete their full life cycle. As it is rare 

for a cohort to be taken through the whole life cycle at NMFS facilities, the results are presented 

for the two distinct periods and entire life cycle survival is estimated from these data.

The survival of sockeye salmon from the green-to-eyed-egg stage at NMFS facilities 

between 1994 and 2008 averaged 62.2% (±3.2) (Figure 20). The lowest green-to-eyed egg 

survival (32.5%) occurred in 1999 and the highest survival (78.3%) in 2002. Green-to-eyed egg 

survival fluctuates from year to year and linear regression indicates there is a significant (P = 

0.000), although slight, increase in survival with time. The r value is 0.189 with the equation 

(egg viability = −2791.150 + 1.425 spawn year), explaining 3.6% of the variation in the data. 

The average survival during this period is less than would be expected for ocean-returned 

Chinook and coho salmon adults in typical production hatcheries (i.e., 90%+) and provides the 

greatest opportunity for improvement, given the brief portion of life cycle it represents.

Figure 20. Average survival from green egg to eyed egg stage of Redfish Lake sockeye salmon by spawn 

year at NWFSC facilities, 1994–2008. 

0

10

20

30

40

50

60

70

80

90

100

1994 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Percent

X = 62.2 ± 3.2
34

The average survival of captive broodstock during the longer eyed-egg-to-maturation life 

stage averaged 61.7% (±5.5) for broodyear cohorts completing their life cycle between 1991 and 

2008 (Figure 21). Linear regression of eyed-egg-to-adult survival against broodyear yielded a 

statistically significant relationship (eyed-to-adult survival = 6,422.75 + 3.245 broodyear, r = 

0.762) that explained 58.0% of the variation. Thus eyed-to-adult survival appears to have 

improved over the course of the program, with the lowest survivals of 22.7% (broodyear 1991) 

and 35.0% (broodyear 1996) occurring in the early years of the program. The survival of all 

cohorts since 1997 never dipped below 59.1% and achieved a maximum of 85.0% in broodyear

2003. As with the green-to-eyed egg data, eyed-egg-to-mature-adult survival data appears to 

become less variable over time. Eyed-egg-to-mature-adult survival is orders of magnitude 

greater than the fish are likely to experience in the wild during this same portion of their life 

cycle.

As mentioned above, full life cycle survival can only be estimated as NMFS data cover 

two conjoined, but nonetheless separate, portions of the entire life cycle. This estimate can be 

derived by multiplying the percentage of fish surviving from green-to-eyed-egg stage by the 

proportion of fish surviving from the eyed-egg-to-mature-adult stage. Using this approach, the 

above 62.2% green-to-eyed egg survival can be multiplied by 0.617 to estimate an overall greenegg-to-adult survival of 38.4%. However, with the improvement in eyed-to-adult survival seen 

over the last decade, one might choose to use a higher proportion to account for the advances in 

fish culture. When the 0.753 mean proportions for the last 5 broodyears (broodyear 2000 to 

broodyear 2004) is substituted into the equation, estimated full life cycle survival increases to 

46.84%. This number, which accounts for program improvements, is probably the better tool for 

predicting future performance of this or other captive broodstocks initiated for rearing sockeye 

salmon. In setting up a new program, at least 38.4 mature adults should be produced for every 

100 green eggs taken into culture. If the program can benefit from the improvements we 

experienced, it will likely produce 46.8 adults from the same 100 green eggs. If these 100 green 

eggs were left in nature, one would expect about 10% of them to survive to smolt and about 

0

10

20

30

40

50

60

70

80

90

100

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

Percent

X = 61.7 ± 5. 51

Figure 21. Average survival by broodyear from eyed egg stage to mature adult for Redfish Lake sockeye 

salmon captive broodstock reared at NWFSC facilities.

X = 61.7 ± 5.51
35

1–3% of the outmigrating smolts to survive to maturation. This would produce less than one 

(0.1–0.3) fish recruiting to the spawning population. Thus even with the lower value (38.4%), 

population amplification from one generation to the next will be more than two orders of 

magnitude higher than if the fish were reared in the wild (Flagg et al. 2004).

Sockeye salmon in NMFS freshwater captive broodstocks typically spawn at a younger 

age than the 4- and 5-year-old anadromous sockeye that returned to Stanley Basin lakes in the 

1960s (Bjorn et al. 1968). The age of maturation for male fish in broodyear 2000, 2001, 2002, 

and 2003 cohorts is illustrated in Figure 22. In these four broodyears, a few males matured as 2-

year-olds, most matured as 3-year-olds, with very few males maturing as 4-year-olds. No 5-

year-old males were produced in any of these broodyears. The presently available data set for 

female sockeye salmon is more extensive, covering broodyears from 1991 to 2004 (Figure 23). 

No freshwater-reared females matured as 2-year-old fish, most matured as 3-year-old fish, a few 

matured as 4-year-old fish, and none matured as 5-year-old fish. The maturation age of females 

appears to be shifting with the passage of time, as the percentage of females maturing as 4-yearolds in the freshwater captive broodstock has decreased in recent years. We have observed that 

adult release sockeye reared in seawater produce many more fish that mature as 4-year-olds than 

their freshwater-reared counterparts. Flagg et al. (1998) speculated that this phenomenon of 

delayed maturation age in seawater was a result of slower and less uniform growth due to the 

cyclic nature of seawater temperature compared to the constant temperature freshwater at 

NWFSC facilities.

Bjorn et al. (1968) reported the average length of 4- and 5-year-old sockeye salmon 

females returning to Stanley Basin lakes to be 546 mm. In the freshwater captive broodstock 

program, the average length of mature 3-year old females ranged from a cohort low of 438 mm 

to a cohort high of 487 mm (Figure 24). As expected, given their younger age, these 3-year-old 

females matured at a smaller size than the 4- and 5-year-old anadromous adults that historically 

returned to the Stanley Basin lakes. The average fork length of 4-year-old females in the NMFS 

0

20

40

60

80

10 0

12 0

20 00 20 01 20 02 20 03

Percent

2 year old

3 year old

4 year old

Figure 22. Percent by broodyear of Redfish Lake sockeye salmon males in the captive broodstock 

program maturing as 2-, 3-, and 4-year-old adults.
36

0

20

40

60

80

100

120

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004

Percent

2 year old

3 year old

4 year old

Figure 23. Percent of broodyear 1991–2004 female Redfish Lake sockeye salmon reared in freshwater at 

NWFSC facilities maturing as 2-, 3-, and 4-year-old fish.

0

100

200

300

400

500

600

700

800

2003 3 yr 2004 3 yr 2004 4 yr 2005 3 yr 2006 3 yr 2007 3 yr 2007 4 yr 2008 3 yr

Millimeters

Figure 24. Average fork length (±SE) for mature 3- and 4-year-old female Redfish Lake sockeye salmon 

spawned at NWFSC freshwater facilities, 2003–2007.
37

captive broodstock ranged from a cohort low of 534 mm to a cohort high of 582 mm (Figure 24),

bracketing the value reported by Bjorn et al. (1968).

The fecundity of 3-year-old Redfish Lake sockeye salmon captive brood females ranged 

from a low of 1,565 to a high of 2,218 eggs per female and averaged 1,765.5 ±84.8 eggs for all 

spawning conducted between 1994 and 2008 (Figure 25). During this same time frame, the 

average fecundity of 4-year-old females averaged 2,349.8 ±359.6 eggs per female and ranged 

from an annual low of 1,788 eggs per fish to a high of 3,275 eggs per female (Figure 26). As is 

apparent, the fecundity of sockeye salmon in the captive broodstock program increases with age. 

Linear regression indicates the fecundity of 3-year-old females significantly increases (P = 

0.000) with spawn year (fecundity = –67,003.387 + 34.321 spawn year). The r value was 0.315,

indicating that regression only explained about 10% of the variation in the data. Regressing 

fecundity against spawn year did not yield a significant (P = 0.185) relationship for 4-year-old 

females.

When fecundity is evaluated on female weight, there is a trend for the number of eggs 

produced per gram of fish to increase with the passage of time (Figure 27). Linear regression 

yields an equation where egg number per gram of 3-year-old fish = −57.218 + 0.029 broodyear 

that is a statistically significant (P = 0.000) relationship with an r value of 0.300 that explains 

about 9.0% of the variation in the data. This same linear regression on the data for 4-year-old 

fish did not yield a statistically significant relationship (P = 0.232). The number of eggs 

produced per gram of 3-year-old fish averaged 1.337 ±0.049 with an annual low of 0.985 

egg/gram of fish in spawn year 2000 and an annual high of 1.524 eggs per gram of fish in spawn 

year 2003.

0

500

1,000

1,500

2,000

2,500

3,000

3,500

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of eggs

Figure 25. Average fecundity (±SD) of 3-year-old Redfish Lake sockeye salmon captive broodstock 

females spawned at NWFSC facilities, 1994–2008.
38

0

500

1,000

1,500

2,000

2,500

3,000

3,500

4,000

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of eggs

Figure 26. Average fecundity (±SD) of 4-year-old Redfish Lake sockeye salmon captive broodstock 

females spawned at NWFSC facilities, 1994–2008.

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

2.0

1996 1997 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Number of eggs

Figure 27. Average number of eggs produced per gram of 3-year-old spawning Redfish Lake sockeye 

salmon captive broodstock, 1996–2008.

Two types of data are available to assess average egg weight. Collection of green egg 

weight, which is a good surrogate for energetic reproductive investment, began in 2003 to 

compare the relative performance of fish in two different maturation environments. Eyed egg 

weight data has been collected as a fish culture tool since 1991 to evaluate female fecundity. 

However, eyed egg weight is a less valuable metric for estimating the energy content of an egg, 
39

as it is affected by the amount of water taken during the water hardening process and the amount 

of organic material lost during respiration. Although not the best proxy for evaluating 

reproductive effort, eyed egg data that are collected in a consistent manner from year to year can 

be used to examine temporal changes in egg weight. Therefore, we present both types of data to 

get a better understanding of how project practices have affected egg weight.

Green eggs from 3-year-old female Redfish Lake sockeye salmon captive broodstock 

averaged 0.084 ±0.001 g. The smallest (0.079 g) green eggs were observed in 2003 and the 

largest (0.087 g) in 2006 (Figure 28). Linear regression indicated no significant (P = 0.285) 

trends in green egg size with the passage of time over the relatively short time frame that these 

data are available.

The average eyed egg weight for 3-year-old females from 1991 to 2005 was 0.107 ±0.004 

g, with a range from 0.085 g for broodyear 2005 females to 0.130 g for broodyear 1997 (Figure 

29). As illustrated in Figure 29, there is a tendency for eyed egg weight to decrease over time. 

Linear regression analysis indicates this trend is statistically significant (P < 0.0005) with an r 

value of 0.563 with regression accounting for 31.7% of the variation in the data. The regression 

equation is eyed egg weight = 4.516 – 0.002 broodyear. Remarkably, average eyed egg weight 

of 4-year-old fish during this same period was an identical 0.107 ± 0.004 g and ranged from 

0.095 to 0.115 g (Figure 30). Linear regression indicates there is also a significant (P = 0.013) 

trend for decreasing eyed egg weight over time for 4-year-old females. The equation generated 

by this regression is eyed egg weight = 16.482 − 0.008 broodyear with an r value of 0.213, which 

explains approximately 4.5% of the variation observed in the data.

Chinook Salmon Culture

The survival of broodyear 1994–2003 Salmon River spring/summer Chinook reared at 

MRS averaged 58.8% ±4.3. The survival of Grande Ronde spring/summer Chinook salmon was 

higher, averaging 67.9% ±3.4 during this same period.

0.0 0

0.0 2

0.0 4

0.0 6

0.0 8

0.1 0

0.1 2

0.1 4

200 3 200 4 200 5 200 6 200 7 200 8

Grams

Figure 28. Average green egg weight (±SE) by spawn year for 3-year-old spawning Redfish Lake 

sockeye salmon captive broodstock, 2003–2008.
40

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

0.16

0.18

0.20

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005

Grams

Figure 29. Average eyed egg weight (±SD) for 3-year-old spawning Redfish Lake sockeye salmon 

captive broodstock, broodyear 1991–2008.

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

0.16

0.18

0.20

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005

Grams

Figure 30. Average eyed egg weight (±SD) for 4-year-old spawning Redfish Lake sockeye salmon 

captive broodstock, 1993–2008.

Figure 31 through Figure 33 illustrate the individual survival of the three Salmon River 

stocks of spring/summer Chinook salmon sent to MRS by IDFG. There is a significant amount 

of broodyear-to-broodyear variation in these data and only one statistically detectable trend over 

time. Lemhi River broodstocks have a slightly higher survival (65.3 ±5.7%) than broodstocks 

from the West Fork Yankee Fork (58.0 ±6.7%) or East Fork (57.4 ±9.5%) of the Salmon River. 

Lemhi River broodstocks are the only stock in which linear regression detected a significant (P < 

0.0005) relationship between in-culture survival and broodyear. The linear equation fit to the

data is percent survival = 772.631 – 0.354 broodyear with r = 0.048 and the regression

explaining a minute amount (0.23%) of the variation in the data. Linear regression of West Fork 
41

Yankee Fork and East Fork Salmon River stocks survival data by broodyear yielded P values of 

0.292 and 0.235, respectively. The variation in in-culture marine survival of these Salmon River 

tributary stocks sourced from three different tributaries within the Salmon River basin provides 

comparative information on how different spring/summer Chinook salmon stocks respond to 

marine culture.

Figure 34 through Figure 36 illustrate the individual survival of the three Grande Ronde 

River spring/summer Chinook salmon stocks sent to MRS by IDFG. The Catherine Creek stock 

showed the highest average survival (73.9% ±7.8), followed by the Lostine River stock (69.0% 

±4.9), and the Grande Ronde River stock (63.4% ±7.8). The survival of the three Grande Ronde 

River stocks from Oregon also shows no clear trends over time. As with the Salmon River 

stocks, the tributary habitat of the Grande Ronde stocks noticeably differ and the response of 

these stocks to in-culture marine survival at MRS provides guidance on the types of variation 

one might expect in see in other spring/summer Chinook salmon stocks within upriver mountain 

basins.

The Snake River spring/summer Chinook salmon reared in seawater at MRS appear to be 

smaller than their wild-reared counterparts. Columbia River stream-type Chinook salmon 

returning from the sea are about 500 mm long when maturing as 3-year-olds and 710 mm long 

when maturing as 4-year-olds (Healey 1991). More specifically in the Grande Ronde River, Boe 

et al. (2005, 2006, 2007a, 2007b, 2009, 2010) report the average fork length ranges 39.6–61.8 

cm for natural 3-year-old jacks, 68.4–76 cm for natural 4-year-old adults, and 80.4–90.4 cm for 

natural 5-year-old returning fish. Sampling conducted by IDFG at Lower Granite Dam indicates 

fork lengths of the majority of 3-year-old adults are 55–60 cm long, 4-year-old adults are 70–85

0

10

20

30

40

50

60

70

80

90

100

1994 1995 1996 1997 1998 1999 2000 2001 2002

Percent

X = 58.0 + 6.7

Figure 31. Percent survival by broodyear for West Fork Yankee Fork stock of Salmon River 

spring/summer Chinook salmon at MRS.
42

0

10

20

30

40

50

60

70

80

90

100

1994 1995 1996 1997 1998 1999 2000 2001 2002

Percent

X = 65.3 +5.7

Figure 32. Percent survival by broodyear for Lemhi River stock of Salmon River spring/summer 

Chinook salmon at MRS.

0

10

20

30

40

50

60

70

80

90

100

1994 1996 1998 1999 2000 2001 2002 2003

Percent

X = 57.4 + 9.5

Figure 33. Percent survival by broodyear for East Fork stock Salmon River spring/summer Chinook 

salmon at MRS.

X = 65.3 ± 5.7
43

0

10

20

30

40

50

60

70

80

90

100

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Percent

X = 69.0 + 4.9

Figure 34. Percent survival by broodyear for Lostine River stock of Grande Ronde River spring/summer 

Chinook salmon at MRS.

0

10

20

30

40

50

60

70

80

90

100

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Percent

4.7X = 73.9 +

Figure 35. Percent survival by broodyear for Catherine Creek stock of Grande Ronde River 

spring/summer Chinook salmon at MRS.

X = 73.9 ± 7.8
44

0

10

20

30

40

50

60

70

80

90

100

1996 1997 1998 2000 2001 2002 2003

Percent

X = 63.4 + 7.8

Figure 36. Percent survival by broodyear for Grande Ronde River stock of Grande Ronde River 

spring/summer Chinook salmon at MRS.

cm long, 5-year-old adults are 85–97 cm long, and most 6-year-old adults 88–99 cm long 

(Copeland et al. 2009). The average fork length of prespawning 3- and 4-year-old adult Salmon 

River fish at Manchester was 374 ±5mm and 489 ±7mm, respectively (Figure 37). Grande 

Ronde 3- and 4-year-old prespawning adults averaged 350 ±30 mm and 470 ±28 mm, 

respectively (Figure 38).

The average weight of 3- and 4-year-old maturing Salmon River spring Chinook salmon 

at MRS was 844.4 ±39.6 g for fish that would spawn as 3-year-olds and 1,811.3 ±86.0 g for fish 

that would spawn as 4-year-olds. Grande Ronde River maturing fish were generally heavier,

weighing an average of 910.3 ±84.6 g for fish that would spawn as 3-year-olds and 2,060.1 

±159.3 g for fish that would spawn as 4-year-olds.

The maturation schedules (Figure 39 and Figure 40) for the Salmon and Grande Ronde 

groups of Snake River spring/summer Chinook salmon stocks reared at MRS suggest that fish 

may be maturing at a younger age than if they had gone to sea. For reference, data collected on 

natural spring Chinook salmon returning to weirs on the Grande Ronde River (Boe et al. 2005, 

2006, 2007a, 2007b, 2009, 2010) indicate few fish mature as 3-year-old jacks (0–16%), most as 

4-year-olds (49–85%), and often many as 5-year-olds (0–47%). Although precocious 2-year-old 

minijacks have been observed in the Grande Ronde, little data is available as to their origin 

(hatchery vs. natural) and numbers. Information collected at Lower Granite Dam on returning 

natural origin Snake River spring/summer Chinook salmon in 2008 indicates 15.7 % returned as 

3-year-olds, 70.5% returned as 4-year-olds, 13.4% returned as 5-year-olds, and 0.5% returned as 

6-year-olds (Copeland et al. 2009).

The 29.735% (±5.238) of the Salmon River fish that matured as precocious 2-year-old 

males seems higher than expected for naturally rearing fish. Age-3 jacks make up 24.461%
45

0

100

200

300

400

500

600

Salmon 3 Grande Ronde 3 Salmon 4 Grande Ronde 4

Millimeters

Figure 37. Average fork length (±SE) of prespawning 3- and 4-year-old adult Salmon River and Grande 

Ronde River spring/summer Chinook salmon at MRS.

0

500

1,000

1,500

2,000

2,500

Salmon 3 Grande Ronde 3 Salmon 4 Grande Ronde 4

Grams

Figure 38. Average weight (±SE) of prespawning 3- and 4-year-old adult Salmon River and Grande 

Ronde River spring/summer Chinook salmon at MRS.
46

0

5

10

15

20

25

30

35

40

45

Age 2 Age 3 Age 4 Age 5 Age 6

Percent

Figure 39. Percent of Salmon River stocks of Snake River spring/summer Chinook salmon reared at 

MRS maturing as 2-, 3-, 4-, 5-, and 6-year-old fish. Data based on broodyears 1994–2003.

0

10

20

30

40

50

Age 2 Age 3 Age 4 Age 5 Age 6

Percent

Figure 40. Percent of Grande Ronde River stocks of Snake River spring/summer Chinook salmon reared 

at MRS maturing as 2-, 3-, 4-, 5-, and 6-year-old fish. Data based on broodyears 1994–2003.
47

(±2.86) of the fish that survived to maturity in the Salmon River stocks, which also seems higher 

than expected for naturally rearing or ocean-ranched Chinook salmon. The percentage of 

Salmon River fish maturing as 4-, 5-, and 6-year-olds was 38.6% ±3.2, 7.3% ±1.828, and 0.1% 

±0.04, respectively. The data for Grande Ronde stocks are less skewed towards younger fish, 

with only 10.5% ±1.9 maturing as 2-year-old precocious males. A greater percentage of the 

younger maturing fish in the Grande Ronde populations became 3-year-old adults (42% ±2.6)

than in the Salmon River populations. The percentage of Grande Ronde Chinook maturing as 4-

year-olds (40% ±2.1) was similar to that in the Salmon River stocks. As with the Salmon River 

stocks, only a few matured as 5-year-old (6.7% ±1.6) or 6-year-old (1.8% ±1.6) fish. The greater 

percentage of fish maturing at a younger age in both Snake River captive broodstock groups may

be the result of higher growth.

Adult Fish Transportation

Snake River Sockeye

From 1996 through 2008, maturing adults from the Snake River captive broodstock 

groups at NWFSC facilities were sorted for maturity in June and July. Seawater-reared adults 

from MRS were transferred back to NMFS freshwater facilities at sorting and held in freshwater 

with the freshwater-reared component until transfer back to the Stanley Basin lakes of central 

Idaho via IDFG or NMFS transport trucks. Adults were released into their natal lakes in 

September of each year for volitional spawning in October as part of sockeye salmon restoration 

efforts by IDFG. During 12 years of adult transfers from NMFS facilities to Redfish Lake 

(1996−2008), there have been no mortality events (Table 2 and Appendix A).

Table 2 provides information on adult transfers from 1996 to 2008. For Redfish Lake 

sockeye salmon, 11 transfers (1 per year) were conducted using the protocols described above 

(see Appendix A for details). Transport container size ranged from 1,900 to 10,220 L (500 to 

2,700 gal) for these transfers. The adults were transported for approximately 10 hours to EFH 

where half of the transfer water was exchanged for fresh well water. After about 1 hour of water 

exchange, the fish were transported another 3 hours to the release site at Redfish Lake. Total 

transport time from NMFS hatcheries to Redfish Lake was approximately 14 hours. At the time 

of release, a small number of adults were radio tagged for tracking fish movements in the lake 

during the approximate 4–6 weeks from release to spawning. Numbers of fish per transfer 

ranged from 61 to 434, transport density ranged 16–60 g/L (0.13−0.50 lb/gal) and had a geomean 

of 31 g/L (0.26 lb/gal). During the 5-year period documented in Appendix A for these transfer 

protocols, only one mortality event was associated with adult fish transfers.

Salmon River Chinook Salmon

From 1997 to 2005, maturing adults from Salmon River captive broodstock groups at 

MRS were sorted for maturity in late April and transferred back to IDFG’s EFH 1 to 2 weeks 

later via IDFG transport truck. The remaining fish were sorted again in late May and transferred 

to EFH in early June via NMFS transport truck. Maturing adults from these transfers were held 

at the hatchery and tagged for release by IDFG into their natal Salmon River system streams for 

volitional spawning in August of each year as part of Chinook salmon restoration efforts.
48

Table 2. Summary of adult fish transfer success from MRS facilities to Oregon and Idaho. Fish transfers were conducted by either NMFS 

personnel with NMFS tanks and trucks or by ODFW or IDFG with state agency tanks and trucks and with NMFS personnel assisting. See 

Appendix A for complete data. 

Stock transfers

No. of 

transfers

Numeric 

values No. of fish

Average 

weight (g) Fish (lb)

Transport 

tank (gal)

Density 

(lb/gal)

Transport 

duration

Survival 

(%)

Snake River sockeye

To Stanley area, 

Idaho 

11 Range 61–434 450–4,039 133–1,734 500–2,700 0.13–0.50 14 98.5–100

Average 201 1,660 740 1,740 0.28 14 98.8

Geomean 665 1,620 588 1,490 0.26 14 99.7

Salmon River Chinook

To Boise area, 

Idaho 

21 Range 12–245 118–3,440 15–648 180–2,700 0.08–0.55 10 100

Average 67 1,495 207 707 0.28 10 100

Geomean 45 1,202 120 492 0.25 10 100

To Stanley area, 

Idaho 

9 Range 30–288 150–2,460 108–957 250–2,100 0.33–0.62 18–22 96.4–100

Average 103 1,645 350 805 0.47 19.8 99.6

Geomean 74 1,622 265 572 0.46 19.7 99.6

Grande Ronde Chinook

To Cascade Locks 

area, Oregon

61 Range 3–204 60–2,699 4–651 70–2,250 0.22–1.11 5 100

Average 71 1,210 194 575 0.30 5 100

Geomean 50 940 104 475 0.22 5 100
49

Table 2 provides information on these transfers from 2002 to 2006, during which a total 

of 21 transfers (2−4 per year) were conducted using the above protocols (see Appendix A for 

details). The transport container size ranged 681−10,220 L (180–2,700 gal). The total transition 

time (transport time) from seawater to freshwater was approximately 10 hours. The numbers of 

fish per transfer ranged from 12 to 245, transport density ranged 10−66 g/L (0.08−0.55 lb/gal) 

and had a geomean of 30 g/L (0.25 lb/gal). During the 5-year period documented in Appendix A

for the transport protocols described above, no direct mortality events were associated with the 

adult fish transfers (Table 2 and Appendix A). Additionally, no posttransfer mortalities were 

noted for these groups of fish at EFH.

In 2006−2008, the maturity sorting and transfer procedure was altered due to hatchery 

construction at EFH. Adults were sorted for maturity in early June, tagged, and held for an 

additional 5 weeks in seawater. In mid-July, fish were loaded on IDFG and NMFS transport 

trucks, transferred to their natal streams, and released for volitional spawning. Nine transfers 

were conducted using the above protocols (Table 2 and Appendix A). Transport container size 

ranged 681–10,220 L (180–2,700 gal). Adults were transported for approximately 10 hours to 

EFH where half of the transfer water was exchanged for fresh well water. After approximately 2

hours of water exchange, the fish were transported another 4 hours to release sites on the West 

Fork Yankee Fork and the East Fork of the Salmon River (total transfer time 18–22 hours). 

Numbers of fish per transfer ranged from 30 to 288, transport density ranged 40−75 g/L (0.33–

0.62 lb/gal) and had a geomean of 55 g/L (0.46 lb/gal). During the 3-year period documented in 

Appendix A for these transfer protocols, only one mortality event occurred (Table 2 and 

Appendix A). In 2007 when the fish were released in the West Fork Yankee Fork during clear 

water conditions, senior IDFG staff noticed they were doing a poor job of holding position in the 

stream. A severe storm event occurred several hours after the release that unleashed into the 

water a tremendous amount of silt and ash from a fire the previous year, which resulted in an 

approximate 35% postrelease mortality of fish released into the West Fork Yankee Fork. Other 

than this instance, no posttransfer mortalities were noted for Snake River Chinook salmon.

Grande Ronde River Chinook Salmon

From 1996 through 2008, maturing adults from Grande Ronde River captive broodstock 

groups were sorted for maturity in spring and early summer and transferred to ODFW’s BFH on 

the same day via ODFW or NMFS transport trucks. Maturing adult fish from these transfers 

were held and spawned at BFH and offspring used by ODFW for Chinook salmon restoration 

efforts in the Grande Ronde River system.

Table 2 provides information on these transfers from 2002 to 2006; during this period a 

total of 61 transfers (1–7 per year) were conducted using the above protocols (see Appendix A

for details). Transport container size ranged 265–8,520 L (70–2,250 gal). Total transition time 

(transport time) from seawater to freshwater was approximately 5 hours. Numbers of fish per 

transfer ranged from 3 to 204, transport density ranged 2–133 g/L (0.02–1.11 lb/gal) and had a 

geomean of 26 g/L (0.22 lb/gal). During the entire 12 years of adult transfers from MRS to BFH

(1997–2008), there have been no mortality events (Table 2 and Appendix A). Additionally, no 

posttransfer mortalities were noted for these groups of fish at BFH.
50

Insights and Recommendations

Fish culture technologies described in this report successfully maintained ESA-listed 

sockeye and Chinook salmon stocks in safety net programs. This has prevented the loss of 

stocks with unique genetic characteristics and generated large numbers of fish that were used in 

restoration actions. The value of broodstock technology can be demonstrated by following the 

theoretical fate of 100 green sockeye salmon eggs. If left for natural spawning and rearing, one 

would expect no more than a single recruit to the next generation (one-to-one replacement in a 

static population). In contrast, if 100 eggs are placed in a safety net captive broodstock program 

using the technology described here, they should produce 46 adults that could be released back 

into their native waters for natural spawning.

The decision to take the population into a safety net program produces a 46-fold

amplification of the population within a single generation. If a decision is then made to retain 

these 46 mature adults in the safety net program and spawn them to produce juveniles for 

reintroduction, one would expect to produce approximately 40,606 green eggs, assuming 23 

females spawned at age 3 with an average fecundity of 1,765.5 eggs/female. If the 40,606 eggs 

were fertilized and reared to the smolt stage with a 50% survival in captivity, assuming a 0.1% 

smolt to adult survival, they would produce more than 20 recruits to the next generation. This is 

a 20-fold amplification over what would occur if 100 green eggs were left in nature. The ability 

to rapidly amplify a population is the main strength of safety net fish culture technology (see 

Flagg and Mahnken 1995 for more information on amplification potentials).

Key factors leading to the success of safety net fish culture technology include pathogen 

free water, onshore tanks, fully enclosed buildings, and a rigorous biosecurity protocol. These 

factors improve fish health and provide higher survivals than when Pacific salmon are reared in 

untreated surface water. In addition, in our case these key factors help ensure out-of-basin stocks 

do not contract local Puget Sound pathogens that could prohibit their return to natal areas under 

existing interstate fish transfer permit requirements. The onshore tanks and fully enclosed 

building not only protect against avian and aerosol-borne pathogens, but also avoid predation 

that may occur when captive broodstocks are reared in net pens (Flagg and Mahnken 1995).

Rearing Chinook and sockeye salmon at low densities in large tanks is critical for 

producing the high survival experienced in this captive broodstock program. Low fish densities 

and large tanks help buffer the low turnover rates associated with the water quantity limitations 

at our freshwater and seawater rearing facilities. They are also crucial in ensuring oxygen, 

ammonia, and temperatures remain adequate when pump failures or other life support 

emergencies develop. Ramped lighting and energy adsorbing netting help prevent fish from 

injury. Rearing Pacific salmon in seawater during the marine portion of their life cycle should 

help promote the retention of anadromous traits within the population. Additionally, we have 

noted that seawater rearing for Chinook salmon in particular produces fish with color and shape 

similar to their naturally reared counterparts. Likewise, when sockeye salmon are placed in 
51

outdoor or greenhouse facilities for final maturation, they develop red coloration similar to 

ocean-returning fish. More natural body shape and coloration should benefit safety net fish 

when they are used in adult reintroductions.

Appropriate rearing water temperature is critical for successful captive broodstock 

programs. The 10°C ground water used to rear sockeye salmon is pathogen free and improves 

in-culture survival and gamete quality, but results in accelerated growth to produce fish that 

mature at a younger age than in nature. We have been able to reduce some precocity in sockeye 

by chilling eggs so that fry emerge near the natural time and grow less overall during their first 

year. The increased precocity observed at MRS in Idaho Chinook salmon stocks may result from 

previous rearing at a higher temperature and for longer times in freshwater at IDFG’s EFH

compared to the Oregon Chinook salmon. The seawater at MRS has more annual variation in 

water temperature than does the ground water at Burley, and does not provide the cool 

environment that sockeye or Chinook salmon experience during their natural oceanic migrations. 

Nonetheless, either the temperature profile or some other characteristic of seawater is sufficient 

to increase the percentage of sockeye salmon maturing as 4-year-olds in adult release groups 

reared at MRS.

Reducing the risk of extinction by maintaining duplicate genetic groups in separate 

facilities is a proven strategy. Duplicate facilities provides insurance that at least one facility 

remains pathogen free if the other experiences disease problems. Duplicate facilities also 

provide an opportunity to expand production if one facility experiences abnormally low survival. 

It is recommended that, as the importance of retaining the stock increases (e.g., has endangered 

vs. threatened listing status), the number of duplicate groups be increased.

Transport protocols for ESA-listed stocks should follow relatively conservative 

guidelines, although little information is available concerning precise requirements for transport 

of maturing salmonids, especially those listed under ESA. Piper et al. (1982) and Pennell and 

Barton (1996) indicate transport limits of about 60−120 g/L (0.5−1.0 lb/gal) for fry size 

salmonids. Piper indicates that loading density can be increased with size to about 300–420 g/L 

(2.5–3.5 lb/gal) for smolt size steelhead (O. mykiss) for 8−10 hour transports. Our loading 

densities were very conservative compared to those described above, ranging 2.4−133 g/L (0.02–

1.11 lb/gal) with a geomean below 30 g/L (0.25 lb/gal). In total we documented 91 successful 

transfers of adult size Chinook salmon and 11 transfers of adult size sockeye salmon under our 

transport protocols, with transports ranging 5−22 hours. Only two minor mortality events were 

associated with any of these transfers, with geomeans for the transfers ranging from 99.6 to 

100% survival. Additionally, no posttransfer transportation-associated mortalities were noted for 

these groups of fish.

In summary, the captive broodstock fish culture technologies described in this report can 

be safely utilized to prevent extinction and amplify populations of salmon for recovery efforts. If 

the results described above for ESA-listed endangered Redfish Lake sockeye salmon can be used 

as a guide, it can be expected that for every 100 green eggs taken into a safety net captive 

broodstock program, more than 40,000 green eggs could be produced to the next generation. 

Those initiating a safety net captive broodstock project for Chinook salmon should expect that 

for every 100 smolts sent to a marine facility for seawater rearing, 58 prespawning adults can be 

produced for use in restoration efforts. At a 1% return rate, this is 58 times the number of 
52

prespawning adults that would be expected if these same 100 smolts had been left in nature to 

complete their marine migration.

At the initiation of present captive broodstock programs for Pacific salmon, Flagg and 

Mahnken (1995) indicated that the technology was in its infancy, without well-described 

standards and with full-term rearing to adult stage problematic. We believe information 

described in the present report provides standards for conducting a successful captive broodstock 

effort. Egg-to-adult survivals of 47% or better can be obtained if captive broodstocks are reared 

in biosecure situations with adequate life support at densities below approximately 1 kg/L/min (9 

lb/gal/min). Salmonid captive broodstocks can safely be reared to adult in either fresh well water 

or sterilized seawater. Although for some species (e.g., Chinook salmon), rearing to adult in 

seawater appears to enhance adult fish quality and body confirmation.
53

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59

Appendix A: Transport Details for Intersite 

Fish Transfers

This appendix consists of three tables listing transport details for transfers from 

NWFSC’s Manchester Research Station in Washington to sites in Oregon and Idaho.
60 

Table A-1. Transport details for intersite fish transfers. 

Date Transfera

Transfer 

time (h) Broodyear No. fish

Average 

weight (g) Fish (lb)

Transfer tank 

(gal)b

Density 

(lb/gal)

Load 

temp.

Release 

temp.

DOc

(mg/L)

Survival (%) Commentd

1996 transfer

8/16/96 MRS to BFH 5 1994 20 10°C 10°C 10–15 100 B, C

1997 transfers

7/24/97 MRS to BFH 5 1994 53 10°C 11°C 15–20 100 B, C

8/19/97 MRS to BFH 5 1994, 1995 16 10°C 11°C 10–20 100 B, C

9/17/97 MRS to BFH 5 1995 1 10°C 11°C 10–20 100 B, C

1998 transfers

6/17/98 MRS to BFH 5 1994, 1995 125 445–1,684 308 750 ODFW 0.41 10°C 11°C 10–15 100 B, C

7/14/98 MRS to BFH 5 1994, 1995 24 445–1,684 67 250 NMFS 0.27 10°C 11°C 10–20 100 B, C

8/17/98 MRS to BFH 5 1994, 1995, 

1996

14 100–1,684 28 500 NMFS 0.06 10°C 12°C 10–20 100 B, C

9/2/98 MRS to BFH 5 1996 5 140 NMFS 10°C 12°C 10–20 100 B, C

1999 transfers

6/2/99 MRS to BFH 5 1994, 1995, 

1996

204 746–2,280 651 1,500 ODFW 0.43 10°C 11°C 15–20 100 B, C

6/23/99 MRS to BFH 5 1994, 1995, 

1996

22 840–1,943 70 500 NMFS 0.14 10°C 11°C 10–20 100 B, C

7/30/99 MRS to BFH 5 1995, 1996 3 820–1,994 8 140 NMFS 0.06 10°C 12°C 10–20 100 B, C

8/12/99 MRS to BFH 5 1997 34 131 10 180 NMFS 0.06 10°C 12°C 10–20 100 B, C

2000 transfers

5/24/00 MRS to BFH 5 1996 118 2,153–2310 583 525 ODFW 1.11 9°C 10°C 15–20 100 B, C

5/25/00 MRS to BFH 5 1994, 1995, 

1997

97 1,161–1923 290 525 ODFW 0.56 9°C 10°C 15–20 100 B, C

5/26/00 MRS to BFH 5 1994, 1995, 

1996, 1997

76 1,087–2,155 277 525 ODFW 0.53 9°C 10°C 15–20 100 B, C

6/22/00 MRS to BFH 5 1995, 1996, 

1997

14 1,133–2,570 62 500 NMFS 0.12 10°C 11°C 10–20 100 B, C

7/19/00 MRS to BFH 5 1998 42 210 NMFS 10°C 12°C 10–20 100 B, C

2001 transfers

5/21/01 MRS to BFH 5 1997 71 2,699 422 750 ODFW 0.56 9°C 10°C 15–20 100 B, C

5/22/01 MRS to BFH 5 1996, 1997 80 2,120–2,618 395 750 ODFW 0.53 9°C 10°C 15–20 100 B, C

5/23/01 MRS to BFH 5 1995, 1996, 

1997, 1998

80 1,374–2,462 280 750 ODFW 0.37 9°C 10°C 15–20 100 B, C
61 

Table A-1 continued. Transport details for intersite fish transfers. 

Date Transfera

Transfer 

time (h) Broodyear No. fish

Average 

weight (g) Fish (lb)

Transfer tank 

(gal)b

Density 

(lb/gal)

Load 

temp.

Release 

temp.

DOc

(mg/L)

Survival (%) Commentd

2001 transfers (continued)

5/24/01 MRS to BFH 5 1998 69 1,066–1,141 166 750 NMFS 0.22 9°C 10°C 10–20 100 B, C

6/29/01 MRS to BFH 5 1997 28 1,017–2,108 115 750 NMFS 0.15 10°C 12°C 10–20 100 B, C

7/2/01 MRS to BFH 5 1998 14 1,093–1,212 36 360 NMFS 0.10 10°C 12°C 10–20 100 B, C

8/9/01 MRS to BFH 5 1999 26 140 NMFS 10°C 12°C 10–20 100 B, C

2002 transfers

4/8/02 MRS to BFH 5 1996, 1997, 

1998, 1999

196 699–2,088 520 2,250 ODFW 0.23 9°C 10°C 15–20 100 B, C

4/11/02 MRS to BFH 5 1999 41 378 34 180 NMFS 0.19 9°C 10°C 10–20 100 B, C

5/20/02 MRS to BFH 5 1998 70 1,202–2,069 278 750 ODFW 0.37 9°C 10°C 15–20 100 B, C

5/20/02 MRS to BFH 5 1997, 1999 31 637–1,817 73 750 NMFS 0.10 9°C 10°C 10–20 100 B, C

7/22/02 MRS to BFH 5 2000 43 210 NMFS 10°C 12°C 10–20 100 B, C

2003 transfers

4/9/03 MRS to BFH 5 1999, 2000 750 ODFW 9°C 10°C 15–20 100 B, C

4/10/03 MRS to BFH 5 1998, 2000 750 ODFW 9°C 10°C 15–20 100 B, C

4/11/03 MRS to BFH 5 1998 750 ODFW 9°C 10°C 15–20 100 B, C

5/28/03 MRS to BFH 5 1999, 2000 9 671–1,187 21 360 NMFS 0.06 10°C 11°C 10–20 100 B, C

7/23/03 MRS to BFH 5 2001 36 60–138 9 180 NMFS 0.05 10°C 12°C 10–20 100 B, C

2004 transfers

4/7/04 MRS to BFH 5 2000 108 1,376–1,465 330 750 ODFW 0.44 9°C 10°C 15–20 100 B, C

4/7/04 MRS to BFH 5 2000 51 1,681 190 350 ODFW 0.54 9°C 10°C 15–20 100 B, C

4/8/04 MRS to BFH 5 2001 152 649–721 229 750 ODFW 0.31 9°C 10°C 15–20 100 B, C

4/8/04 MRS to BFH 5 2001 82 732 132 350 ODFW 0.38 9°C 10°C 15–20 100 B, C

4/9/04 MRS to BFH 5 1999 6 1,787 24 140 NMFS 0.17 10°C 10°C 10–20 100 B, C

5/26/04 MRS to BFH 5 2000, 2001 21 255–1,357 48 220 NMFS 0.22 10°C 10°C 10–20 100 B, C

7/30/04 MRS to BFH 5 2002 59 86 12 500 NMFS 0.02 10°C 12°C 10–20 100 B, C

2005 transfers

4/4/05 MRS to BFH 5 2001 92 1,102–1,277 231 750 ODFW 0.31 9°C 10°C 15–20 100 B, C

4/5/05 MRS to BFH 5 2000, 2001 90 1,197–1,277 235 750 ODFW 0.31 9°C 10°C 15–20 100 B, C

4/13/05 MRS to BFH 5 2002 164 582–789 274 750 NMFS 0.37 10°C 10°C 10–20 100 B, C
62 

Table A-1 continued. Transport details for intersite fish transfers. 

Date Transfera

Transfer 

time (h) Broodyear No. fish

Average 

weight (g) Fish (lb)

Transfer tank 

(gal)b

Density 

(lb/gal)

Load 

temp.

Release 

temp.

DOc

(mg/L)

Survival (%) Commentd

2005 transfers (continued)

5/25/05 MRS to BFH 5 2000, 2001, 

2002

39 225–1,453 85 440 NMFS 0.19 10°C 10°C 10–20 100 B, C

7/18/05 MRS to BFH 5 2003 85 105–112 20 210 NMFS 0.10 10°C 12°C 10–20 100 B, C

2006 transfers

4/24/06 MRS to BFH 5 2002, 2003 136 793–1,366 338 750 ODFW 0.45 9°C 10°C 15–20 100 B, C

4/25/06 MRS to BFH 5 2002, 2003 133 829–1,287 307 750 ODFW 0.41 9°C 10°C 15–20 100 B, C

4/27/06 MRS to BFH 5 2001, 2002, 

2003

82 721–891 158 750 NMFS 0.21 10°C 10°C 10–20 100 B, C

6/9/06 MRS to BFH 5 2002, 2003 28 793–1,365 77 250 NMFS 0.31 10°C 10°C 10–20 100 B, C

7/26/06 MRS to BFH 5 2004 38 88–100 8 140 NMFS 0.06 10°C 12°C 10–20 100 B, C

2007 transfers

4/24/07 MRS to BFH 5 2003, 2004 139 1,123–1,681 434 750 ODFW 0.58 9°C 10°C 15–20 100 B, C

4/25/07 MRS to BFH 5 2003, 2004 164 909–1,965 472 750 ODFW 0.63 9°C 10°C 15–20 100 B, C

4/27/07 MRS to BFH 5 2002, 2003 62 1,004–1,965 245 750 NMFS 0.33 10°C 10°C 10–20 100 B, C

5/24/07 MRS to BFH 5 2002, 2003, 

2004

20 909–1,965 55 500 NMFS 0.11 10°C 11°C 10–20 100 B, C

7/25/07 MRS to BFH 5 2005 21 82 4 70 NMFS 0.06 10°C 12°C 10–20 100 B, C

2008 transfers

4/22/08 MRS to BFH 5 2004 62 1,786 244 750 ODFW 0.33 9°C 10°C 15–20 100 B, C

4/23/08 MRS to BFH 5 2005 87 988 190 500 ODFW 0.38 9°C 10°C 15–20 100 B, C

4/24/08 MRS to BFH 5 2004 89 2,014 395 750 ODFW 0.53 9°C 10°C 15–20 100 B, C

5/2/08 MRS to BFH 5 2002, 2003 15 1,362–1,497 47 360 NMFS 0.13 10°C 11°C 10–20 100 B, C

a

MRS = Manchester Research Station, Washington; BFH = Bonneville Fish Hatchery, Oregon.

b

ODFW = Oregon Department of Fish and Wildlife; NMFS = National Marine Fisheries Service. c

DO = dissolved oxygen.

d

B = Stop every 2–3 hours to check dissolved oxygen level, temperature, and fish condition; C = Fish transferred in 25% seawater and 75% freshwater. 
63 

Table A-2. Transport details for intersite fish transfers, Salmon River spring Chinook salmon (Oncorhynchus tshawytscha). 

Date Transfera

Transfer 

time (h) Broodyear No. fish

Average 

weight (g) Fish (lb)

Transfer tank 

(gal)b

Density 

(lb/gal)

Load 

temp

Release 

temp

DOc

(mg/L)

Survival (%) Commentd

2002 transfers

4/23/02 MRS to EFH 10 1998 52 3,073 352 1,000 IDFG 0.35 10°C 11°C 10–15 100 A, C

4/23/02 MRS to EFH 10 1997, 1998 98 2,305 498 900 IDFG 0.55 10°C 11°C 10–15 100 A, C

4/23/02 MRS to EFH 10 1997, 1999 113 790–2,088 229 800 IDFG 0.29 10°C 11°C 15–20 100 A, C

4/23/02 MRS to EFH 10 1998 17 1,263–2,309 70 440 NMFS 0.16 10°C 11°C 10–20 100 A, B, C

4/23/02 MRS to EFH 10 1999 23 841 43 180 NMFS 0.25 10°C 11°C 10–20 100 A, B, C

6/11/02 MRS to EFH 10 1998 15 2,169 72 250 IDFG 0.29 10°C 12°C 10–15 100 A, C

6/11/02 MRS to EFH 10 1998, 1999 49 409–2,375 164 690 NMFS 0.24 10°C 12°C 10–20 100 A, B, C

2003 transfers

5/6/03 MRS to EFH 10 1999 135 1,730–2,100 583 2,700 IDFG 0.22 10°C 12°C 10–15 100 A, C

5/6/03 MRS to EFH 10 1998 22 1,870 91 250 IDFG 0.36 10°C 12°C 10–15 100 A, C

5/6/03 MRS to EFH 10 2000 37 1,690 138 250 IDFG 0.55 10°C 12°C 10–15 100 A, C

5/6/03 MRS to EFH 10 1998, 2000 40 1,580–3,440 235 750 NMFS 0.31 10°C 12°C 10–15 100 A, B, C

6/12/03 MRS to EFH 10 1999, 2000 12 1,209–1,541 36 360 NMFS 0.10 10°C 12°C 10–15 100 A, B, C

2004 transfers

5/6/04 MRS to EFH 10 2000 116 1,992–2,906 648 1,900 IDFG 0.34 10°C 11°C 10–15 100 A, C

5/6/04 MRS to EFH 10 1999, 2001 13 670 19 250 IDFG 0.08 10°C 11°C 10–15 100 A, C

5/6/04 MRS to EFH 10 1998, 1999, 

2001

20 718–2,386 72 250 IDFG 0.29 10°C 11°C 10–15 100 A, C

7/8/04 MRS to EFH 10 2002 49 143 15 180 NMFS 0.08 10°C 12°C 10–20 100 A, B, C

2005 transfers

5/4/05 MRS to EFH 10 2001, 2002 33 1,018 74 250 IDFG 0.30 10°C 11°C 10–15 100 A, C

5/4/05 MRS to EFH 10 2001, 2002 32 1,022 72 250 IDFG 0.29 10°C 11°C 10–15 100 A, C

5/4/05 MRS to EFH 10 2001, 2002 151 782 260 750 NMFS 0.34 10°C 11°C 10–20 100 A, B, C

7/21/05 MRS to EFH 10 2003 125 174 48 360 NMFS 0.13 10°C 12°C 10–20 100 A, B, C

2006 transfers

7/12/06 MRS to Stanley, 

Idaho

20 2002, 2003, 

2004

245 118–2,100 621 2,100 IDFG 0.30 10°C 14°C 10–15 100 A, C

7/12/06 MRS to Stanley, 

Idaho

20 2002 81 1,587 283 750 NMFS 0.38 10°C 14°C 10–20 100 A, B, C
64 

Table A-2 continued. Transport details for intersite fish transfers, Salmon River spring Chinook salmon. 

Date Transfera

Transfer 

time (h) Broodyear No. fish

Average 

weight (g) Fish (lb)

Transfer tank 

(gal)b

Density 

(lb/gal)

Load 

temp

Release 

temp

DOc

(mg/L)

Survival (%) Commentd

2007 transfers

7/11/07 MRS to Stanley, 

Idaho

20 2002, 2003, 

2004

288 150–2,460 957 2,100 IDFG 0.46 10°C 16°C 10–15 100 A, C

7/11/07 MRS to Stanley, 

Idaho

22 2002, 2003, 

2004, 2005

192 150–2,111 446 750 NMFS 0.59 10°C 14°C 10–20 96.4 A, B, C, D

7/11/07 MRS to Stanley, 

Idaho

22 2003, 2004 39 1,100–2,068 156 250 IDFG 0.62 10°C 16°C 10–15 100 A, C, D

7/11/07 MRS to Stanley, 

Idaho

22 2003, 2004 38 1,100–2,068 152 250 IDFG 0.61 10°C 16°C 10–15 100 A, C, D

2008 transfers

7/9/08 MRS to Stanley, 

Idaho

18 2003, 2004, 

2005

160 990–1,960 632 1,900 IDFG 0.33 10°C 12°C 10–15 100 A, C

7/9/08 MRS to Stanley, 

Idaho

18 2003, 2004, 

2005

71 990–1,960 306 750 NMFS 0.41 10°C 12°C 7–24 100 A, C

7/9/08 MRS to Stanley, 

Idaho

18 2004 30 1,635 108 250 IDFG 0.43 10°C 12°C 10–15 100 A, C

7/9/08 MRS to Stanley, 

Idaho

18 2004 30 1,635 108 250 IDFG 0.43 10°C 12°C 10–15 100 A, C

a

MRS = Manchester Research Station; EFH = Eagle Fish Hatchery. b

IDFG = Idaho Department of Fish and Game; NMFS = National Marine Fisheries Service.

c

DO = dissolved oxygen.

d

A = Water exchange at Eagle Hatchery ID after 10 hour drive; B = Stop every 2–3 hours to check dissolved oxygen level, temperature, and fish condition; 

C = Fish transferred in 25% seawater and 75% freshwater; and D = Postrelease mortality was 45% due primarily to severe environmental conditions at time of 

release.
65 

Table A-3. Transport details for intersite fish transfers, Snake River (Redfish Lake) sockeye salmon (O. nerka). 

Date Transfera

Transfer

time (h) Broodyear No. fish

Average 

weight (g) Fish (lb)

Transfer tank 

(gal)

Density 

(lb/gal)

Load 

temp

Release 

temp

DOb

(mg/L)

Survival (%) Commentc

1996 transfer

9/10/96 MRS to Stanley, 

Idaho

14 1993 80 1,510 266 2,000 IDFG 0.13 10°C 14°C 10–15 100 A, B, E

1997 transfer

9/11/97 MRS to Stanley, 

Idaho

14 1993, 1994 120 1,866 493 2,000 IDFG 0.25 10°C 14°C 10–15 100 A, B, E

2000 transfer

9/5/00 MRS to Stanley, 

Idaho

14 1997 61 990 133 500 NMFS 0.27 10°C 14°C 10–15 100 A, B, E

2001 transfer

9/9/01 MRS to Stanley, 

Idaho

14 1997 66 2,498 363 2,000 IDFG 0.18 10°C 14°C 10–15 98.5 A, B, E

2002 transfer

9/11/02 MRS to Stanley, 

Idaho

14 1999 131 1,390 401 2,000 IDFG 0.20 10°C 14°C 10–15 100 A, B, E

2003 transfer

9/16/03 MRS to Stanley, 

Idaho

14 2000 280 1,395–1,743 1,001 2,700 IDFG

750 NMFS

0.29 10°C 14°C 10–15 100 A, B, E 

2004 transfer

9/7/04 MRS to Stanley, 

Idaho

14 2000, 2001 241 1,437–3,413 1,007 2,700 IDFG

750 NMFS

0.29 10°C 14°C 10–15 100 A, B, E

2005 transfer

9/7/05 MRS to Stanley, 

Idaho

14 2000, 2001, 

2002

177 1,200–2,244 671 2,700 IDFG

750 NMFS

0.19 10°C 14°C 10–15 100 A, B, E

2006 transfer

9/8/06 MRS to Stanley, 

Idaho

14 2002, 2003, 

2004

434 450–3,300 1,734 2,700 IDFG

750 NMFS

0.50 10°C 14°C 10–15 100 A, B, E

2007 transfer

9/5/07 MRS to Stanley, 

Idaho

14 2002, 2003, 

2004

367 1,253–3,200 1,341 2,100 IDFG

750 NMFS

0.47 10°C 14°C 10–15 98.9 A, B, E

2008 transfer

9/10/08 MRS to Stanley, 

Idaho

14 2003, 2004, 

2005

253 982–4,039 726 2,100 IDFG 0.35 10°C 14°C 10–15 100 A, B, E

a

MRS = Manchester Research Station. b

DO = dissolved oxygen.

c

A = Water exchange at Eagle Hatchery, ID, after 10-hour drive; B = Stop every 2–3 hours to check dissolved oxygen level, temperature, and fish condition; and 

E = Fish transferred in 100% freshwater.

Recent NOAA Technical Memorandums

published by the

Northwest Fisheries Science Center

NOAA Technical Memorandum NMFS-NWFSC116 Lian, C.E. 2012. West Coast open access groundfish and salmon troller survey: Protocol and results 

for 2005 and 2006. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-116, 52 p. NTIS 

number PB2012-107486.

115 Plummer, M.L., W. Morrison, and E. Steiner. 2012. Allocation of fishery harvests under the 

Magnuson-Stevens Fishery Conservation and Management Act: Principles and practice. U.S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-115, 84 p. NTIS number PB2012-107485.

114 Bradburn, M.J., A.A. Keller, and B.H. Horness. 2011. The 2003 to 2008 U.S. West Coast bottom 

trawl surveys of groundfish resources off Washington, Oregon, and California: Estimates of distribution, 

abundance, length, and age composition. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC114, 323 p. NTIS number PB2012-105507.

113 Ford, M.J. (ed.). 2011. Status review update for Pacific salmon and steelhead listed under the 

Endangered Species Act: Pacific Northwest. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC113, 281 p. NTIS number PB2012-104687.

112 Skidmore, P.B., C.R. Thorne, B.L. Cluer, G.R. Pess, J.M. Castro, T.J. Beechie, and C.C. Shea. 

2011. Science base and tools for evaluating stream engineering, management, and restoration proposals. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-112, 255 p. NTIS number PB2012-104660.

111 Leonard, J., and P. Watson. 2011. Description of the input-output model for Pacific Coast fisheries. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-111, 64 p. NTIS number PB2011-113405.

110 Ainsworth, C.H., I.C. Kaplan, P.S. Levin, R. Cudney-Bueno, E.A. Fulton, M. Mangel, P. TurkBoyer, J. Torre, A. Pares-Sierra, and H.N. Morzaria Luna. 2011. Atlantis model development for the 

northern Gulf of California. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-110, 293 p. 

NTIS number PB2011-113404.

109 Levin, P.S., and F.B. Schwing (eds.). 2011. Technical background for an integrated ecosystem 

assessment of the California Current: Groundfish, salmon, green sturgeon, and ecosystem health. U.S. 

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-109, 330 p. NTIS number PB2011-112724.

108 Drake, J.S., E.A. Berntson, J.M. Cope, R.G. Gustafson, E.E. Holmes, P.S. Levin, N. Tolimieri, 

R.S. Waples, S.M. Sogard, and G.D. Williams. 2010. Status review of five rockfish species in Puget 

Sound, Washington: Bocaccio (Sebastes paucispinis), canary rockfish (S. pinniger), yelloweye rockfish 

(S. ruberrimus), greenstriped rockfish (S. elongatus), and redstripe rockfish (S. proriger). U.S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-108, 234 p. NTIS number PB2011-107576.

Most NOAA Technical Memorandums NMFS-NWFSC are available at the

Northwest Fisheries Science Center Web site, http://www.nwfsc.noaa.gov