Final Restoration Plan

for the 

Anadromous Fish Restoration Program

A Plan to Increase Natural Production of Anadromous Fish in the 

Central Valley of California

Released as a Revised Draft on May 30, 1997

and Adopted as Final on January 9, 2001
UPDATES*

* This page is not included in the Final Restoration Plan for the AFRP. The purpose of this page is to track 

possible changes in the Plan as more information becomes available. 

The following updates have been identified:

Appendix B-1 and Table E-1: The referred winter Chinook salmon run in the Calaveras 

River is not considered an authentic salmon run in this river and may have been mistaken 

by a late fall-run (Yoshiyama et al. 2001). Alternative production targets for other 

salmonids in the Calaveras River are being evaluated in the AFRP project: Lower 

Calaveras River salmonid life history limiting factor analysis. Updated production 

targets for salmonids in the Calaveras River will be reported here at the completion of 

that study (Last updated September 3, 2002).

References

Yoshiyama, R.M., E.R. Gertstung, F.W. Fisher and P.B. Moyle. 2001. Historical and present distribution of 

Chinook salmon in the Central Valley of California. California Department of Fish and Game. Fish 

Bulletin 179(1): 71-176.
FINAL RESTORATION PLAN

FOR THE

ANADROMOUS FISH RESTORATION PROGRAM

APLAN TO INCREASE NATURAL PRODUCTION OF ANADROMOUS FISH

IN THE CENTRAL VALLEY OF CALIFORNIA

Prepared for the Secretary of the Interior by the

United States Fish and Wildlife Service with assistance from

the Anadromous Fish Restoration Program Core Group

under authority of the Central Valley Project Improvement Act.

 

 January 9, 2001
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 i

PREFACE

The Central Valley Project Improvement Act (CVPIA) directs the Secretary of the

Interior to develop and implement a program that makes all reasonable efforts to double

natural production of anadromous fish in Central Valley streams (Section 3406(b)(1)). 

The program is known as the Anadromous Fish Restoration Program (AFRP).

The document you have before you is the Restoration Plan. The Restoration Plan is a

programmatic-level description of the AFRP in broad and general terms, and will be used

to guide the long-term development of the AFRP. The Restoration Plan presents the

goal, objectives, and strategies of the AFRP; describes how the AFRP identified and

prioritized reasonable actions and evaluations; lists those actions and evaluations; and

notes those actions and evaluations that are already underway or that may be

implemented in the near future.

An initial draft was released for review and comment in December 1995 and a revised

draft was released for review and comment in 1997. This Final Plan incorporates those

1997 comments to the extent the Department of the Interior (Interior) deemed

appropriate. The Programmatic Environmental Impact Statement (PEIS) required by

Section 3409 of the CVPIA has been completed.

The AFRP will use all the authority and resources provided by the CVPIA to restore

anadromous fish and will rely heavily on local involvement and partnerships with

property owners, watershed workgroups, public and private organizations, county and

local governments, and state and federal agencies. To make restoration efforts as

efficient as possible, the AFRP will coordinate restoration efforts with those by other

groups, such as the California Department of Fish and Game, Category III of the BayDelta Agreement, the San Joaquin River Management Program, and the CALFED BayDelta Program. Successful implementation of the Restoration Plan will depend on the

continued participation of the public and interested parties and support of involved state

and federal agencies.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 ii

ACKNOWLEDGMENTS

The Restoration Plan is the responsibility of the USFWS as the lead agency for the AFRP. The 

USFWS thanks the AFRP=s Core Group, including Randy Brown of the California Department of 

Water Resources, Jim Bybee of the National Marine Fisheries Service (NMFS), Susan Hatfield and 

Bruce Herbold of the United States Environmental Protection Agency (USEPA), Ken Lentz of the 

USBR, and Terry Mills and Alan Barraco of the California Department of Fish and Game. However, 

this plan does not commit any Core Group members= agency to implement any of the actions noted 

herein. The USFWS thanks Laura King of the USBR, Gary Stern of the NMFS, Tom Hagler of the 

USEPA, and Dana Jacobsen of the Office of the Solicitor, and the members of Interior=s Washington 

Office Policy Group, including Ted Boling of the Office of the Assistant Secretary for Fish and Wildlife 

and Parks, Dana Cooper of the Office of the Assistant Secretary for Water and Science, Barbara 

Geigle of the Office of the Solicitor, Rowan Gould of the USFWS, and Steve Magnuson of the USBR; 

and the staffs at the Central Valley Fish and Wildlife Restoration Program, including Roger Dunn, Roger 

Guinee, Andy Hamilton, Jim McKevitt, and Larry Puckett; the Sacramento Field Office, including Rick 

Morat and Mike Thabault; the Northern Central Valley Fish and Wildlife Office, including Jim Smith; 

and the Sacramento-San Joaquin Estuary Fishery Resource Office, including Pat Brandes, Dan 

Castleberry, Kathy Corbin, John Icanberry, Marty Kjelson, Yvette Leatherman, Sam Lohr, Gary 

Rensink, Scott Spaulding, and John Wullschleger; for their contributions toward completion of this plan. 

 The USFWS also thanks the many public and private organizations and individuals that took time to 

help prepare this plan by attending public workshops, meeting on a local watershed or interest level, or 

writing or calling to voice their concerns.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 iii

TABLE OF CONTENTS

PREFACE..........................................................................................................................................i

ACKNOWLEDGMENTS ................................................................................................................ ii

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

STATUTORY SCHEME......................................................................................................1

COMPLIANCE WITH RELATED STATUTES...................................................................2

National Environmental Policy Act..............................................................................2

Endangered Species Act ............................................................................................3

PURPOSES ..........................................................................................................................3

GOAL AND OBJECTIVES..................................................................................................4

STRATEGIES.......................................................................................................................4

Implementation principles...........................................................................................5

Contribution to natural production...................................................................5

Species status................................................................................................5

Restoring natural habitat values.......................................................................6

Modifying CVP operations.............................................................................6

Implementing supporting measures in the CVPIA............................................6

Implementation approach...........................................................................................6

Partnerships...................................................................................................7

Local involvement ..........................................................................................7

Public support................................................................................................7

Adaptive management....................................................................................7

Flexibility.......................................................................................................8

DEVELOPING RESTORATION PLAN ACTIONS........................................................................8

IDENTIFYING THE SCIENTIFIC KNOWLEDGE BASE - THE WORKING PAPER......8

DEVELOPING THE DRAFT RESTORATION PLAN......................................................10

DEVELOPING THE REVISED DRAFT RESTORATION PLAN.....................................13

DEVELOPING SPECIFIC IMPLEMENTATION PLANS ................................................14

IMPLEMENTATION PROCESS...................................................................................................16

CRITERIA TO PRIORITIZE REASONABLE ACTIONS.................................................16

Watershed priority...................................................................................................16

Action priority..........................................................................................................17

IMPLEMENTING RESTORATION PLAN ACTIONS.....................................................18

Tools in the CVPIA.................................................................................................18
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 iv

Cooperation with others...........................................................................................22

MONITORING AND EVALUATION...............................................................................25

Action-specific.........................................................................................................26

Watershed-specific ..................................................................................................26

Systemwide and long-term.......................................................................................26

DEALING WITH VARYING DEGREES OF SCIENTIFIC CERTAINTY........................27

PUBLIC INVOLVEMENT.................................................................................................29

Approach ................................................................................................................29

Programmatic public involvement activities to date.....................................................30

Future public involvement opportunities.....................................................................32

Programmatic...............................................................................................32

Action-specific.............................................................................................32

Public involvement mechanisms.................................................................................32

ACTIONS AND EVALUATIONS.................................................................................................33

SACRAMENTO RIVER BASIN........................................................................................35

Upper mainstem Sacramento River...........................................................................35

Upper Sacramento River tributaries..........................................................................

Clear Creek.................................................................................................40 

Cow Creek..................................................................................................42

Bear Creek..................................................................................................43 

Cottonwood Creek......................................................................................44 

Battle Creek ................................................................................................45 

Paynes Creek .............................................................................................. 48 

Antelope Creek ........................................................................................... 48 

Elder Creek................................................................................................. 49 

Mill Creek...................................................................................................50 

Thomes Creek.............................................................................................51 

Deer Creek ................................................................................................5..4 

Stony Creek ................................................................................................55 

Big Chico Creek..........................................................................................55 

Butte Creek................................................................................................. 58 

Colusa Basin Drain.......................................................................................66 

Miscellaneous small tributaries......................................................................67 

LOWER SACRAMENTO RIVER AND DELTA TRIBUTARIES.....................................67 

Feather River...........................................................................................................67

Yuba River.............................................................................................................. 69 

Bear River ...............................................................................................................71 

American River........................................................................................................73 

Mokelumne River..................................................................................................... 76 

40
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 v

Cosumnes River....................................................................................................... 78 

Calaveras River........................................................................................................80 

SAN JOAQUIN BASIN.....................................................................................................81 

Merced River...........................................................................................................81 

Tuolumne River........................................................................................................83 

Stanislaus River........................................................................................................ 86 

Mainstem San Joaquin River..................................................................................... 89 

SACRAMENTO-SAN JOAQUIN DELTA........................................................................92 

CENTRAL VALLEY-WIDE............................................................................................101 

OCEAN ............................................................................................................................104 

REFERENCES CITED .................................................................................................................105 

APPENDICES .............................................................................................................................A-1

A. AFRP Position Paper..................................................................................................A-1

B. Production targets for chinook salmon in each stream....................................................B-1

C. Contacts and sources of information.............................................................................C-1

D. Template for organization of detailed information on specific actions..............................D-1

E. Summary of information used to prioritize watersheds....................................................E-1

F. Projected funding resources. .........................................................................................F-1

G. List of acronyms and abbreviations. .............................................................................G-1
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 vi

H. Responses to public comments received on the December 6, 1995 

Draft Anadromous Fish Restoration Plan.............................................................. H-1

1

I. Public comments received on the December 6, 1995 Draft

Anadromous Fish Restoration Plan.........................................................................I-1

1

 

1Appendices H and I are bound as separate documents. Appendix H presents paraphrased 

comments and the USFWS=s responses to each of the comments that we received during the 

designated comment period on the December 6, 1995 draft of the Restoration Plan. Appendix I 

presents the summarized oral comments and complete written comments that we paraphrased for 

Appendix H. Although Appendix H provides insight to help the reader further understand the 

Restoration Plan, it is not essential for using the Restoration Plan. Appendix I is intended to help 

interested parties see how their comments and the comments of others were paraphrased and 

represented by the USFWS in Appendix H. Appendices H and I are available upon request from the 

Program Manager for the AFRP at (209) 946-6400 or at the address listed in Appendix C.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 1

INTRODUCTION

Since settlement of the Central Valley in the mid-1800s, populations of native anadromous fishes (i.e., 

chinook salmon, steelhead, white sturgeon, and green sturgeon) have declined dramatically. Declines 

have been so dramatic that several species may be in danger of extinction. At present, winter-run 

chinook salmon are listed as endangered under the federal and state Endangered Species acts, and all 

other races of chinook salmon and steelhead have been petitioned for either federal or state listing.

American shad and striped bass were introduced into the Sacramento-San Joaquin system in the 1870s. 

 Both species supported valuable sport and commercial fisheries throughout much of this century, but 

California Department of Fish and Game (CDFG) data indicate that populations have declined since the 

mid-1960s.

Habitat degradation is the primary cause of these declines. Hydraulic mining for gold was the first 

human activity that resulted in large-scale habitat degradation due to sedimentation and diversion of 

water in many Central Valley streams. Hydraulic mining was prohibited in 1894, but habitat 

degradation has continued. Habitat quantity and quality have declined due to construction of barriers to 

migration and levees, modification of natural hydrologic regimes by dams and water diversions, elevated 

water temperatures, and water pollution. Causes of declines in habitat quality and quantity are examples 

of factors that may potentially reduce natural production of anadromous fish below levels that would 

occur in the absence of the factor, and are sometimes called limiting factors or stressors. Although the 

effects of habitat degradation on fish populations were evident by the 1930s, rates of decline for most 

anadromous fish species increased following completion of major water project facilities.

Other factors that may have adversely affected natural stocks of anadromous fish include overharvest, 

illegal harvest, hatchery production, and introduction of competitors, predators and diseases. Fish 

populations may also vary due to natural events. Droughts and poor ocean conditions, such as El Niño, 

may reduce populations. However, populations in healthy habitats typically recover within a few years 

after natural events. The decline of fish populations has continued through cycles of beneficial and 

adverse natural conditions, indicating the need to improve habitat.

STATUTORY SCHEME

Section 3406(b)(1) of the Central Valley Project Improvement Act (CVPIA) requires the Secretary of 

the Department of the Interior (Secretary) to Adevelop within three years of enactment and implement a 

program which makes all reasonable efforts to ensure that, by the year 2002, natural production of 

anadromous fish in Central Valley rivers and streams will be sustainable, on a long-term basis, at levels 

not less than twice the average levels attained during the period of 1967 - 1991...@ Section 3406(b)(1) 

also states that Athis goal shall not apply to the San Joaquin River between Friant Dam and the Mendota 

Pool.@ Further, Section 3406(b)(1)(A) requires that the program Agive first priority to measures which 
2 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

protect and restore natural channel and riparian habitat values through habitat restoration actions, 

modifications to Central Valley Project operations, and implementation of the supporting measures 

mandated by this subsection; shall be reviewed and updated every five years; and shall describe how 

the Secretary intends to operate the Central Valley Project to meet the fish, wildlife and habitat 

restoration goals and requirements set forth in this title and other project purposes.@

The Secretary directed the U.S. Fish and Wildlife Service (USFWS) and the U.S. Bureau of 

Reclamation (USBR) to jointly implement the CVPIA, and Section 3406(b)(1) in particular. The 

USFWS and USBR are approaching implementation of this directive through development of an 

Anadromous Fish Restoration Program (AFRP) to address those species identified for restoration in the 

CVPIA. Those six anadromous fish species are chinook salmon (Oncorhynchus tshawytscha), 

steelhead (O. mykiss), striped bass (Morone saxatilis), American shad (Alosa sapidissima), white 

sturgeon (Acipenser transmontanus), and green sturgeon (A. medirostris). The term AAFRP@ is the 

umbrella term for all of the components of the Department of the Interior=s (Interior) and its agency and 

private partner=s efforts to make all reasonable efforts to at least double the natural production of 

anadromous fish. This Restoration Plan presents the goal, objectives, and strategies of the AFRP; 

describes processes the AFRP used to identify, develop, and select restoration actions; and lists actions 

and evaluations determined, at a programmatic level, to be reasonable to implement as part of the 

AFRP.

COMPLIANCE WITH RELATED STATUTES

A number of related statutes affect the development and implementation of this Restoration Plan under 

the CVPIA. The most important of these related statutes are the National Environmental Policy Act 

(NEPA) and the Endangered Species Act (ESA).

National Environmental Policy Act

This Restoration Plan was developed to comply with Section 3406(b)(1) of the CVPIA. The impacts 

of this programmatic-level Restoration Plan are being analyzed in the Programmatic Environmental 

Impact Statement (PEIS), which is being prepared pursuant to NEPA and to Section 3409 of the 

CVPIA. The revised Restoration Plan remains subject to change, based on the results of the PEIS, as 

well as through adaptive management of the actions during the life of the Restoration Plan. 

While the PEIS is being finalized, Interior will continue to manage the water dedicated by Section 

3406(b)(2) of the CVPIA for the primary purpose of implementing the fish, wildlife, and habitat 

restoration purposes of the CVPIA, as determined by the Ninth Circuit Court of Appeals in Westlands 

v. United States, 43 F. 3d 457 (9th Cir. 1994). The court in that case concluded that the requirements 

in certain sections of the CVPIA to take action immediately upon enactment of the CVPIA created an 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 3

irreconcilable conflict with the requirements of NEPA. The court concluded, therefore, that NEPA 

analysis of the dedication and management of the 3406(b)(2) water was not required.

The impacts of implementing individual actions identified in the Restoration Plan pursued under authority 

other than Section 3406(b)(2) will be analyzed in site-specific NEPA documentation, as appropriate.

Endangered Species Act

Section 7(a) of the ESA states in part that AThe Secretary shall review other programs administered by 

him and utilize such programs in furtherance of the purposes of this Act.@ For example, in March 1993 

the USFWS listed the delta smelt as a threatened species pursuant to the ESA. In December 1994, 

critical habitat was designated for the delta smelt. In November 1996, the USFWS published the Final 

Recovery Plan for the Sacramento-San Joaquin Delta Native Fishes (DNFRP) (USFWS 1996). The 

DNFRP identifies both flow and non-flow actions. The flow actions identified in the DNFRP are 

classified as Apriority one actions,@ meaning that they are actions considered necessary for the recovery 

of the species. Many actions in this Restoration Plan are flow-related, and the life stages of many of the 

anadromous species overlap with critical life stages of the delta smelt and other native fishes in the Delta. 

 The implementation schedule for actions within the DNFRP are immediate and ongoing. Therefore, 

many actions in the Restoration Plan will contribute towards recovery of Delta native fishes.

Actions within the Restoration Plan may have effects not foreseen at this time. All actions implemented 

through the AFRP will need to be reviewed for their effects on listed and proposed species. Any such 

actions that may affect those species will be subject to further review under the Secretary's authorities 

under Section 7(a)(2) of the ESA. It is Interior's intention that the USFWS, National Marine Fisheries 

Service (NMFS), and CDFG work closely together to coordinate actions in the implementation and 

recovery plans for anadromous fish and listed and proposed species.

PURPOSES

The AFRP is an opportunity for the USFWS and USBR to collaborate with other agencies, 

organizations and the public to increase natural production of anadromous fish in the Central Valley by 

augmenting and assisting restoration efforts presently conducted by local watershed workgroups, the 

CDFG, and others. Purposes of the CVPIA (Section 3402) relevant to the AFRP are:

• To protect, restore, and enhanc e fish, wildlife, and associated habitats in the Central Valley;

• To address impacts of the Central Valley Project (CVP) on fish, wildlife, and associated 

habitats;

• To improve the operational flexibility of the CVP;

• To contribute to the State of California =s interim and long-term efforts to protect the San 

Francisco Bay and Sacramento-San Joaquin Delta Estuary; and
4 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

• To achieve a reasonable balance among competing demands for the use of CVP water, 

including the requirements of fish and wildlife, agricultural, municipal and industrial, and power 

contractors.

GOAL AND OBJECTIVES

The goal of the AFRP, as stated in Section 3406(b)(1) of the CVPIA, is to Adevelop within three years 

of enactment and implement a program which makes all reasonable efforts to ensure that, by the year 

2002, natural production of anadromous fish in Central Valley rivers and streams will be sustainable, on 

a long-term basis, at levels not less than twice the average levels attained during the period of 1967-

1991.@ Section 3406(b)(1) also states that Athis goal shall not apply to the San Joaquin River between 

Friant Dam and the Mendota Pool.@

Six general objectives need to be met to achieve the program goal:

• Improve habitat for all life stages of anadromous fish through provision of flows of suitable 

quality, quantity, and timing, and improved physical habitat;

• Improve survival rates by reducing or eliminating entrainment of juveniles at diversions;

• Improve the opportunity for adult fish to reach their spawning habitats in a timely manner;

• Collect fish population, health, and habitat data to facilitate evaluation of restoration actions;

• Integrate habitat restoration efforts with harvest and hatchery management; and

• Involve partners in the implementation and evaluation of restoration actions.

STRATEGIES

Fishery managers must address complex biological, economic, social, and technological issues to 

substantially restore natural production of anadromous fish in the Central Valley. Restoration will be 

costly and require changing the way aquatic resources and habitats are managed. Because the challenge 

is great, the AFRP requires solid strategies to select and implement effective restoration actions.

The AFRP strategies consist of two components, implementation principles and an implementation 

approach. Implementation principles are the tenets guiding selection and prioritization of actions. The 

implementation approach describes key aspects of how restoration actions will be implemented.

Implementation principles

Restoration actions are being selected and prioritized based on the magnitude of the contribution to 

doubling natural production, the status of target species and races, and on Section 3406(b)(1)(A) of the 

CVPIA, which directs the AFRP to give first priority to:
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 5

• Measures which protect and restore natural channel and riparian habitat values through habitat 

restoration actions;

• Modifications to Central Valley Project operations; and

• Implementation of the supporting measures mandated by subsection 3406(b) of the CVPIA.

These principles are discussed below.

- Contribution to natural production

Placing priority on actions that result in large increases in natural production will most efficiently 

contribute to meeting target production levels.

- Species status

Placing priority on actions that benefit species and races whose abundance is precariously low will help 

maintain the genetic diversity of anadromous fish in the Central Valley. Maintaining genetic diversity will 

preserve adaptability and resilience, which are essential if natural production is to be sustainable on a 

long-term basis.

Winter-run chinook salmon are listed as endangered under the federal and state ESAs. Spring-run, 

late-fall-run, and fall-run chinook salmon have been petitioned for threatened or endangered status 

throughout their range in Washington, Oregon, California, and Idaho, under the federal ESA (NMFS 

1995). The California Fish and Game Commission will take regulatory action concerning the candidacy 

of spring-run chinook salmon as an endangered species under the state ESA soon. Steelhead have 

been petitioned for threatened or endangered status throughout its range in Washington, Oregon, 

California, and Idaho, under the federal ESA (NMFS 1994). A proposed determination by NMFS 

identified steelhead in the Central Valley as an evolutionary significant unit, and recommended listing as 

an endangered species (NMFS 1996). A final determination will be made in August 1997. White 

sturgeon, green sturgeon, striped bass and American shad have also suffered significant, long-term 

declines.

- Restoring natural habitat values

Protecting and restoring natural channel and riparian habitat values promotes natural processes that 

regulate geomorphic characteristics, nutrient dynamics, and production capabilities of streams, rivers, 

and estuaries. Restoring natural processes is essential to ensure that both physical and biological 

ecosystem components can resist declines and recover after both natural and anthropogenic 

perturbations, thus contributing to long-term sustainability of natural production.
6 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

- Modifying CVP operations

Placing priority on actions that modify CVP operations will directly help minimize impacts on fish, 

wildlife, and associated habitats; help balance competing demands for the use of CVP water, including 

the requirements of fish and wildlife; and will focus restoration efforts where the Secretary has the 

authority to be most effective.

- Implementing supporting measures in the CVPIA

Placing priority on implementing the supporting measures mandated by subsection 3406(b) of the 

CVPIA focuses restoration efforts where the Secretary has the authority to be most effective.

The implementation principles can be used to compare actions that address a common limiting factor 

(for example, to compare two actions that address a lack of suitable spawning substrate) as well as to 

compare actions that address different limiting factors (for example, to compare an action that addresses 

lack of suitable spawning substrate with an action that addresses illegal harvest) within a watershed. In 

applying these principles, the AFRP will support actions that contribute to increasing the natural 

production of anadromous fish through restoration of natural habitat values before supporting actions 

that increase production by other means.

Implementation approach

The AFRP approach to making all reasonable efforts to at least double natural production of 

anadromous fish will include partnerships, local involvement, public support, adaptive management, and 

flexibility.

- Partnerships

A single entity cannot double natural production of anadromous fish throughout the Central Valley. 

Partnerships are needed. Voluntary collaborations to achieve mutual goals and objectives will 

accelerate accomplishments, increase available resources, reduce duplication of efforts, encourage 

innovative solutions, improve communication, and increase public involvement and support through 

shared authority and ownership of restoration actions. The AFRP will seek partners to facilitate 

restoration.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 7

- Local involvement

The AFRP will encourage local citizens and groups to share or take the lead in implementing restoration 

actions. Influences on anadromous fish production in specific watersheds are often related to local 

water management and land use, which are typically controlled by local individuals and groups. Local 

people may have innovative approaches to solving problems, and may be able to implement those 

solutions most efficiently. This approach is consistent with ACalifornia=s Coordinated Regional Strategy 

to Conserve Biological Diversity@ (MOU 1991), in which 26 state and federal agencies emphasize 

regional solutions to regional problems.

The AFRP will encourage local involvement by joining with existing local restoration groups and 

supporting the formation of new groups.

- Public support

Public support is both a product and a prerequisite of partnerships and local involvement. Public 

sentiment is an indicator of perceived economic and social effects of restoration actions. Public support 

for an action will facilitate implementation and attract partners for future actions. The AFRP will seek 

opportunities for the public to assist in planning and implementing restoration actions.

- Adaptive management

The AFRP will employ adaptive management to increase the effectiveness of restoration actions and to 

address scientific uncertainty. Adaptive management is an approach that allows resource managers to 

learn from past experiences through formal experiment or by altering actions based on their measured 

effectiveness. Monitoring programs are the foundation of the adaptive management approach.

- Flexibility

Implementation of restoration actions needs to be flexible so that unforeseen opportunities can be 

pursued if they meet the intent of the CVPIA. Also, flexibility will help the AFRP address unforeseen 

factors that arise or problems that intensify in the future. For example, although there is just one 

evaluation in this plan that addresses the effects of nuisance, non-native aquatic organisms such as the 

zebra mussel, this may become a problem that will potentially intensify in unforeseen ways in the future. 

The AFRP has the flexibility to work with partners to develop actions consistent with the intent of the 

CVPIA to address specific problems as they arise or intensify. This flexibility will facilitate efforts to 

maximize the effects of restoration efforts and to sustain benefits to fish production that accrue from 

these restoration efforts and other management activities.
8 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

DEVELOPING RESTORATION PLAN ACTIONS

The AFRP is being developed in three steps: (1) attain the best available scientific and commercial data; 

(2) develop a long-term Restoration Plan that identifies the general approaches and actions to attain the 

goal; and (3) develop short-term (three-to-five years) implementation plans tiered off the Restoration 

Plan. One important implementation plan will be the Water Management Plan that will outline how 

Interior will manage CVP water resources to implement the AFRP. These implementation plans can be

modified at any time in response to new information acquired through monitoring or new research; 

Interior presently anticipates revisions at least every three-to-five years. The long-term Restoration Plan 

will be reviewed and updated every five years as required by Section 3406(b)(1)(A) of the CVPIA.

IDENTIFYING THE SCIENTIFIC KNOWLEDGE BASE - THE WORKING PAPER

The first step in developing the AFRP was accomplished through development and dissemination of the 

"Working Paper on Restoration Needs--Habitat Restoration Actions to Double Natural Production of 

Anadromous Fish in the Central Valley of California (May9, 1995)" (the Working Paper, USFWS 

1995). The Working Paper was developed under the direction of a scientific Core Group composed of 

representatives of the USFWS, USBR, NMFS, U.S. Environmental Protection Agency (USEPA), 

CDFG, and California Department of Water Resources (CDWR). The Working Paper focused on 

identifying the best available science, without regard to whether CVPIA tools might reasonably be 

brought to bear on the identified scientific issues.

The scientific basis for the AFRP is founded in numerous pre-AFRP research, planning, management, 

and restoration activities, and the resulting body of information that was produced documenting these 

activities. In carrying out the development of the AFRP, Interior used information available from a 

variety of sources. These include published literature on the species, CDFG reports such as ARestoring 

Central Valley Streams: A Plan For Action@ (Reynolds et al. 1993) and subsequent AStatus of 

Implementation@ (Mills 1995), the San Joaquin River Management Program=s document title ASan 

Joaquin River Management Plan@ (SJRMP), Category III of the Bay-Delta Agreement=s list of actions, 

as well as input from stakeholders and the scientific community in general. The Core Group also sought 

input from individuals with expertise in the fisheries of the Delta and Central Valley to develop actions 

deemed necessary to at least double natural production of anadromous fish. The Working Paper listed 

potential factors or stressors that may limit natural production of anadromous fish and restoration actions 

that, if implemented, would address these factors and likely result in at least doubling natural production 

of anadromous fish. Reasonableness was not considered in developing the restoration actions because 

reasonableness would be addressed in development of this Restoration Plan.

The Working Paper actions included both non-flow actions (such as gravel restoration or use of fish 

screens) and flow actions. The Working Paper also included estimates of target levels of long-term, 

average production for four races of chinook salmon, steelhead, striped bass, American shad, and white 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 9

and green sturgeon. Production was defined in Appendix A of the Restoration Plan as the number of 

fish recruited to the adult population, including those harvested. Estimates of target production levels 

are summarized in Table 1.

The Working Paper was intended to establish a list of restoration actions that, if implemented in its 

entirety, would likely result in at least doubling the natural production of anadromous fish. The Working 

Paper relied on the scientific research that was available, with acknowledgment that scientific uncertainty 

was a reality in many areas. As noted above, the Working Paper did not attempt any consideration of 

whether the actions were reasonable as required under the CVPIA. Doubling production by 

implementing a reasonable set of actions (that is, a subset of the Working Paper actions) is less certain 

than if all the actions were implemented, but it still may be possible to double production of some 

species and streams. For example, doubling production of fall-run chinook salmon in a small tributary 

of the upper Sacramento River may be relatively easy, whereas doubling production of striped bass will 

likely be difficult because of the potential quantity of water that could be required to provide adequate 

conditions for doubling.

Table 1. Target production levels for anadromous fish

in Central Valley rivers and streams.

Species Target

Chinook salmon, all racesa990,000

Fall run 750,000

Late-fall run 68,000

Winter run 110,000

Spring run 68,000

Steelheadb13,000

Striped bassc2,500,000

American shadd4,300

White sturgeon 11,000

Green sturgeon 2,000
10 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

a

 Appendix B lists production targets for each race of chinook salmon for each of the streams in the Central 

Valley. Because of rounding errors, targets for individual races of chinook salmon do not add up to the 

target for all races.

b

 Production target for steelhead spawning upstream of Red Bluff Diversion Dam. Additional steelhead 

spawned naturally elsewhere in the Central Valley during 1967 through 1991, but no data exist from which to 

calculate a target production level. Absence of a production target for a species in a specific area (for 

example, steelhead downstream of Red Bluff Diversion Dam) does not mean that actions to benefit that 

species in that area will not be considered, and in fact this Restoration Plan includes several actions for 

species in reaches that do not have associated production targets.

c

 Production target for striped bass is expressed as the abundance of legal-sized striped bass estimated 

annually by the CDFG. Estimates of legal-sized fish are used as a surrogate for adult fish because these are 

the best available data for developing a production target. However, the estimate includes some legal-sized 

fish that are not sexually mature and does not include some sub-legal-sized fish that are sexually mature.

d

 Production target for American shad is expressed as the juvenile index as derived from the CDFG fall 

midwater trawl in the Delt a.

DEVELOPING THE DRAFT RESTORATION PLAN

The second step in developing an AFRP was the development and release of a draft Restoration Plan 

on December 6, 1995. The draft Restoration Plan served several functions. First, the draft Restoration 

Plan reflected the public comments that had been received after release of the Working Paper. In order 

to inform the public about the Working Paper and solicit comments, Interior held public workshops in 

five cities throughout northern California in June 1995. In addition, between May and November 1995, 

AFRP staff participated in over 30 technical workshops to discuss the Working Paper and potential 

provisions of the Restoration Plan. Information that was developed as a result of this outreach effort 

was included in the draft Restoration Plan. 

The second major function of the draft Restoration Plan was to present specific target flows to be 

implemented in the Delta and on the CVP-controlled Central Valley streams (Sacramento River, Clear 

Creek, American River, and Stanislaus River). The draft Restoration Plan also included non-flow 

actions for all Central Valley streams (CVP-controlled and non-CVP-controlled streams).

Finally, in developing the draft Restoration Plan, Interior began its analysis of the reasonableness of 

AFRP actions and evaluations at the programmatic level. To assess the reasonableness of proposed 

AFRP actions and evaluations, Interior conducted two parallel processes. In the first process, Interior 

reviewed a multi-step process to evaluate each proposed action. This review, which identified 

reasonable actions, and which will also be used to consider proposed actions in the future, sequentially 

considered six steps (Figure 1) to address the following three broad categories of questions:
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 11

The first category of questions concerned the intent and technical and legal basis of an action. Specific 

questions Interior addressed were whether the action would benefit natural production consistent with 

the provisions of the CVPIA; whether key technical and scientific issues were resolved; and whether the 

action complied with applicable laws and regulations (steps one and two, Figure 1). If any question was 

not affirmed, the action was either referred to other programs, modified for reconsideration, or 

eliminated. Otherwise, actions were subjected to the second category of questions.

The second category of questions considered authority to implement the action. If the CVPIA 

specifically authorizes or directs Interior to implement the action and it does not require a partner (step 

three, Figure 1), it was considered reasonable for inclusion in the Restoration Plan. For example, 

Section 3406(b) includes a number of specific actions or programs to be implemented by the Secretary. 

 The actions and programs determined consistent with the goal and objectives of the AFRP were 

considered reasonable. This same conclusion applies to certain explicit measures in the CVPIA that are 

also Atools@ for attaining the goal of the AFRP. That is, Interior believes that it is reasonable, at a 

programmatic level, to conclude that using the tools in subsections 3406 (b)(1)(B), (b)(2) and (b)(3) --

reoperation of the CVP, use of the 800,000 acre-feet of dedicated water for fish and wildlife 

restoration, and acquisition of additional water from willing sellers -- is reasonable for purposes of this 

programmatic level analysis.
12 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

If the action requires a partner with 

the authority to implement it, and the 

partners support implementation, then 

the action was considered reasonable 

(step four, Figure 1). Otherwise the 

action was subjected to the third 

category of questions.

The third category of questions 

concerned support from the 

interested public for actions that 

would require partnerships to 

implement but the partnerships were 

not yet established. For example, 

some of the proposed actions require 

a cost-share partner as either 

stipulated in the CVPIA or due to the 

nature of the action. In these cases, 

Interior evaluated whether the 

interested public has expressed 

sufficient support for a particular 

action that it may be reasonable to 

assume that a cost-share partner will 

eventually come forward (step five, 

Figure 1). If partners were likely to 

come forward, an action was 

considered reasonable. Otherwise, 

an action was either modified for reconsideration or 

eliminated. Forming partnerships will be a dynamic and ongoing process continuing through the 

implementation phase of the AFRP, as described below.

A second reasonableness evaluation process was also being conducted during the development of the 

draft Restoration Plan. As noted above, the draft Restoration Plan included specific flows targets to be 

implemented in the Delta and on the four major CVP-controlled Central Valley streams. These flows 

will be addressed in the PEIS. To evaluate the reasonableness of these flows, the AFRP staff consulted 

with the staff developing the PEIS in an iterative process. The process resulted in modeling a range of 

flows, which was based on a series of assumptions considering the relative availability of water and the 

expected benefits to fish of flows on CVP-controlled streams and the Delta. Although the flows 

modeled by the PEIS may not exactly match the targets in this Restoration Plan, a range of flow regimes 

Refer to other 

programs for

implementation

1) Would the action ben efit

natural production of anadromous

YES

NO

NO

3) Does the CVPIA specifically

authorize and direct interior to

2) Have the key technical and

scientific issues been resolved 

NO

YES

4) Is the action supported by all

partners necessary to implement

the action?

NO

NO 6) Either resolve 

5) Has the interested public shown

sufficient support to suggest a partner

YES

Figure 1. Process used to identify reasonable 

restoration actions for inclusion in the Restoration Plan

(see explanation in text).

.

Proposed

Restoration 

action

fish in a manner consistent with

the provisions and intent of CVPIA?

and does the action comply with

applicable laws and regulations?

implement the action, and can it be

implemented without a partner?

will be identified in the future?

Action considered reasonable for

inclusion in the Restoration Plan

legal, or partnership

issues and reconsider 

the revised action or 

eliminate the 

YES

YES

technical, scientific, 

consideration. 

ac tion from further
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 13

encompassing the targets are analyzed that more realistically portrays possible water use and acquisition 

scenarios than was given in the Working Paper. Differences are due primarily to the fact that the PEIS, 

as a NEPA document, has to take the final evaluative step of estimating how implementation of the 

AFRP would occur in the future.

In addition, the Restoration Plan does not contain flow targets for non-CVP-controlled streams, but the 

PEIS modeled stream flows that would likely result from a reasonable level of water acquisition. To 

model stream flows, the PEIS made a series of assumptions about water availability and funding 

availability.2 There is no need for this programmatic Restoration Plan to make similar projections, 

because the availability of water or funding for particular actions is something that will become known 

with certainty as the AFRP is implemented over the years.

DEVELOPING THE REVISED DRAFT RESTORATION PLAN

After release of the draft Restoration Plan in December 1995, Interior engaged in a substantial public 

outreach effort to describe the draft and solicit public comments. This effort began with general public 

workshops in four cities in northern California in early 1996, and has continued throughout 1996 and 

early 1997 as AFRP staff has attended over 50 technical workshops and meetings to discuss various 

aspects of the draft Restoration Plan.

 

2

For purposes of the PEIS to estimate how implementation of the AFRP would occur in the future and to 

model flows primarily on non-CVP-controlled streams, Interior will rely on four fundamental criteria to forecast the 

implementation of the water acquisition program consistent with the Restoration Plan. These include: (1) biological 

priorities (AFRP staff provided the PEIS staff with these priorities and the resulting guidelines for allocation of 

acquired water in a document titled ADraft guidelines for allocation of water acquired pursuant to Section 3406(b)(3) 

of the Central Valley Project Improvement Act,@ dated October 22, 1996); (2) water availability; (3) cost of water; and 

(4) fund availability.

The Revised Draft Restoration Plan includes summarized oral comments and copies of the written 

comments received from the public (Appendix I), along with a comprehensive response-to-comments 

document prepared by the AFRP staff (Appendix H). The release of the draft Restoration Plan 

generated substantial response from potential partners on those actions that will require a partner for 
14 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

implementation. Again, as was done with the draft, information about the availability or absence of a 

necessary partner is reflected in this Revised Draft Restoration Plan, even though this action-specific 

information more appropriately belongs in the detailed implementation plans described below. The 

AFRP staff have concluded that including this additional information about specific proposed actions 

presents a more complete portrayal of the current status of the AFRP, even though it risks confusing the 

programmatic-level analyses with action-specific detail.

DEVELOPING SPECIFIC IMPLEMENTATION PLANS

The third step in developing an AFRP will take place in the near future as Interior develops specific 

implementation plans. One of these will be the Implementation Plan, wherein Interior will identify 

specific actions from the Restoration Plan that are deemed the highest priority and the most readily 

implementable in the three-to-five year period. Interior will work closely with stakeholders, the 

interested public, and the CALFED Restoration Coordination Program of the CALFED Bay-Delta 

Program to identify the short-term priorities for the Implementation Plan.

Information contained in the Implementation Plan will primarily be organized into two categories, general 

and action-specific. The general information will include a more detailed description of the overall 

AFRP than this Restoration Plan; including processes such as public involvement and partnerships, 

proposal submission, environmental compliance, implementation, coordination and integration with other 

restoration programs, and coordination and integration among restoration actions.

Action-specific information will include current data concerning individual actions that are underway or 

have high potential for implementation in the near future. The information for each action will be 

organized in a format similar to the template in Appendix D of this Restoration Plan, and will include the 

action=s location, relevance to the AFRP, description, objectives, background, monitoring, costs, 

schedule, and involved parties. The Implementation Plan will also describe evaluations and monitoring 

activities supported by the AFRP.

In developing the Implementation Plan, USFWS and USBR are interested in receiving substantial input 

from interested parties and potential partners. To encourage input, the Implementation Plan will be 

developed in an open forum. Initial drafts of the various components of the Implementation Plan will be 

available on the AFRP Internet homepage (http:\\www.delta.dfg.ca.gov\usfws\afrp\afrp.html), and will 

be available in hard copy on request. Comments on any component are invited. In addition, USFWS 

and USBR will continue to consider action proposals they receive and to solicit action proposals to 

address specific problems. Proposals should be submitted to the Program Manager of the USFWS=s 

Central Valley Fish and Wildlife Restoration Program (CVFWRP) at the address listed in Appendix C, 

using a format similar to that described in Appendix D.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 15

Interior anticipates that a first draft of the Implementation Plan will be released in 1997, but it will 

continue to be a living document. Because both general and action-specific details are in various stages 

of development and likely to evolve as information is gathered, partnerships are formed, and actions are 

implemented, the Implementation Plan must be responsive to change. The Implementation Plan will 

continue to be maintained on the Internet to allow interested parties and partners the opportunity to 

receive and comment on the most current information available concerning the AFRP and its 

implementation. Hard copies of the entire Implementation Plan will be made periodically to provide a 

record of its status, and it will be distributed to individuals upon request. Following development of the 

first Implementation Plan, the scope of the Implementation Plan will expand to include a three-to-five 

year period from the present.

One component of Restoration Plan implementation will be discussed in a separate implementation plan, 

the Water Management Plan. This Water Management Plan will guide Interior=s management of water 

for environmental purposes, including use of the water dedicated or acquired for environmental 

purposes under Sections 3406(b)(2) and (b)(3) of the CVPIA. The Water Management Plan will use a 

longer planning horizon (three-to-five years at a minimum), so as to enable water project operators to 

efficiently plan project operations to maximize environmental benefits while minimizing water supply 

impacts. Interior also intends that the Water Management Plan will contain a detailed description of the 

process for accounting for the dedication of (b)(2) water, and will include the basis for any potential 

Secretarial findings that (b))(2) water may not be necessary in certain circumstances under Section 

3406(b)(2)(D) of the CVPIA.

Interior will make its final conclusions about the reasonableness of particular AFRP actions in these 

implementation plans. There are several possible reasons why an action that is reasonable at the 

programmatic level may become unreasonable at the specific action implementation level. First, in the 

process of developing specific implementation plans for actions and implementing the action, additional 

information will be collected on the action, including information developed during feasibility analyses 

and the environmental documentation process. This new information may show actions that were 

considered to be reasonable at the programmatic level to be unreasonable to implement. Second, the 

cost-sharing partner identified in the CVPIA for many of the actions or categories of actions may not be 

able or willing to participate on a particular project. Third, many actions in the Restoration Plan will be 

implementable only with the assistance and cooperation of state, local, or private party partners (for 

example, granting or selling easements or screening diversions). For actions that require the assistance 

or cooperation of partners, the Restoration Plan actions will be reasonable only to the extent that 

Interior can identify willing partners for cooperative projects. Finally, Interior recognizes that an 

authorized program that is reasonable at the programmatic level may become unreasonable if the 

particular implementation is carried out in an arbitrary manner as these plans prioritize the particular

implementation scenarios.
16 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

IMPLEMENTATION PROCESS

This section of the Restoration Plan provides a general description of the implementation process, 

including prioritizing and implementing actions, monitoring and evaluating the effects of actions, dealing 

with varying degrees of scientific certainty, and public involvement. The implementation process is 

based on the implementation principles and approaches described in the strategies section of this 

Restoration Plan.

CRITERIA TO PRIORITIZE REASONABLE ACTIONS

Because resources are not sufficient to implement all reasonable actions simultaneously, an attempt will 

be made to implement high-priority items first. Prioritie s will be used to focus initial efforts. Monitoring 

will provide information to help in reevaluating priority for remaining actions. However, the 

implementation schedule should be flexible so the AFRP can take advantage of unique opportunities, 

even if it results in implementing actions that are not the highest priority.

Prioritization criteria primarily include biological considerations, which are derived from the 

implementation principles described in the strategies section of this Restoration Plan. In the following 

sections, watersheds are prioritized, followed by a list of criteria to prioritize types of actions within each 

watershed.

Watershed priority

Watersheds, or parts of watersheds, are prioritized based on a combination of biological and nonbiological factors. Biological factors include the capacity to increase natural production within each 

watershed and the presence of species and races of anadromous fish with special status. Information 

used to prioritize watersheds are summarized in Appendix E.

Watersheds with a high capacity to increase fish production, relative to production during the baseline 

period, are assigned priority over those watersheds with a lower capacity to increase production. Thus, 

higher priority is generally placed on watersheds with severely degraded habitat than those with less 

severely degraded habitat.

Watersheds that support, or have the potential to support species or races of special status are assigned 

priority over those watersheds that do not.

A non-biological consideration is the ability of the Secretary to facilitate restoration. Because the 

CVPIA directs the AFRP to address effects of the CVP on anadromous fish and habitat, and provides 

more tools to the USFWS and USBR to implement restoration actions for such streams and facilities 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 17

than elsewhere, streams with CVP facilities or flows controlled primarily by the CVP are considered 

high priority.

The watershed of highest priority for restoration is assigned to the Sacramento-San Joaquin Delta 

because it is highly degraded, many anadromous fish rear in the Delta, and all anadromous fish in the 

Central Valley must pass through it as both juveniles and adults.

The following watersheds are assigned equal priority but rank below the Delta:

• The Sacramento River because it provides habitat for endangered winter-run chinook salmon, is 

the primary area for production of most species and races, and is strongly influenced by 

operation of the CVP.

• Tributaries of the upper Sacramento River that have high potential for sustaining natural 

production of spring-run chinook salmon and steelhead, and for promoting genetic diversity. 

These streams include Clear, Battle, Antelope, Mill, Deer, Big Chico, and Butte creeks.

• The American River because it is strongly influenced by operation of the CVP.

• The mainstem San Joaquin River and its tributaries below Mendota Pool, because fall-run 

chinook salmon there may be distinct from fall run in the Sacramento River, production of San 

Joaquin fall-run chinook salmon often falls to very low levels, and the tributaries are highly 

degraded.

Action priority

Within each watershed actions are prioritized. The criteria to prioritize actions address factors that limit 

natural production of anadromous fish. Limiting factors have been identified in the Working Paper 

(USFWS 1995) and through substantial comments and data supplied by various groups. In addition, 

these priorities comply with Section 3406(b)(1)(A) of the CVPIA and recognize the authorities of 

Interior.

In general, actions scored as a high priority if they promote natural channel and riparian habitat values 

and natural processes, such as those affecting stream flow, water temperature, water quality, and 

riparian areas. Actions are assigned a medium priority if they affect emigration or access to streams, 

such as sites of entrainment into diversions and migration barriers. Actions score a low priority if they 

do not directly affect habitat, such as hatchery practices and harvest regulations. Hatchery production 

should only be used as a last resort to supplement or to re-establish natural production, and then only 

after investigations on the desirability of developing and implementing additional hatchery production. In 

a few cases, actions that are likely to provide benefits disproportionate to the priority they would be 

assigned based on these criteria are assigned the appropriate priority. Where this occurs, the rationale 

for the assigned priority is given in a footnote. For example, in some watersheds, factors associated 

with fish access to habitat, rather than habitat quality, may be identified as the primary limiting factor. In 

these cases, actions to improve fish passage may be elevated to high priority, and so noted in a footnote 

to the action in the Actions and Evaluations section of this Restoration Plan.
18 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

IMPLEMENTING RESTORATION PLAN ACTIONS

The Secretary has several tools available to implement actions. These tools include the tools in the 

CVPIA and cooperating with others. Because these tools are in various stages of development and are 

likely to evolve as they are used and partnerships are formed, this section of the Restoration Plan 

describes these tools in general terms. We expect to provide detail as it becomes available on these 

tools in implementation plans.

Tools in the CVPIA

Tools available to the Secretary for achieving the goal of the AFRP include implementing all sections of

the CVPIA. Sections 3406(b)(1)(B) through (21) of the CVPIA authorize and direct the Secretary, in 

consultation with other state and federal agencies, Indian tribes, and affected interests, to take specific 

actions. These actions are briefly described below. Details are provided in the CVPIA.

3406(b)(1)(B) -Modify CVP operations based on recommendations of USFWS after

consultation with CDFG.

3406(b)(2) - Manage 800,000 acre-feet of CVP yield for fish, wildlife, and habitat restoration 

purposes after consultation with USBR and CDWR and in cooperation with CDFG.

3406(b)(3) - Acquire water to supplement the quantity of water dedicated for fish and wildlife 

water needs under (b)(2), including modifications of CVP operations; water banking; 

conservation; transfers; conjunctive use; and temporary and permanent land 

fallowing, including purchase, lease, and option of water, water rights, and associated 

agricultural land.

3406(b)(4) - Mitigate for Tracy Pumping Plant operations.

3406(b)(5) - Mitigate for Contra Costa Canal Pumping Plant operations.

3406(b)(6) - Install temperature control device at Shasta Dam.

3406(b)(7) - Meet flow standards that apply to CVP.

3406(b)(8) - Use pulse flows to increase migratory fish survival.

3406(b)(9) - Eliminate fish losses due to flow fluctuations of the CVP.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 19

3406(b)(10) - Minimize fish passage problems at Red Bluff Diversion Dam.

3406(b)(11) - Implement Coleman National Fish Hatchery Development Plan and modify Keswick 

Dam Fish Trap.

3406(b)(12) - Provide increased flows and improve fish passage and restore habitat in Clear 

Creek.

3406(b)(13) - Replenish spawning gravel and restore riparian habitat below Shasta, Folsom, and 

New Melones reservoirs.

3406(b)(14) - Install new control structures at the Delta Cross Channel and Georgiana Slough.

3406(b)(15) - Construct, in cooperation with the State and in consultation with local interests, a 

seasonally operated barrier at head of Old River.

3406(b)(16) - In cooperation with independent entities and the State, monitor fish and wildlife 

resources in the Central Valley.

3406(b)(17) - Resolve fish passage and stranding problems at Anderson-Cottonwood Irrigation 

District Diversion Dam.

3406(b)(18) - If requested by the State, assist efforts to restore the striped bass fishery in the BayDelta estuary.

3406(b)(19) - Reevaluate carryover storage criteria for reservoirs on the Sacramento and Trinity 

rivers.

3406(b)(20) - Participate with the State and other federal agencies in the implementation of the ongoing program to mitigate for the Glenn-Colusa Irrigation District=s Hamilton City 

Pumping Plant.

3406(b)(21) - Assist the State in efforts to avoid losses of juvenile anadromous fish resulting from 

unscreened or inadequately screened diversions.

In addition to these actions, Section 3406(e)(1 through 6) directs the Secretary to investigate and 

provide recommendations on the feasibility, cost, and desirability of implementing the actions listed 

below.
20 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

3406(e)(1) - Measures to maintain suitable temperatures for anadromous fish survival by 

controlling or relocating the discharge of irrigation return flows and sewage effluent, 

and by restoring riparian forests.

3406(e)(2) - Opportunities for additional hatchery production to mitigate the impacts of water 

development and operations on, or enhance efforts to increase Central Valley 

fisheries; Provided, That additional hatchery production shall only be used to 

supplement or to re-establish natural production while avoiding adverse effects on 

remaining wild stocks.

3406(e)(3) - Measures to eliminate barriers to upstream and downstream migration of salmonids.

3406(e)(4) - Installation and operation of temperature control devices at Trinity Dam and 

Reservoir.

3406(e)(5) - Measures to assist in the successful migration of anadromous fish at the Delta Cross 

Channel and Georgiana Slough.

3406(e)(6) - Other measures to protect, restore, and enhance natural production of salmon and 

steelhead in tributary streams of the Sacramento and San Joaquin rivers.

Finally, Section 3406(g) of the CVPIA directs the Secretary, in cooperation with the state of California, 

to develop models and data to evaluate the ecologic and hydrologic effects of existing and alternate 

operations of public and private water facilities and systems to improve scientific understanding and 

enable the Secretary to fulfill requirements of the CVPIA.

The CVPIA establishes the ACentral Valley Project Restoration Fund@ and gives the Secretary the 

authority to use the fund Ato carry out the habitat restoration, improvement and acquisition (from willing 

sellers) provisions@ of the CVPIA (Section 3407), including the actions listed above. Focus areas for 

expenditure of the Restoration Fund are being developed in coordination with interested parties and will 

be described in a report to Congress in mid-1997 pursuant to sections 3407(a) and (f) of the CVPIA.

Some of the tools provided in the CVPIA involve the supplementation of stream flows on specific 

stream reaches. To guide the acquisition of water on both CVP and non-CVP streams, USFWS 

released a document titled ADraft guidelines for allocation of water acquired pursuant to Section 

3406(b)(3) of the Central Valley Project Improvement Act,@ dated October 22, 1996. These guidelines 

are intended for use in developing the long-term Water Management Plan and the implementation plan 

for the water acquisition program, and were used in developing alternatives for analysis in the PEIS.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 21

The specific instream flows implemented on non-CVP streams will be the result of water acquired from 

willing sellers as authorized by Section 3406(b)(3) of the CVPIA. Considerable uncertainty 

characterizes the water acquisition process due to the many complex factors influencing the sale of 

water. The PEIS analyzed stream flows on non-CVP streams that would likely result from a reasonable 

level of water acquisition based on the draft guidelines for allocation of acquired water and considering 

water availability, cost of water and fund availability in its modeling. While stream flows on a long-term 

basis on non-CVP streams are difficult to predict, water acquisition decisions will be defined in annual 

implementation plans.

Restoration actions using the tools listed above will be implemented by the USFWS and USBR to 

contribute to doubling production of anadromous fishes. Each of these tools is being managed 

separately under the coordination of the Program Manager for the CVFWRP. Actions not directly 

addressed by tools in the CVPIA will be managed by the AFRP Program Manager (address listed in 

Appendix C), and their implementation will depend on partnership with local watershed workgroups 

and other agencies, especially the CDFG. Managers of these tools and the AFRP will use this plan as a 

guide to help establish priorities and identify actions. Specific actions will be selected according to the 

overall strategies stated in the Introduction to this Restoration Plan. These managers will ensure that 

actions conducted pursuant to the CVPIA will be coordinated with and complementary to ongoing 

restoration actions of other groups in the Central Valley and Bay-Delta, such as CDFG, Category III of 

the Bay-Delta Agreement, the San Joaquin River Management Program, mitigation agreements, and ad 

hoc groups such as the Spring-Run Chinook Salmon Workgroup.

Several tools may contribute to goals other than increasing natural production of anadromous fish. For 

example, 3406(b)(18) and (e)(2) may include artificial production, or other contributions to total 

production, such as pen rearing of salvaged striped bass, that would not directly contribute to natural 

production (see the AFRP Position Paper in Appendix A for definition of natural production). In fact, 

some fishery interests believe that artificial production is needed to supplement reasonable habitat 

restoration actions to stabilize or increase total production of fall-run chinook salmon in the San Joaquin 

tributaries and striped bass. While the AFRP can not directly support artificial production and pen 

rearing, it will coordinate its efforts with these and similar efforts conducted under other subsections of 

the CVPIA to achieve the greatest benefit for fish and wildlife.

Tools available to the Secretary to implement actions on streams and in the Delta where flows are 

controlled primarily by CVP structures are greater than the tools available on streams where flows are 

not controlled by CVP structures. For example, modification of CVP operations (Section 

3406(b)(1)(B)) and use of (b)(2) water (the 800,000 acre-feet of CVP yield dedicated for fish and 

wildlife and habitat restoration by Section 3406(b)(2)) are limited to CVP-controlled streams and the 

Delta. The CVP-controlled streams include the Sacramento, American, Stanislaus, and San Joaquin 

rivers and Clear Creek. (Restoration of anadromous fish habitat on the San Joaquin River is limited to 
22 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

the section downstream of Mendota Pool.) In addition, the CVP controls exports at the Tracy Pumping 

Plant, located in the south Delta.

The long-term Water Management Plan and water accounting system are being developed and will 

focus on modifications to CVP operations, accounting for the management of (b)(2) water, and 

acquisition of supplemental water (Section 3406(b)(3)) to provide flows of suitable quality, quantity, 

and timing to meet fish, wildlife, and habitat restoration purposes. This long-term Water Management 

Plan, as well as appropriate annual water management plans (i.e., annual CVP operational forecasts), 

will integrate upstream and Delta flows to make efficient use of the water resources available.

During 1993 through 1997, the approach described in the May 28, 1996 memorandum titled 

AGuidelines for Section 3406(b)(2) Water for Fish and Wildlife Restoration@ (the approach was initially 

described in a December 1994 letter of agreement between the USFWS and USBR, also known as the 

Awhite paper@) was used to manage (b)(2) water, wherein the USFWS submitted annual habitat and 

flow objectives to the USBR for implementation in the Sacramento, American, and Stanislaus rivers, 

and the Delta. In 1995 through 1997, flow objectives for Clear Creek were also submitted to USBR. 

These objectives considered the projected hydrologic conditions and were developed annually in 

coordination with CDFG, CDWR, USBR, and other interested parties.

Cooperation with others

In most streams of the Central Valley, the Secretary does not have direct authority to implement actions 

to restore anadromous fish production because the CVP does not control facilities or flows. Streams 

not controlled by the CVP include Battle, Antelope, Mill, Deer, Big Chico, and Butte creeks and 

Feather, Yuba, Bear, Cosumnes, Mokelumne, Calaveras, Tuolumne and Merced rivers, as well as a 

portion of the Delta. Private land owners, public and private irrigation districts, utilities, the State Water 

Project (SWP), municipalities, and industry manage facilities and flows on these streams. To assist in 

restoration of these streams, the Secretary will need the cooperation of others. Cooperation through 

partnerships of the USFWS and USBR with other entities that have the authority, interests, or resources 

to facilitate restoration, provides a tool to implement actions. The USFWS and USBR encourage 

potential partners to enter into voluntary relationships with the agencies to conduct restoration actions. 

Potential partners needing CVPIA resources to implement habitat restoration actions consistent with the 

AFRP should send a request to the Program Manager of the CVFWRP at the address listed in 

Appendix C.

Mechanisms under which the USFWS and USBR can establish cooperative relationships are discussed 

in AConservation Partnerships: A Field Guide to Public-Private Partnering for Natural Resource 

Conservation@ (MIEB 1993). Selection of the appropriate mechanism will depend on the role of the 

USFWS or USBR in relation to the partners. Figure 2 is a guide for selecting mechanisms, which are 

briefly explained below:
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 23

• Interagency agreements--used when one 

agency is providing payments, goods or 

services to another agency. For federal 

agencies, the Economy Act allows for this if an 

efficiency gain can be realized.

• Procurement arrangements--used when an 

agency pays to receive a direct benefit. It is 

treated as a procurement action.

• Memoranda of understanding--most commonly 

used to establish partnerships and document 

specific responsibilities; signatories agree to 

work toward mutual goals, perform joint work, 

or share research results, but no obligation of 

funds may be included.

• Grants--allow the USFWS and USBR to 

transfer money, property, services or anything 

of value to an outside group for a project of 

mutual interest where substantial agency 

involvement is not anticipated.

• Cooperative agreements --allow the USFWS 

and USBR to transfer money, property, 

services or anything of value to an outside 

group for a project of mutual interest where 

substantial agency involvement is anticipated.

• Challenge cost-sharing--allow the USFWS and USBR and other federal agencies to receive 

funds and requires recipients to match this money with non-federal funds, labor, materials, 

equipment or land and water, typically of one-to-one.

Through these mechanisms, the USFWS and USBR can make agreements and direct funds, including a 

portion of the Restoration Fund, or services to partners. The partners could then implement specific 

restoration actions. The CVPIA (Section 3407(e)) provides the Secretary with the flexibility to use 

several of the mechanisms for working together to fund non-federal partners by stating:

AIf the Secretary determines that the State of California or an agency or subdivision thereof, an 

Indian tribe, or a non-profit entity concerned with restoration, protection, or enhancement of fish, 

Interagency

agreement

Is other agency YES

more efficient?

Start

NO

Procurement

arrangement

Memorandum of

understanding

YES

Are resources NO

being exchanged?

Is USFWS or USBR

 paying for direct benefit?

YES

NO

Is USFWS or USBR

substantially involved

in execution?

Grant

NO

YES

Cooperative

agreement

(does not need a match)

Challenge

cost-share

(needs a match)

Is there joint YES

performance of actions?

YES

Figure 2. Mechanisms for working together

(adapted from MIEB 1993).
24 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

wildlife, habitat, or environmental values is able to assist in implementing any action authorized by 

this title in an efficient, timely, and cost effective manner, the Secretary is authorized to provide 

funding to such entity on such terms and conditions as he deems necessary to assist in implementing 

the identified action.@

Funds dispersed through this section are subject to cost-share requirements contained in other sections 

of the CVPIA. Potential partners and possible mechanisms for working together are:

Local agencies and groups--Watershed workgroups, conservation groups, water districts, non-profit 

groups, organized school groups, and individual property owners can help implement restoration 

actions. Agreements can be reached with these groups, or funds and services can be directed to them 

through memoranda of understanding, grants, cooperative agreements, and challenge cost-sharing. In 

areas where there is local support but no watershed workgroups, the USFWS and USBR may provide 

funds and help for forming one. Information on forming and supporting local watershed workgroups is 

contained in the ACalifornia Coordinated Resource Management and Planning Handbook@ (CCRMP 

1990). In addition, the USFWS and USBR are developing a grant program, Project Double, designed 

to allow small groups to participate in restoration actions.

State agencies--The CDFG, CDWR, Reclamation Board, State Water Resources Control Board 

(SWRCB), and other state agencies have expertise, abilities, experience, and are willing to assist in 

implementing many restoration actions. The USFWS and USBR can enter into procurement 

arrangements, memoranda of understanding, grants, and cooperative agreements with state agencies.

Other federal agencies--The Natural Resources Conservation Service (NRCS), U.S. Forest Service 

(USFS), Bureau of Land Management (BLM), NMFS, U.S. Geologic Survey (USGS), U.S. Army 

Corps of Engineers (COE), Western Area Power Administration and other federal agencies likely have 

specific expertise and abilities, and are willing to help implement specific actions. Through interagency 

and procurement arrangements, the USFWS and USBR can enter into agreements with other federal 

agencies to provide funding or services for development, review, and implementation of restoration 

actions.

MONITORING AND EVALUATION

Monitoring, using standardized and validated methods, is essential to obtain data on anadromous fish 

production and associated habitats to facilitate an evaluation of the effects of restoration actions. When 

possible, data collection should begin before specific restoration actions are implemented so that an 

adequate baseline is established. Data collected after implementation of actions can then be compared 

to the baseline. These data are essential for evaluating the contribution of actions to doubling natural 

production.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 25

Most data used to establish the AFRP production targets were derived from sampling programs 

conducted by the CDFG (Mills and Fisher 1994). These programs consisted primarily of carcass 

counts, angler surveys, and ocean harvest records of salmonids; adult and juvenile population estimates 

and angler surveys of striped bass; an index of juvenile abundance of American shad; and adult 

population estimates of both white sturgeon and green sturgeon. These data represent the most 

complete data set on anadromous fish in most Central Valley streams and the Bay-Delta. The AFRP 

recommends that these programs continue and that efforts be made to refine methods and integrate the 

CDFG monitoring with that needed by the AFRP. This would reduce duplication and effectively 

allocate funding by both entities for monitoring throughout the Central Valley.

AFRP and CDFG monitoring will also be integrated and coordinated with existing programs such as the 

Interagency Ecological Program (IEP) and associated real-time monitoring, and others initiated to 

comply with mitigation requirements for specific projects. An oversight committee or forum is needed 

to coordinate activities of all those involved and to ensure that efforts are complementary, encourage an 

open exchange of information, and establish a repository or clearinghouse for data. An additional 

function of such a group would be to help direct monitoring activities by identifying deficiencies in the 

current data base. The IEP is an appropriate entity for coordinating monitoring in the Bay-Delta and for 

managing all data. An IEP project work team or similar forum, which would include experts in various 

watersheds, should be established to provide oversight for Central Valley streams. A scientific peer 

review process should be used to aid in evaluating the effects of restoration actions.

A diverse array of data will be required to fully evaluate restoration actions in the Central Valley and the 

Bay-Delta. The AFRP proposes a hierarchical approach to monitoring, from fine to coarse spatial and 

temporal scales (for example, action-specific, watershed-specific, and system-wide scales, and shortversus long-term temporal scales). Monitoring at all scales is needed so that restoration can be 

adaptively modified and refined.

Action-specific

Monitoring the effects of specific restoration actions shall facilitate evaluation at the finest spatial, and 

possibly temporal resolution. This could be a short-term process, intended to determine the immediate 

effectiveness of restoration actions. For example, the effectiveness of a fish screen, the revegetation of a 

restored streambank, and the effects of an operational change on flow and temperature would all be 

monitored. Results of action-specific evaluations will contribute to an evaluation of the overall success 

of Section 3406(b) of the CVPIA (described below).

Restoration actions implemented pursuant to Section 3406(b) of the CVPIA will include a plan to 

assess the effectiveness of each action. Ensuring that each action includes monitoring will be the 

responsibility of the AFRP, designated agencies, and partners.
26 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Watershed-specific

The purpose of monitoring at the watershed level would be to evaluate the cumulative effects of all 

restoration actions within a single watershed. Data collected specifically for a watershed may span a 

short or long period, and should address the overall results of multiple actions. For example, monitoring 

at the watershed level could answer whether there has been an improvement in the abundance, timing, 

health and distribution of juvenile anadromous fish, or in selected habitat variables. The effectiveness of 

restoration actions in specific watersheds will be determined primarily by evaluation of indices of 

abundance, health and survival of juvenile life-history stages and estimates of adult production. Results 

of watershed-specific evaluations will also contribute to an evaluation of the overall success.

Systemwide and long-term

The long-term effects of restoration actions need to be assessed throughout the Central Valley and BayDelta. For example, the primary biological measure may be production of adult fish, but it could also 

include measures of abundance at adult or juvenile life stages. Production of adult fish should be 

monitored in all watersheds.

Systemwide monitoring needs to include hatchery-produced fish, primarily chinook salmon and 

steelhead. All or a constant fraction of hatchery salmonids released from Central Valley hatcheries 

should be uniquely marked according to site of origin and site and date of release. This would allow 

managers to differentiate between wild and hatchery fish spawning in streams, clarify the distribution of 

hatchery fish in the system, determine their relative contribution to commercial and sport harvest, and 

evaluate factors affecting fish survival. Specific studies should be designed to determine how hatchery 

fish interact with naturally produced fish so that the effects of hatchery practices on population genetics 

and dynamics can be evaluated.

Other components of the Central Valley ecosystem that will be monitored include long-term changes in 

characteristics of stream channels, riparian areas, and water quality. Additional sampling of fish 

assemblages could be incorporated into sampling protocols, and the resulting data used to evaluate fish 

community responses to restoration actions through time.

Section 3406(b)(16) of the CVPIA directs the Secretary to Aestablish in cooperation with independent 

entities and the State of California, a comprehensive assessment program to monitor fish and wildlife 

resources in the Central Valley to assess the biological results and effectiveness of actions implemented 

pursuant to this subsection.@ The Comprehensive Assessment and Monitoring Program (CAMP) was 

initiated pursuant to Section 3406(b)(16) and will assist in directing future monitoring activities. A draft 

implementation plan prepared for CAMP uses a watershed-specific approach for evaluating long-term 

trends in anadromous fish. Therefore, CAMP will not address action- or site-specific monitoring. It 

will rely on information from other monitoring programs to provide the basis for evaluating the overall 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 27

success of restoration actions. Because the AFRP restoration targets are based on natural production 

of adult anadromous fish, CAMP will emphasize this attribute in selected watersheds. However, 

measures of hatchery production and harvest will be needed to determine success toward doubling 

natural production of anadromous fish.

DEALING WITH VARYING DEGREES OF SCIENTIFIC CERTAINTY

Biological resource management decisions are always made with varying degrees of scientific certainty. 

Primary factors contributing to scientific certainty are the variability of biological processes and the 

physical conditions on which they depend, and our ability to quantify variability. For anadromous fish, 

their large geographic range and long life-span restrict the ability of resource managers to employ many 

control and replicate groups in studies, as is common in other fields of science (Hilborn and Ludwig 

1993). It is often difficult or impossible to gather enough data to describe key processes, evaluate 

important variables, and predict results of management actions with absolute certainty. Thus, analyses 

are subject to different interpretations by interest groups, and professional judgement plays a role in 

management decisions.

By acknowledging varying degrees of scientific certainty in making decisions, biological resource 

managers engage in risk assessment. Anyone making a decision must balance the certainty of a 

predicted effect of a management action with the need to act. An example is the certainty of effects 

resulting from acting to recover winter-run chinook salmon in the Sacramento River compared to the 

probable results of not acting, which are continued decline and likely extinction of the race. However, 

managers must also consider the human dimension as part of the system in making decisions. That is, 

they must assess the relationship between human activities and the resource, such as potential economic 

and social effects of implementing management actions versus not implementing management actions.

An approach to address scientific certainty about the effects of restoration actions is to employ adaptive 

management. The essence of adaptive management is that in the face of uncertainty, management 

actions should be treated as experiments, intended to yield information as well as to meet other goals. 

This approach can be separated into three phases:

• First, implement initial actions, based on available data and professional judgement.

• Second, monitor initial actions to evaluate their effectiveness.

• Third, modify actions, if necessary and reasonable, to improve their benefits, stop unnecessary 

actions, and respond to improved scientific certainty.

Actions in the Restoration Plan correspond to the first phase of adaptive management. To address the 

second phase, every action will be monitored so its effectiveness can be assessed. An additional benefit 

of monitoring is increased certainty of an action=s effects on anadromous fish and their habitats. Many 

activities in the Restoration Plan are evaluations of potential problems affecting anadromous fish. 

Evaluations will provide insight into restoration opportunities by improving scientific certainty. The third 
28 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

phase will be addressed through annual evaluations and continued interaction with interest groups. 

Where appropriate, scientific peer review will be used in the adaptive management approach.

Evaluations are important for contested issues, especially where questions of scientific certainty 

surrounding an issue prevents progress toward restoration. The AFRP will encourage interest groups 

involved in such issues to agree in advance to take specific actions contingent upon the results of 

evaluations.

It is the position of the USFWS and USBR that the levels of scientific certainty used in developing the 

Restoration Plan are sufficient to support the recommended actions at the programmatic level. 

Considering the status of listed and potentially listed species and races of anadromous fish and the 

substantial declines in others, there is a real urgency for action to reverse these trends. In addition, 

delays to restore some anadromous fish stocks may ultimately reduce future management options, 

relegating options to more costly actions.

The USFWS and USBR will continue to use the best available scientific information to make and 

implement management decisions. In the biological sciences and in managing natural ecosystems, 

varying degrees of scientific certainty is a reality. Therefore, professional judgement will continue to be 

employed to make the best possible recommendations, especially when the need for restoration is great.

PUBLIC INVOLVEMENT

Section 3406(b)(1) of the CVPIA presents two great challenges. First, Congress directed the 

Secretary to determine actions that are reasonable to implement. Second, the Secretary=s authority is 

limited. This limitation emphasizes the need for voluntary partnerships to restore natural production in 

the Central Valley. Even for actions that the Secretary is authorized to take, partnerships are important 

if the actions are to be performed efficiently. Public support and local involvement are integral parts of 

the AFRP=s strategies and implementation.

The USFWS and USBR are committed to involving the public as much as possible in planning and 

implementing restoration actions.

Approach

There are two levels of public involvement for the AFRP. The first level is programmatic, and involves 

planning a comprehensive program. At this level, all areas of the Central Valley are included. To plan 

and implement a comprehensive program, the AFRP will require ongoing, intensive public involvement. 

The USFWS and USBR will work with the public to nurture a process which ensures consistent 

participation of interested parties.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 29

The second level is action-specific and involves implementing specific actions in individual watersheds. 

At the action-specific level, the AFRP will work with local watershed workgroups, local agencies and 

interested parties to plan and implement actions. These local watershed workgroups involve local 

citizens, property owners, and public and private organizations in the planning and implementation of 

actions within their watershed. In 1996, the AFRP partnered with local watershed workgroups, 

including the Mill Creek, Deer Creek Watershed, and Butte Creek Watershed conservancies and the 

Lower Tuolumne River Technical Advisory Committee, and with Category III of the Bay-Delta 

Agreement to fund eleven actions, including funding to support planning efforts by several of the local 

watershed workgroups. The AFRP will continue to coordinate with local watershed workgroups, the 

CALFED Restoration Coordination Program of the CALFED Bay-Delta Program, and other partners 

to implement actions in the Restoration Plan.

Environmental documentation is an important public process that addresses both programmatic and 

action-specific restoration efforts. NEPA and California Environmental Quality Act (CEQA) processes 

require public involvement in the planning and assessment of actions prior to implementation. The PEIS 

provides a mechanism for programmatic-level public involvement in determining the broad impacts of 

implementing actions in the Restoration Plan. NEPA and CEQA processes will also be required prior 

to implementation of many of the individual actions, providing additional opportunity for public 

involvement at the action-specific level.

Programmatic public involvement activities to date

CVPIA signed by President Bush. October 1992

Draft Plan of Action for the Central Valley Anadromous Fish 

Restoration Program released.

August 1993

Coalition of senior fish experts from the USFWS, USBR, 

NMFS, USEPA, CDFG, and CDWR formed the Core Group to 

direct the development of the AFRP.

October 1993

Public workshops held in Oakland, Fort Bragg, Sacramento, 

Fresno, and Red Bluff to introduce the AFRP and to discuss the 

draft Plan of Action.

October-November 1993

Core Group initiated efforts to develop actions deemed necessary 

to at least double natural production of anadromous fish.

March 1994

Final Plan of Action for the Central Valley Anadromous Fish May 1994
30 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Restoration Program rele ased.

Public workshop held in Sacramento to discuss the final Plan of 

Action.

May 1994

Draft Position Paper for Development of the Anadromous Fish 

Restoration Program released.

July 1994

Public workshop held in Sacramento to discuss the draft Position 

Paper.

July 1994

Central Valley Anadromous Sport Fish Annual Run-size, Harvest, 

and Population Estimates, 1967 through 1991, Third Draft, 

released by CDFG.

August 1994

Public workshop held in Stockton to discuss CDFG=s Central 

Valley Anadromous Sport Fish Annual Run-size, Harvest, and 

Population Estimates.

October 1994

Working Paper on Restoration Needs released. May 1995

Public workshops held in Oakland, Redding, Sacramento, 

Modesto, and Monterey to discuss the Working Paper on 

Restoration Needs; opportunity extended to public to comment 

orally or in writing on Working Paper.

June 1995

AFRP staff attended over 30 technical workshops and meetings 

to discuss the Working Paper and development of the draft 

Anadromous Fish Restoration Plan.

May-November 1995

Draft Anadromous Fish Restoration Plan released. December 1995

Public workshops held in Oakland, Sacramento, Modesto, and 

Chico to discuss the draft Restoration Plan; opportunity extended 

to public to comment orally or in writing on the Restoration Plan.

January-February 1996

Public workshop held in Sacramento to release the draft 

guidelines for allocation of water acquired pursuant to Section 

3406(b)(3) of the CVPIA.

October 1996
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 31

Public workshop held in Sacramento to review the proposed fish 

flow and habitat objectives and priorities for those Central Valley 

rivers and the Delta upon which the CVP has direct influence due 

to their operational facilities.

October 1996

AFRP staff attended over 50 technical workshops and meetings 

to discuss the draft Restoration Plan, development of the revised 

draft Restoration Plan, and implementation of actions in the 

Restoration Plan.

January 1996-

 February 1997

Revised Draft Restoration Plan for the AFRP released, including 

Appendix H which provides AFRP responses to comments on 

the December 1995 draft Restoration Plan.

May 1997

Future public involvement opportunities

- Programmatic

Develop and refine the Implementation Plan. Beginning summer 1997

- Action-specifi

Implementation of specific actions in the Restoration Plan, 

including partnership formation, planning, environmental 

documentation, and permitting.

 Ongoing

Public involvement mechanisms

Public participation is critical to successful implementation of the Restoration Plan. The following are 

public involvement mechanisms established to facilitate public input to the AFRP:

• Draft document review- Allows the public to contribute to document development.

• Final document- Reports progress and offers the public a road map for implementation.

• Press releases- Announce significant events and the opportunity for involvement.

• Letters to interested parties- Provide information.
32 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

• Workshops and meetings- Offer an informal, public setting for discussion and learning to occur 

both for the AFRP and the attending public.

• Educational materials- Provide summary or pertinent information about anadromous fish and the 

AFRP.

• Records of comments and responses- Summarize comments and AFRP responses. 

• Environmental documentation- NEPA and CEQA compliance affords structured public 

involvement in scoping and review.

• Permitting- If required, regulatory permitting affords the public structured public involvement.

• Grapevine- Toll-free and automated information line that provides information on meeting 

schedules, document releases, workshop announcements, and other events. To reach this 

service, dial (800) 742-9474 or (916) 979-2330 and dial extension 542 after the recorded 

message begins.

• Internet home page- Provides up-to-date information on the AFRP and access to USFWS 

public release files. The Internet address is:

http://www.delta.dfg.ca.gov/usfws/afrp/afrp.html

• Implementation Plan- Afford public the opportunity to receive and comment on implementation.

• Mailing lists- Will be maintained and updated as requested.

• Action implementation partnerships- The implementation program for specific actions will seek 

to effect public involvement in the form of action-oriented partnerships, preferably local 

watershed workgroups.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 33

ACTIONS AND EVALUATIONS

The actions and evaluations that follow came from several sources, including the AFRP Working Paper, 

public and private organizations, and individual contributors. They were subjected to the process to 

determine reasonable actions described earlier in this Restoration Plan. Some actions from the Working 

Paper were determined to be unreasonable or in need of further evaluation, and are not included here. 

Some of those actions were replaced, while others were changed to evaluations rather than actions. 

With some actions, the language and intent were changed, perhaps reducing their potential biological 

benefit, to make them reasonable but still maintaining their contribution to increasing natural production 

of anadromous fish. Others were combined.

Actions and evaluations are categorized by stream or geographic area. Streams are categorized by 

basin, starting with the Sacramento River basin, moving to the lower Sacramento River and Delta 

tributaries, then to the San Joaquin basin, and finally the Delta. Within each basin, streams are 

organized geographically, generally starting upstream and moving downstream. For the Delta, which 

was assigned the highest priority in the watershed priority section, and for those streams that were 

assigned high priority, the priority is listed flush to the right margin on the same line as the header for the 

section on that stream or geographic area. Separate lists of actions and evaluations are presented 

Central Valley-wide and for the ocean. In general, actions identified in this plan are activities that will 

contributed to increases in natural production of anadromous fish. Evaluations are activities that 

generate information that may help define or contribute to development of actions for future 

implementation.

Under each stream or geographic area, actions and evaluations appear in separate tables. The tables 

consist of four columns. The first column describes the action or evaluation in one or two brief 

sentences. The second column lists the potential involved parties, including local watershed 

workgroups, and public and private organizations expected to be involved in implementation. The list of 

potential involved parties is not meant to limit involvement to the listed parties, rather the intention is to 

help start the process of partnership formation. The third column lists the CVPIA tools. The last 

column lists the priority for the action or evaluation in relation to others in the watershed.

Actions and evaluations with an arrow (•) preceding their description in the first column are underway or 

have high potential for implementation in the near future. These are actions that the USFWS and 

USBR, partners, or individual sponsors have indicated they are implementing or could begin to 

implement in the near future. In most cases, considerable design and engineering work, feasibility 

studies, environmental compliance documentation, or contract administration will be required prior to 

on-site activity.

It is important to note that the number of actions that can be implemented in the near future will be 

constrained by the resources available from the USFWS, USBR, and potential partners. This is true for 
34 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

both flow management actions that are greatly influenced by annual rainfall, snow pack, carryover 

storage, and willing sellers, and other habitat actions that rely on the availability of partners and funding. 

The Restoration Fund, along with additional agency and other partnership funds, will support 

implementation of the AFRP restoration actions (See Appendix F for a brief summary of CVPIA 

resources available in the near future for implementation of restoration actions).

Direct benefits to fish may not be immediately observed even though implementation has begun. In 

addition, costs to implement, operate and maintain a specific action often are greater than envisioned. 

Hence, it is likely that the number of actions implemented may be fewer than desired. Greater 

accomplishments may be possible through cost sharing with partners.

A total of 172 actions and 117 eva luations are identified. Of these, 103 actions and 40 evaluations 

have high potential for implementation in the near future.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 35

SACRAMENTO RIVER BASIN

Upper mainstem Sacramento River

Action Involved parties Tools Priority

•1. Implement a river flow regulation plan that 

balances carryover storage needs with instream flow 

needs consistent with the 1993 biological opinion for 

winter-run chinook salmon based on runoff and 

storage conditions, including the following minimum 

recommended flows at Keswick and Red Bluff 

Diversion dams.

Recommended minimum Sacramento River flows (cfs) at Keswick Dam for 

October 1 to April 30 based on October 1 carryover storage in Shasta Reservoir 

and critically dry runoff conditions (driest decile runoff of 2.5 maf) to produce a 

target April 30 Shasta Reservoir storage of 3.0-3.2 maf for temperature control.

Carryover storage (maf) Keswick release (cfs)

1.9 to 2.1 3,250

2.2 3,500

2.3 3,750

2.4 4,000

2.5 4,250

2.6 4,500

2.7 4,750

2.8 5,000

2.9 5,250

3 5,500

USFWS, 

USBR, NMFS, 

CDFG, 

Tehama-Colusa 

Canal Authority 

(TCCA)

3406(b)(1)(B), 

3406(b)(2), 

3406(b)(3)

High

•2. Implement a schedule for flow changes that 

avoids, to the extent controllable, dewatering redds 

and isolating or stranding juvenile anadromous 

salmonids, consistent with SWRCB Order 90-5.

USFWS, 

USBR, CDFG, 

SWRCB, 

NMFS

3406(b)(9) High

•3. Continue to maintain water temperatures at or 

below 56°F from Keswick Dam to Bend Bridge to 

the extent controllable, consistent with the 1993 

USFWS, 

USBR, CDFG, 

SWRCB, 

3406(b)(1)(B) High
36 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved parties Tools Priority

biological opinion for winter-run chinook salmon and 

with SWRCB Order 90-5.

NMFS

•4. Continue to raise the gates of the Red Bluff 

Diversion Dam (RBDD) for a minimum duration from 

September 15 through at least May 14 to protect 

adult and juvenile chinook salmon migrations, 

consistent with the 1993 biological opinion for winterrun chinook salmon and with SWRCB Order 90-5, 

and accommodate water delivery using appropriate 

pumping facilities.

USFWS, 

USBR, 

SWRCB, 

NMFS, CDFG, 

TCCA

3406(b)(6) High3

•5. Construct an escape channel for trapped adult 

chinook salmon and steelhead from the Keswick Dam 

stilling basin to the Sacramento River, as designed by 

NMFS and USBR.

USFWS, 

USBR, NMFS, 

CDFG

3406(b)(11) Medium

•6. Continue to implement the Anadromous Fish 

Screen Program.4

Diverters, 

USFWS, 

USBR, NMFS, 

CDFG, CDWR

3406(b)(21) High5

•7. Implement structural and operational modifications 

to the Glenn-Colusa Irrigation District=s (GCID) water 

diversion facility to minimize impingement and 

entrainment of juvenile salmon.

GCID, 

USFWS, 

USBR, CDFG, 

NMFS, CDWR

3406(b)(20) High6

 3

Although Action 4 addresses fish passage, it was assigned high priority because it significantly increases 

fish productivity. These findings are based on unpublished data and reports located in the Northern Central Valley 

Fish and Wildlife Office, USFWS, Red Bluff, California (Rich Johnson, personal communication 1995).

4 Priorities for screening are being determined by the Anadromous Fish Screen Program.

5

Although Action 6 addresses fish passage, it was assigned a high priority because it has a high potential 

to significantly increase fish production.

6

Although Action 7 addresses solutions to impingement and entrainment of juvenile salmon, it was 

assigned a high priority because solutions can significantly enhance fish production on the upper mainstem 

Sacramento River.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 37

Action Involved parties Tools Priority

•8. Remedy water quality problems from toxic 

discharges associated with Iron Mountain Mine and 

water quality problems associated with metal sludges 

in Keswick Reservoir, consistent with the 

Comprehensive Environmental Response, 

Compensation, and Liability Act and the Clean Water 

Act.

USEPA, 

SWRCB 

USFWS, 

USBR, NMFS, 

CDFG

High

•9. Pursue opportunities, consistent with efforts 

conducted pursuant to Senate Bill 1086 (SB 1086), to 

create a meander belt from Keswick Dam to Colusa 

to recruit gravel and large woody debris, to moderate 

temperatures and to enhance nutrient input.

Upper 

Sacramento 

River Fisheries 

and Riparian 

Habitat 

Advisory 

Council 

(USRFRHAC), 

CDFG, COE, 

USFWS, 

USBR, CDWR, 

NMFS

3406(b)(1)(B), 

3406(b)(13) 

High

•10. Implement operational modifications to 

Anderson-Cottonwood Irrigation District=s (ACID) 

diversion dam to eliminate passage and stranding 

problems for chinook salmon and steelhead adults and 

early life stages; eliminate toxic discharges from the 

canal and implement structural modifications to 

improve the strength of the fish screens.

ACID, 

USFWS, 

USBR, CDFG, 

RWQCB, 

NMFS

3406(b)(17) Medium

•11. Develop and implement a program for restoring 

and replenishing spawning gravel, where appropriate, 

in the Sacramento River.

CDFG, 

USFWS, 

USBR, NMFS, 

CDWR

 3406(b)(13) High
38 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Evaluation

Involved 

parties

Tools Priority

•1. Continue study to refine a river 

regulation program, consistent with 

SB 1086, that balances fish habitats with 

the flow regime and addresses 

temperatures, flushing flows, attraction 

flows, emigration, channel and riparian 

corridor maintenance.

USFWS, 

USBR, 

CDFG, 

SWRCB, 

NMFS, 

USRFRHAC

3406(e)(1) High

•2. Evaluate opportunities to incorporate 

flows to restore riparian vegetation from 

Keswick Dam to Verona that are 

consistent with the overall river regulation 

plan.

USFWS, 

USBR, 

NMFS, 

CDFG, 

USRFRHAC

3406(b)(13), 3406(e)(1) High

•3. Continue the evaluation to identify 

solutions to passage at RBDD, including 

measures to improve passage when the 

RBDD gates are in the raised position from 

September 15 through at least May 14.

USFWS, 

USBR, 

CDFG, 

TCCA, 

NMFS

3406(b)(10) High

4. Evaluate the contribution of large 

woody debris and boulders in the upper 

mainstem Sacramento River to salmonid 

production and rearing habitat quality.

CDFG, 

USFWS, 

USBR, 

CDFG, 

RWQCB,

NMFS

3406(e)(6) Medium7

•5. Identify opportunities for restoring 

riparian forests in channelized sections of 

the upper mainstem Sacramento River that 

are appropriate with flood control and 

USRFRHAC, 

The Nature 

Conservancy 

(TNC), 

3406(b)(13) High

 

7

Although Action 4 contributes to natural habitat, it was assigned medium priority because of a lack of 

evidence of benefits to fish production.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 39

Evaluation

Involved 

parties

Tools Priority

other water management constraints. CDFG, COE, 

USFWS, 

USBR, 

CDWR, 

NMFS

•6. Identify and attempt to maintain 

adequate flows for white sturgeon and 

green sturgeon from February to May for 

spawning, emigration, egg incubation and 

rearing, consistent with actions to protect 

chinook salmon and steelhead and when 

hydrologic conditions are adequate to 

minimize adverse effects to water supply 

operations.

USFWS, 

USBR, 

NMFS, 

CDFG 

3406(b)(1)(B),3406(b)(2), 

3406(b)(3)

High

•7. Identify and attempt to maintain

adequate flows from April to June for 

spawning, incubation, and rearing of 

American shad, consistent with actions to 

protect chinook salmon and steelhead and 

when hydrologic conditions are adequate 

to minimize adverse effects to water supply 

operations.

USFWS, 

USBR, 

NMFS, 

CDFG 

3406(b)(1)(B),3406(b)(2), 

3406(b)(3)

 High

8. Identify and implement actions that will 

maintain mean daily water temperatures 

between 61°F and 65°F for at lease one 

month between April 1 and June 30 for 

American shad spawning below RBDD, 

consistent with actions to protect chinook 

salmon and steelhead and when hydrologic 

conditions are adequate to minimize 

adverse effects to water supply operations.

USFWS, 

USBR, 

NMFS, 

CDFG

3406(b)(2), 3406(b)(3) High

9. Identify the extent of entrainment of USFWS, Medium
40 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Evaluation

Involved 

parties

Tools Priority

juvenile sturgeon at diversions and pumps 

and minimize entrainment, if substantial.

USBR, 

CDFG, 

NMFS

•10. Identify green sturgeon spawning 

sites and evaluate the availability, adequacy 

and use by adult sturgeon.

USFWS, 

USBR, 

CDFG, 

NMFS

High

11. Determine the effects of poaching and 

fishing on the number of spawning 

sturgeon.

USFWS, 

USBR, 

CDFG, 

NMFS

Low

Upper Sacramento River tributaries

- Clear Creek

Action Involved 

parties

Tools Priority

•1. Release 200 cfs October 1 to June 1 from 

Whiskeytown Dam for spring-, fall- and late fall-run chinook 

salmon spawning, egg incubation, emigration, gravel 

restoration, spring flushing and channel maintenance; release 

150 cfs, or less, from July through September to maintain 

60°F temperatures in stream sections utilized by spring-run 

chinook salmon. Both releases should be within the average 

total annual unimpaired flows to the Clear Creek watershed.

CDFG, 

USFWS, 

USBR, 

SWRCB

3406(b)(12)

High

•2. Halt further habitat degradation and restore channel 

conditions from the effects of past gravel mining.

CDFG, 

USFWS, 

USBR, BLM, 

3406(b)(12) High

<_
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 41

Action Involved 

parties

Tools Priority

Western 

Shasta 

Resource 

Conservation 

District 

(WSRCD), 

NPS NRCS

•3. Remove sediment from behind McCormick-Saeltzer 

Dam and provide fish passage, either by removing the dam 

or improving fish passage facilities.

McCormickSaeltzer Dam 

owners, 

CDFG, 

USFWS, 

USBR, 

NRCS, 

WSRCD

3406(b)(12) High8

•4. Develop an erosion control and stream corridor 

protection program to prevent habitat degradation due to 

sedimentation and urbanization.

CDFG, 

USFWS, 

USBR, 

NRCS, 

BLM, 

WSRCD

3406(b)(12) High

•5. Replenish gravel and restore gravel recruitment blocked 

by Whiskeytown Dam.

CDFG, 

USFWS, 

USBR, BLM, 

WSRCD

3406(b)(13) High

•6. Preserve the productivity of habitat in the Clear Creek 

watershed through cooperative watershed management and 

development of a watershed management analysis and plan.

CDFG, 

USFWS, 

USBR, BLM, 

High

 8

Although Action 3 address fish passage, it was assigned a high priority because implementation of other 

high priority actions in Clear Creek are dependent on completion of fish passage facilities over McCormick-Saeltzer 

Dam.
42 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

WSRCD

Evaluation Involved 

parties

Tools Priority

•1. Evaluate the feasibility of reestablishing habitat 

for spring-run chinook salmon and steelhead; 

including ensuring that water temperatures five 

miles downstream of Whiskeytown Dam do not 

exceed upper temperature limits for each of the 

life history stages present in the creek from June 1 

to November 1, <60°F for holding of 

prespawning adults and for rearing of juveniles, 

and 56°F for egg incubation.

CDFG, 

USFWS, 

USBR

3406(b)(1)(B),3406(b)(7), 

3406(b)(12)

High

- Cow Creek

Action Involved 

parties

Tools Priority

1. Supplement flows with water acquired from willing 

sellers consistent with applicable guidelines or negotiate 

agreements to provide flows for suitable passage and 

spawning for fall-run chinook salmon adults and adequate 

summer rearing habitat for juvenile steelhead.

Diverters, 

CDFG, 

USFWS, 

USBR, 

SWRCB

3406(b)(3) High

•2. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

 

_

<_
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 43

Action Involved 

parties

Tools Priority

•3. Improve passage at agricultural diversion dams. Diverters, 

CDFG, 

USFWS, 

USBR

Medium

•4. Fence select riparian corridors within the watershed to 

exclude livestock.

NRCS, 

Landowners, 

CDFG, 

USFWS, 

USBR

High

- Bear Creek

Action Involved 

parties

Tools Priority

1. Supplement flows with water acquired from willing sellers 

consistent with applicable guidelines or negotiate agreements to 

allow suitable passage of juvenile and adult chinook salmon 

and steelhead during spring and early fall.

Diverters, 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

•2. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

 USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium
44 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

1. Establish limits on instream gravel mining operations by 

working with state and local agencies to protect spawning 

gravel and enhance recruitment of spawning gravel to the 

Sacramento River in the valley sections of Cottonwood Creek.

COE, Shasta

and Tehama 

counties, 

California 

Division of 

Mines, 

CDFG, 

USFWS, 

USBR

High

2. Restore the stream channel to prevent ACID Siphon from 

becoming a barrier to migration of spring- and fall-run chinook 

salmon and steelhead.

ACID, 

Gravel 

miners, 

USFWS, 

USBR

Medium

3. Eliminate adult fall-run chinook stranding by stopping 

attraction flows in Crowley Gulch or by constructing a barrier 

at the mouth of Crowley Gulch.

ACID, 

CDFG, 

USFWS, 

USBR

Medium

4. Facilitate watershed protection and restoration to reduce 

water temperatures and siltation to improve holding, spawning, 

and rearing habitats for salmonids.

Landowners, 

CDFG, 

USFWS, 

USBR 

High

5. Establish, restore, and maintain riparian habitat on 

Cottonwood Creek.

ACID, 

Gravel 

miners, 

Landowners, 

USFWS, 

USBR

High

- Cottonwood Creek
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 45

- Battle Creek

Action Involved 

parties

Tools Priority

•1. Continue to allow adult spring-run chinook salmon and 

steelhead passage above the Coleman National Fish Hatchery 

(CNFH) weir. After a disease-safe water supply becomes 

available to the CNFH, allow passage of fall- and late-fall-run 

chinook salmon and steelhead above the CNFH weir. In the 

interim, prevent anadromous fish from entering the main 

hatchery water supply by blocking fish ladders at Wildcat 

Canyon, Eagle Canyon, and Coleman diversion dams.

CDFG, 

USFWS, 

USBR

3406(b)(11)

High9

•2. Acquire water from willing sellers consistent with applicable 

guidelines or negotiate agreements to increase flows past 

PG&E's hydropower diversions in two phases to provide 

adequate holding, spawning and rearing habitat for anadromous 

salmonids.

Diversion Months Flow (cfs)c

Keswick ditchb All year 30

North Battle Creek feeder b September-November

January-April

May-August

40

40

30

Eagle Canyon a May-November

December-April

30

50

Wildcat a May-November

December-April

30

50

South b May-November

December-April

20

30

Inskip b May-November

December-April

30

40

Coleman a September-April

May-August

50

30

 a

First phase flows required to support winter- and spring-run chinook salmon between the 

Coleman Powerhouse and Eagle Canyon Diversion Dams while a disease-safe water supply is 

being developed for CNFH.

b

Second phase flows required to support fall-run chinook salmon and steelhead above the 

CNFH weir, Coleman Powerhouse and Eagle Canyon Diversion Dams, after a disease-safe 

water supply is available to CNFH.

c

Flows are intended as indicators of magnitude and subject to revision based on additional 

analyses.

CDFG, 

PG&E, 

USFWS, 

USBR, 

NMFS, 

FERC

3406(b)(3) High

 9

Although Action 1 addresses fish passage, it was assigned high priority because a disease-safe water 

supply to CNFH substantially enhances production of anadromous salmonids by allowing them unrestricted access 

to the upper reaches of Battle Creek.
46 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

•3. Construct barrier racks at the Gover Diversion dam and 

waste gates from the Gover Canal to prevent adult chinook 

salmon from entering Gover Diversion.

Gover 

Diversion 

Dam 

owners, 

CDFG, 

USFWS, 

USBR

3406(b)(21) Medium

•4. Screen Orwick Diversion to prevent entrainment of 

juvenile salmonids and straying of adult chinook salmon.

Orwick 

Diversion 

Dam 

owners, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR, 

BLM

3406(b)(21) Medium

•5. Screen tailrace of Coleman Powerhouse to eliminate 

attraction of adult chinook salmon and steelhead into an area 

with little spawning habitat and contamination of the CNFH 

water supply.

CDFG, 

PG&E, 

USBR, 

USFWS

3406(b)(21) Medium

•6. Construct fish screens on all PG&E diversions, as 

appropriate, after both phases of upstream flow actions (see 

Action 1) are completed and fish ladders on Coleman and 

Eagle Canyon diversion dams are opened.

PG&E, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

•7. Improve fish passage in Eagle Canyon by modifying a 

bedrock ledge and boulders that are potential barriers to adult 

salmonids, and rebuild fish ladders on Wildcat and Eagle 

Canyon diversion dams.

CDFG, 

USFWS, 

USBR

Medium
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 47

Action Involved 

parties

Tools Priority

•8. Screen CNFH intakes 2 and 3 to prevent entrainment of 

juvenile chinook salmon and steelhead.

USFWS, 

USBR, 

CDFG, 

WSRCD

3406(b)(21) Medium

Evaluation Involved 

parties

Tools Priority

•1. Evaluate the effectiveness of fish ladders at PG&E 

diversions.

CDFG, 

PG&E, 

USFWS, 

USBR

3406(e)(3) Medium

•2. Evaluate the feasibility of establishing naturally spawning 

populations of winter-run and spring-run chinook salmon and 

steelhead through a comprehensive plan to restore Battle 

Creek.

CDFG, 

USFWS, 

USBR, 

NMFS

3406(e)(6) High10

•3. Evaluate alternatives for providing a disease-safe water 

supply to CNFH so that winter-, spring- and fall-run chinook 

salmon and steelhead would have access to an additional 41 

miles of Battle Creek habitat.

USFWS, 

USBR, 

CDFG, 

NMFS

3406(e)(6)

High

•4. Develop a comprehensive restoration plan for Battle Creek 

that integrates CNFH operations.

WSRCD, 

CDFG, 

USFWS, 

USBR

High

 10Although action priority criteria do not directly address endangered species, Action 2 was rated high 

because restoration of winter-run chinook salmon requires high priority restoration actions, flow enhancement and 

habitat and water quality improvements.
48 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

- Paynes Creek

Action Involved 

parties

Tools Priority

1. Supplement flows with water acquired from willing sellers 

consistent with applicable guidelines or negotiate agreements to 

improve spawning, rearing and migration opportunities for fallrun chinook salmon and steelhead.

Diverters, 

CDFG, 

BLM, 

USFWS, 

USBR, 

Tehama 

County 

RCD

3406(b)(3) High

2. Restore and enhance spawning gravel. CDFG, 

BLM, 

USFWS, 

USBR, 

Tehama 

County 

RCD

High

- Antelope Creek

Action Involved 

parties

Tools Priority

•1. Supplement flows with water acquired from willing sellers 

consistent with applicable guidelines or negotiate agreements to 

allow passage of juvenile and adult spring-, fall- and late-fall-run 

chinook salmon and steelhead.

Diverters, 

CDFG, 

USFWS, 

USBR, 

USFS

3406(b)(3) High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 49

Evaluation Involved 

parties

Tools Priority

•1. Evaluate the creation of a more defined stream channel to 

facilitate fish passage by minimizing water infiltration into the 

streambed and maintaining flows to the Sacramento River.

Landowners, 

CDFG, 

USFWS, 

USBR

3406(e)(3) Medium

- Elder Creek

Action Involved 

parties

Tools Priority

1. Work with Tehama County to develop an erosion control 

ordinance to minimize sediment input into Elder Creek.

Tehama 

County, 

CDFG, 

USFWS, 

USBR, 

Tehama 

County 

RCD, 

NRCS

High

Evaluation Involved 

parties

Tools Priority

1. Evaluate the feasibility of constructing a fish passage 

structure over the Corning Canal Siphon.

CDFG, 

USFWS, 

USBR, 

TCCA

3406(e)(3) Medium
50 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

- Mill Creek

Action Involved 

parties

Tools Priority

•1. Continue to provide instream flows in the valley reach of 

Mill Creek to facilitate the passage of adult and juvenile 

spring-, fall- and late-fall-run chinook salmon and steelhead.

Mill Creek 

Conservancy 

(MCC), 

Landowners, 

CDFG, 

USFWS, 

USBR, 

CDWR

3406(b)(3) High

•2. Preserve the habitat productivity of Mill Creek through 

cooperative watershed management and development of a 

watershed strategy.

CDFG, 

MCC, 

USFWS, 

USBR, Vina 

RCD

High

•3. Improve spawning habitats in lower Mill Creek for fallrun chinook salmon.CDFG, 

MCC, 

USFWS, 

USBR, 

USFWS, 

Vina RCD

High

•4. Establish, restore, and maintain riparian habitat the 

riparian habitat along the lower reaches of Mill Creek. County 

agencies, 

California 

State 

University at 

Chico, 

CDFG, 

USFWS, 

USBR, 

MCC, Los 

Molinos 

School 

High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 51

Action Involved 

parties

Tools Priority

District, Vina 

RCD

Evaluation Involved 

parties

Tools Priority

•1. Develop and implement an interim fish passage solution at 

Clough Dam until such time that a permanent solution is 

developed and accepted by landowners.

Diverters, 

MCC, Los 

Molinos 

Municipal 

Water 

Company, 

CDFG, 

CDWR, 

USFWS, 

USBR, 

Vina RCD

3406(e)(3) Medium

- Thomes Creek

Action Involved 

parties

Tools Priority

1. Modify gravel mining methods to reduce their effects on 

salmonid spawning habitats.

Gravel 

miners, 

Tehama 

County 

Planning 

Commission, 

CDFG, 

CDWR, 

USFWS, 

USBR

High
52 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

2. Employ the most ecologically sound timber extraction 

practices by implementing the Forest Plan on federal lands 

within the drainage.

Landowners, 

USFWS, 

USBR, 

USFS, 

California 

Department 

of Forestry 

and Fire 

Protection, 

TCCA

High

3. Modify and employ the most ecologically sound grazing 

practices by implementing the Forest Plan on federal lands and 

through partnerships on private and state-owned land within the 

drainage.

Landowners, 

USFS, 

USFWS, 

USBR, 

Tehama 

Colusa RCD

High

4. Reduce use of seasonal diversion dams that may be barriers 

to migrating chinook salmon and steelhead. 

Henleyville 

and Paskenta 

diversion dam 

operators, 

CDFG, 

USFWS, 

USBR

Medium

Evaluation Involved 

parties

Tools Priority

1. Identify and evaluate restoring highly erodible watershed 

areas.

CDFG, 

USFWS, 

USBR

3406(e)(6) High

2. Monitor water quality throughout the creek and identify CDFG, 

 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 53

Evaluation Involved 

parties

Tools Priority

limiting conditions for salmon. USFWS, 

USBR

High
54 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

- Deer Creek

Action Involved 

parties

Tools Priority

•1. Acquire water from willing sellers consistent with 

applicable guidelines or negotiate agreements to supplement 

instream flows in the lower ten miles of Deer Creek to ensure 

passage of adult and juvenile spring- and fall-run chinook 

salmon and steelhead over three diversion dams.

Deer Creek 

Watershed 

Conservancy 

(DCWC), 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

•2. Develop a watershed management plan to preserve the 

chinook salmon and steelhead habitat in Deer Creek through 

cooperative watershed management.

DCWC, 

CDFG, 

USFWS, 

USBR

High

•3. Improve spawning habitats in lower Deer Creek for falland late-fall-run chinook salmon.DCWC, 

CDFG, 

USFWS, 

USBR, Vina 

RCD

High

•4. Negotiate long-term agreements to restore and preserve 

riparian habitats along Deer Creek.

Landowners, 

DCWC, 

CDFG, 

USFWS, 

USBR, Vina 

RCD

High

•5. Plan and coordinate required flood management activities 

with least damage to the fishery resources and riparian 

habitats of lower Deer Creek; and establish, restore, and 

maintain riparian habitat on Deer Creek.

Tehama 

County Flood 

Control, 

DCWC, 

COE, 

CDFG, 

USFWS, 

USBR

High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

 

55

- Stony Creek

Evaluation Involved 

parties

Tools Priority

1. Determine the feasibility of restoring anadromous salmonids 

by evaluating water releases from Black Butte Dam, water 

exchanges with the Tehama-Colusa Canal, interim and longterm water diversion solutions at Red Bluff Diversion Dam, 

water quality improvements, spawning gravel protection and 

restoration, riparian habitat protection and restoration, creek 

channel creation, and passage improvements at water 

diversions.

Stony 

Creek 

Task 

Force, 

TCCA, 

CDFG, 

COE, 

USFWS, 

USBR

3406(e)(1), 

3406(e)(3), 

3406(e)(6)

High

- Big Chico Creek

Action Involved 

parties

Tools Priority

•1. Relocate and screen the M&T Ranch diversion. M&T Ranch 

owners, 

Western 

Canal Water 

District 

(WCWD), 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) High11

 11Although Action 1 addresses a diversion, it was assigned a high priority because relocating the diversion 

and associated water rights from Big Chico Creek to the Sacramento River results in an additional 40 cfs in the upper 

reaches of Butte Creek, providing a significant benefit to spring-run chinook salmon production.
56 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

•2. Repair the Iron Canyon fish ladder. CDFG, 

USFWS, 

USBR, Big 

Chico Creek 

Task Force 

(BCCTF)

Medium

•3. Replenish spawning gravel in reaches modified for flood 

control.

Chico Parks 

Department, 

CDFG, 

USFWS, 

USBR, 

BCCTF

High

•4. Repair the Lindo Channel weir and fishway at the Lindo 

Channel box culvert at the Five-Mile Diversion.

Chico Parks 

Department, 

CDFG, 

CDWR, 

COE, 

USFWS, 

USBR, 

BCCTF

Medium

•5. Improve cleaning procedures at One-Mile Pool. City of 

Chico, 

CDFG, 

USFWS, 

USBR

High

•6. Protect spring-run chinook salmon summer holding 

pools by obtaining from willing sellers titles or conservation 

easements on lands adjacent to the pools.

Landowners, 

CDFG, 

USFWS, 

USBR

High

•7. Cooperate with local landowners to encourage 

revegetation of denuded stream reaches; and establish, 

Landowners, 

Sacramento 

River 

High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 57

Action Involved 

parties

Tools Priority

restore, and maintain riparian habitat on Big Chico Creek. Preservation 

Trust, 

CDFG, 

California 

Department 

of Parks and 

Recreation, 

USFWS, 

USBR

•8. Preserve the productivity of the habitat on Big Chico 

Creek through cooperative watershed management and 

development of a watershed management plan.

USFS, 

CDFG, 

USFWS, 

USBR

High

Evaluation Involved 

parties

Tools Priority

1. Evaluate the water management operations between Big 

Chico Creek and Lindo Channel.

City of 

Chico, 

CDFG, 

CDWR, 

USFWS, 

USBR

3406(e)(6) Medium

2. Evaluate the replenishment of gravel in the flood-diversion 

reach of Mud Creek.

Butte 

County, 

CDFG, 

CDWR, 

USFWS, 

USBR

3406(e)(6) High
58 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

- Butte Creek

Action Involved 

parties

Tools Priority

•1. Obtain additional instream flows from Parrott-Phelan 

Diversion.

Diverters, 

Butte Creek 

Watershed 

Conservancy 

(BCWC), 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

•2. Maintain a minimum 40 cfs instream flow below 

Centerville Diversion Dam.

BCWC, 

CDFG, 

PG&E, 

USFWS, 

USBR

3406(b)(3) High

•3. Purchase existing water rights from willing sellers. Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR, 

SWRCB

3406(b)(3) High

•4. Build a new high water volume fish ladder at Durham 

Mutual Dam.

Durham 

Mutual Water 

Company 

(DMWC), 

BCWC, 

CDFG, 

TNC, 

USFWS, 

USBR

Medium

•5. Install fish screens on both diversions at Durham Diverters, 3406(b)(21) Medium
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 59

Action Involved 

parties

Tools Priority

Mutual Dam. DMWC, 

TNC, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

•6. Remove the Western Canal Dam and construct the 

Western Canal Siphon.

Western 

Canal Water 

District 

(WCWD), 

BCWC, 

TNC CDFG, 

USBR, 

USFWS

3406(b)(21) High12

•7. Remove McPherrin and McGowan dams and provide 

an alternate source of water as part of the Western Canal 

Dam removal and siphon construction.

Diverters, 

WCWD, 

BCWC, 

CDFG, 

USBR, 

USFWS

3406(b)(3), 

3406(b)(21)

High13

•8. As available, acquire water rights as a part of the 

Western Canal Siphon project.

WCWD, 

BCWC, 

CDFG, 

SWRCB, 

3406(b)(3) High

 12Although Action 6 addresses fish passage, it was assigned a high priority because the removal of 

Western Canal Dam and construction of the Western Canal Siphon returns the stream to natural conditions and 

enhances anadromous salmonid access to spawning habitats.

13Although Action 7 addresses fish passage, it was assigned high priority because removal of McPherrin 

and McGowan dams returns the stream channel to natural conditions and enhances anadromous salmonid access to 

spawning habitats.
60 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

USBR

9. Adjudicate water rights and provide water master 

service for the entire creek.

Diverters, 

BCWC, 

CDFG,

CDWR, 

SWRCB, 

USFWS, 

USBR

High

•10. Build a new high water volume fish ladder at Adams 

Dam.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

Medium

•11. Install fish screens on both diversions at Adams Dam. Diverters, 

BCWC, 

CDFG, 

CDWR, 

NMFS, 

USFWS, 

USBR

3406(b)(21) Medium

•12. Build a new high water volume fish ladder at Gorrill 

Dam.

Diverters, 

CDFG, 

USFWS, 

USBR

Medium

•13. Install a fish screen on the Gorrill Dam diversion. Diverters, 

BCWC, 

CDFG, 

CDWR, 

NMFS, 

USFWS, 

USBR

3406(b)(21) Medium

•14. Install a fish screen at White Mallard Dam.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 61

Action Involved 

parties

Tools Priority

Diverters, 

BCWC, 

CDFG, 

CDWR, 

NMFS, 

USFWS, 

USBR

3406(b)(21) Medium

•15. Eliminate chinook salmon stranding at White Mallard 

Duck Club outfall.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

Medium

16. Rebuild and maintain existing culvert and riser at 

Drumheller Slough outfall.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

Medium

•17. Install screened portable pumps in Butte Creek as an 

alternative to the Little Dry Creek diversion.

Diverters, 

BCWC, 

CDFG, 

CDWR,

NMFS, 

USFWS, 

USBR

3406(b)(21) Medium

18. Install a high water volume fish ladder at White Mallard 

Dam.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR 

Medium

•19. Develop land use plans that create buffer zones 

between the creek and agricultural, urban, and industrial 

developments; and restore, maintain, and protect riparian 

and spring-run chinook salmon summer-holding habitat 

City and 

county 

government 

agencies, 

 3406(e)(6) High
62 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

along Butte Creek. Conservation 

groups, 

BCWC, 

CDFG, 

USFWS, 

USBR

•20. Install fish screens and fish ladder at Parrott-Phelan 

Diversion Dam.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR 

3406(b)(21) Medium

•21. Develop a watershed management program. BCWC, 

CDFG, 

USFWS, 

USBR

High

22. Establish operational criteria for Sanborn Slough 

Bifurcation.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

Medium

23. Establish operational criteria for the East Barrow pit 

and West Barrow pit.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

Medium

24. Establish operational criteria for Nelson Slough. Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

Medium
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 63

Evaluation Involved 

parties

Tools Priority

1. Develop and evaluate operational criteria and potential 

modifications to Butte Slough outfall.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

2. Evaluate alternatives or build a new high water volume fish 

ladder at East-West Diversion Weir.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

3. Evaluate operational alternatives and establish operational 

criteria for Sutter Bypass Weir #2.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

4. Evaluate operational alternatives and establish operational 

criteria for Sutter Bypass Weir #1.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

•5. Evaluate alternatives to help fish passage, including the 

installation of a fish screen, at Sanborn Slough Bifurcation 

Structure.

Diverters, 

BCWC, 

CDFG, 

CDWR, 

NMFS, 

USFWS, 

USBR

3406(e)(3) High14

6. Evaluate alternatives to help fish passage, including the 

installation of fish screens, within Sutter Bypass where 

Diverters, 

BCWC, 

3406(e)(3) Medium

 14Although Evaluation 5 addresses fish passage, it was assigned a high priority because passage and 

screening solutions at the Sanborn Slough Bifurcation Structure can significantly enhance Butte Creek productivity.
64 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Evaluation Involved 

parties

Tools Priority

necessary. CDFG, 

CDWR, 

NMFS, 

USFWS, 

USBR

7. Evaluate operational alternatives and establish operational 

criteria for Sutter Bypass Weir #5.

Diverters, 

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

8. Evaluate alternatives to help fish passage, including the 

installation of a high water volume fish ladder, on Sutter 

Bypass Weir #2.

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

9. Evaluate alternatives to help fish passage, including the 

installation of a high water volume fish ladder, on Sutter 

Bypass Weir #1.

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

10. Evaluate alternatives to help fish passage, including the 

installation of a high water volume fish ladder, on Sutter 

Bypass Weir #5.

BCWC, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

Medium

11. Evaluate alternatives to help fish passage, including the 

installation of a high water volume fish ladder, on Sutter 

Bypass Weir #3.

BCWC, 

CDFG, 

USFWS, 

3406(e)(3), 

3406(e)(6)

Medium
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 65

Evaluation Involved 

parties

Tools Priority

USBR

•12. Evaluate enhancement of fish passage at a natural 

barrier below the Centerville Diversion Dam.

BCWC, 

PG&E, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

High15

•13. Evaluate fish passage enhancement at PG&E diversion 

dams and other barriers above Centerville Diversion Dam.

BCWC, 

Spring-run 

Chinook 

Salmon 

Workgroup, 

PG&E, 

CDFG, 

USFWS, 

USBR

3406(e)(3), 

3406(e)(6)

High15

•14. Evaluate the juvenile life history of spring-run chinook 

salmon.

BCWC, 

CDFG, 

USFWS, 

USBR

Medium

15. Evaluate juvenile and adult chinook salmon stranding in 

Sutter Bypass and behind Tisdale, Moulton, and Colusa 

weirs during periods of receding flows on the upper mainstem 

Sacramento River.

BCWC, 

CDFG, 

USFWS, 

USBR

Medium

 15Although evaluations 12 and 13 address fish passage, they were assigned high priority because actions 

resulting from these evaluations could provide access to four miles of deep holding pools and three miles of 

spawning habitat for spring-run chinook salmon in the vicinity of Centerville and Butte Creek diversion dams 

(Holtgrieve, D.G. and G.W. Holtgrieve. 1995. Physical stream survey: upper Butte Creek, Butte County, California. 

The Nature Conservancy and the Spring-run Chinook Salmon Work Group).
66 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

- Colusa Basin Drain (westside tributaries)

Action Involved 

parties

Tools Priority

1. Install an adult exclusion device at the Knights Landing 

outfall for Colusa Basin Drain as an interim action pending 

completion of Colusa Basin Drain Evaluation 1.

CDFG, 

USFWS, 

USBR

3406(e)(1), 

3406(e)(6)

Medium

Evaluation Involved 

parties

Tools Priority

1. Investigate the feasibility of restoring the access of 

anadromous fish to westside tributaries through development of 

defined migrational routes, sufficient flows, and adequate water 

temperatures.

CDFG, 

USFWS, 

USBR

3406(e)(1), 

3406(e)(6)

Medium
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 67

- Miscellaneous small tributaries

Evaluation Involved 

parties

Tools Priority

•1. Evaluate the contribution of small Sacramento River 

tributaries as rearing areas for juvenile winter-, spring-, fall- and 

late-fall-run chinook salmon and steelhead.

CDFG, 

USFWS, 

USBR, 

Chico State 

University

3406(e)(6) High

LOWER SACRAMENTO RIVER AND DELTA TRIBUTARIES

Feather River

Action Involved 

parties

Tools Priority

•1. Supplement flows with water acquired from willing sellers 

consistent with applicable guidelines or negotiate agreements to 

improve conditions for all life history stages of fall- and springrun chinook salmon and steelhead.

CDWR, 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

2. Improve flows for American shad migration, spawning, 

incubation and rearing from April to June, consistent with actions 

to protect chinook salmon and steelhead and when hydrologic 

conditions are adequate to minimize adverse effects to water 

supply operations.

Diverters, 

CDWR, 

CDFG,

USFWS, 

USBR

3406(b)(3) High

•3. Develop and utilize a temperature model as a tool for river 

management.

CDWR High

Evaluation Involved 

parties

Tools Priority

•1. Evaluate the response of spawning salmonids to increased 

flows in the low-flow channel.

CDWR, 

CDFG

High
68 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Evaluation Involved 

parties

Tools Priority

•2. Evaluate the quality of spawning gravel in areas used by 

chinook salmon, and if indicated, consider gravel renovation or 

supplementation to enhance substrate quality.

CDWR High

•3. Evaluate the distribution of Feather River Fish Hatchery 

chinook salmon in Central Valley stocks and determine the 

genetic integrity of Feather River spring-run chinook salmon.

CDWR, 

CDFG

Low

4. Identify and attempt to maintain adequate flows and 

temperatures for white sturgeon and green sturgeon migration, 

spawning, incubation and rearing from February to May, 

consistent with actions to protect chinook salmon and steelhead 

and when hydrologic conditions are adequate to minimize 

adverse effects to water supply operations.

CDFG,

CDWR

High

5. Identify and remove physical and water quality barriers that 

impede access for white sturgeon and green sturgeon to 

spawning habitat or facilitate passage around these barriers.

CDFG, 

CDWR

Medium

6. Identify the extent of white sturgeon and green sturgeon 

entrainment at diversions and pumps and reduce or eliminate 

entrainment if found to be substantial.

CDFG, 

CDWR

Medium

7. Identify white sturgeon and green sturgeon spawning sites 

and evaluate the availability and use by adult sturgeon of 

spawning habitat.

CDFG, 

CDWR

High

8. Determine the effects of poaching and fishing on the number 

of spawning white sturgeon and green sturgeon.

CDFG Low

9. Identify and implement actions that maintain mean daily water 

temperatures between 61 F and 65 F for at least one month 

from April 1 to June 30 for American shad spawning, consistent 

with actions to protect chinook salmon and steelhead and when 

hydrologic conditions are adequate to minimize adverse effects 

to water supply operations.

CDFG, 

CDWR

High

° °
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 69

Yuba River

Action Involved 

parties

Tools Priority

•1. Supplement flows with water acquired from willing 

sellers consistent with applicable guidelines or negotiate 

agreements to improve conditions for all life history stages 

of chinook salmon and steelhead.

Yuba County 

Water 

Agency 

(YCWA), 

SWRCB, 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

2. Improve flows for American shad migration, spawning, 

incubation and rearing from April to June, consistent with

actions to protect chinook salmon and steelhead and when 

hydrologic conditions are adequate to minimize adverse 

effects to water supply operations.

YCWA, 

SWRCB, 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

3. Reduce and control flow fluctuations to avoid and 

minimize adverse effects to juvenile salmonids.

YCWA, 

PG&E, 

SWRCB, 

CDFG

High

4. Maintain adequate instream flows for temperature 

control.

YCWA, 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

•5. Improve efficiency of screening devices at HallwoodCordua and Brophy-South Yuba water diversions, and 

construct screens at the Brown=s Valley water diversion and 

other unscreened diversions.

Diverters, 

SWRCB, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

6. Construct or improve the fish bypasses at Hallwood- Diverters, Medium
70 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

Cordua and Brophy-South Yuba water diversion. SWRCB, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

•7. Facilitate passage of spawning adult salmonids by 

maintaining appropriate flows through the fish ladders, or by 

modifying the fish ladders at Daguerre Point Dam.

YCWA, 

CDFG, 

COE, 

USFWS, 

USBR

3406(b)(3) Medium

8. Purchase streambank conservation easements to 

improve salmonid habitat and instream cover.

Landowners, 

YCWA, 

BLM, 

USFWS, 

USBR

High

9. Facilitate passage of juvenile salmonids by modifying the 

dam face of Daguerre Point Dam.

YCWA, 

CDFG, COE

Medium

10. Operate reservoirs to provide adequate water 

temperatures for anadromous fish.

Yuba River 

Water 

Temperature 

Advisory 

Committee, 

SWRCB

High

Evaluation Involved 

parties

Tools Priority

1. Evaluate the effectiveness of pulse flows to facilitate 

successful juvenile salmonid emigration.

YCWA, 

CDFG, 

USFWS, 

USBR

3406(e)(6) High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 71

Evaluation Involved 

parties

Tools Priority

2. Evaluate whether enhancement of water temperature control 

via shutter configuration and present management of the cold 

water pool at New Bullards Bar Dam is effective, and modify 

the water release outlets at Englebright Dam if enhancement of 

water temperature control via shutter configuration is effective.

YCWA, 

CDFG, 

PG&E, 

USFWS, 

USBR

3406(e)(6) High

3. Identify and attempt to implement actions that will maintain 

mean daily water temperatures between 61°F and 65°F for at 

least one month from April 1 to June 30 for American shad, 

consistent with actions to protect chinook salmon and steelhead 

and when hydrologic conditions are adequate to minimize 

adverse effects to water supply operations.

YCWA, 

CDFG, 

USFWS, 

USBR

3406(g) High

•4. Evaluate the benefits of restoring stream channel and 

riparian habitats of the Yuba River, including the creation of side 

channels for spawning and rearing habitats for salmonids.

YCWA, 

PG&E, 

CDFG, 

USFWS

3406(e)(6) High

Bear River

Action Involved 

parties

Tools Priority

1. Supplement flows with water acquired from willing sellers 

consistent with applicable guidelines or negotiate agreements to 

improve conditions for all life history stages of chinook salmon 

and steelhead.

South 

Sutter 

Water 

District 

(SSWD), 

SWRCB, 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

2. Provide adequate water temperatures for all life-stages of 

chinook salmon and steelhead.

SSWD, 

SWRCB, 

High
72 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

CDFG

3. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

 USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

•4. Negotiate removal or modification of the culvert crossing 

at Patterson Sand and Gravel and other physical and chemical 

barriers impeding anadromous fish migration.

Patterson 

Sand and 

Gravel, 

CDFG, 

USFWS, 

USBR

Medium

Evaluation Involved 

parties

Tools Priority

1. Determine and evaluate instream flow requirements that 

ensure adequate flows for all life stages of all salmonids.

SSWD, 

CDFG, 

USFWS, 

USBR

High

2. Evaluate the extent that white sturgeon and green sturgeon 

use the Bear River for spawning and rearing.

CDFG, 

USFWS

High

3. Monitor water quality, particularly at agricultural return 

outfalls, and evaluate potential effects on anadromous fish.

Diverters, 

CDFG

High

4. Evaluate the extent that poaching or fishing reduces the 

numbers of adult sturgeon.

CDFG, 

USFWS

Low
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 73

American River

Action Involved 

parties

Tools Priority

•1. Develop and implement a river regulation plan that meets 

the following flow objectives by modifying CVP operations, 

using (b)(2) water, and acquiring water from willing sellers as 

needed.

American River minimum flow objectivesa Month (cfs)

Wetb Above and 

below normal

Dry and 

critical

Critical 

relaxation

October 2,500 2,000 1,750 800

NovemberFebruary2,500 2,000 1,750 1,200

March -May 4,500 3,000 2,000 1,500

June 4,500 3,000 2,000 500

July 2,500 2,500 1,500 500

August 2,500 2,000 1,000 500

September 2,500 1,500 500 500

 a

 A multi-agency and interested party management team should be formed to review and 

adjust flows in consideration of carryover storage and hydrologic conditions as needed to 

provide for the long-term needs of anadromous fish. Flow objectives should be met for the 

entire reach of the American River downstream of Nimbus Dam.

b

 Year types should be based on an American River index, or on consideration of carryover 

storage and hydrologic conditions in the American River watershed.

Sacramento 

Area Water 

Forum 

(SAWF), 

CDFG, 

USBR, 

USFWS

3406(b)(1)(

B), 

3406(b)(2), 

3406(b)(3)

High

•2. Develop a long-term water allocation plan for the 

American River watershed.

SAWF, 

CDFG, 

Other water 

users, 

USFWS, 

USBR

3406(b)(1)(

B), 

3406(b)(2), 

3406(b)(3)

High

•3. Reduce and control flow fluctuations to avoid and 

minimize adverse effects on juvenile salmonids. USFWS, 

USBR, 

CDFG

3406(b)(9) High

•4. Reconfigure Folsom Dam shutters for improved 

management of Folsom Reservoir's cold water pool and 

better control over the temperature of water released 

downstream.

County of 

Sacramento, 

Sacramento 

Area Flood 

3406(b)(1)(

B)

High
74 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

Control 

Association 

(SAFCA), 

USFWS, 

USBR, 

CDFG

5. Replenish spawning gravel and restore existing spawning 

grounds.

USFWS, 

USBR, 

CDFG

3406(b)(13) High

6. Improve the fish screen at Fairbairn Water Treatment

Plant.

City of 

Sacramento, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

7. Modify the timing and rate of water diverted from the river 

annually to reduce entrainment losses of juvenile salmonids.

City of 

Sacramento, 

Other water 

users, 

CDFG, 

USFWS, 

USBR

3406(b)(1)(B) Medium

8. Develop a riparian corridor management plan to improve 

and protect riparian habitat and instream cover.

SAFCA, 

COE, 

USFWS, 

USBR, 

CDFG

3406(b)(13) High

9. Terminate current programs that remove woody debris 

from theriver channel.

County of 

Sacramento, 

City of 

Sacramento, 

High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 75

Action Involved 

parties

Tools Priority

SAFCA, 

COE, 

USFWS, 

USBR, 

CDFG

•10. Increase flows for American shad migration, spawning, 

incubation and rearing from April to June, by modifying CVP 

operations, by using dedicated water, and by acquiring water 

from willing sellers, consistent with actions to protect chinook 

salmon and steelhead and when hydrologic conditions are 

adequate to minimize adverse effects to water supply 

operations.

SAWF, 

USFWS, 

USBR, 

CDFG

3406(b)(1)(

B), 

3406(b)(2), 

3406(b)(3)

High

Evaluation Involved 

parties

Tools Priority

1. Evaluate the effectiveness of pulse flows to facilitate 

successful emigration of juvenile salmonids.

USFWS, 

USBR, 

CDFG

High

2. Evaluate and refine a river regulation plan that provides flows 

to protect all life stages of anadromous fish based on water 

storage at Folsom Reservoir and predicted hydrologic conditions 

in the American River watershed.

SAWF, 

CDFG, 

USFWS, 

USBR

3406(g) High

3. Identify and implement actions that maintain mean daily water 

temperatures between 61 F and 65 F for at least one month 

from April 1 to June 30 for American shad spawning, consistent 

with action to protect chinook salmon and steelhead and when 

hydrologic conditions are adequate to minimize adverse effects 

to water supply operations. 

CDFG, 

CDWR

High

°

° °
76 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Mokelumne River

Action Involved 

parties

Tools Priority

1. Supplement flows with water acquired from willing 

sellers consistent with applicable guidelines or negotiate 

agreements to improve conditions for all life history stages 

of chinook salmon and steelhead.

East Bay 

Municipal 

Utility District 

(EBMUD), 

SWRCB, 

Woodbridge 

Irrigation 

District 

(WID), 

FERC, 

CDFG, 

USFWS

3406(b)(3) High

•2. Replenish gravel suitable for salmonid spawning habitat. CDFG, 

EBMUD

High

•3. Cleanse spawning gravel of fine sediments and prevent 

sedimentation of spawning gravel.

CDFG, 

EBMUD

High

4. Reduce and control flow fluctuations to avoid and 

minimize adverse effects to juvenile salmonids.

CDFG, 

EBMUD

High

5. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

CDFG, 

CDWR, 

USFWS, 

USBR, 

NMFS

3406(b)(21) Medium

6. Maintain suitable water temperatures for all salmonid life 

stages.

EBMUD, 

CDFG

High

7. Enhance and maintain the riparian corridor to improve 

streambank and channel rearing habitat for juvenile 

salmonids.

Landowners, 

CDFG

High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 77

Action Involved 

parties

Tools Priority

8. Establish and enforce water quality standards to

provide optimal water quality for all life history stages of 

salmonids.

CDFG High

9. Eliminate or restrict gravel mining operations in the 

Mokelumne River flood plain to prevent damage to 

potential spawning areas and encroachment of vegetation.

Gravel 

miners, 

CDFG

High

Evaluation Involved 

parties

Tools Priority

1. Evaluate the effectiveness of pulse flows to facilitate 

successful emigration of juvenile salmonids in the spring, and 

determine the efficacy in all water year types.

EBMUD, 

CDFG, 

USFWS, 

USBR

3406(e)(6) High

2. Evaluate and facilitate passage of spawning adult salmonids 

in the fall and juvenile salmonids in the spring past Woodbridge 

Irrigation District Diversion Dam and Lodi Lake.

WID, City 

of Lodi, 

EBMUD, 

CDFG, 

USFWS

3406(e)(3) Medium

3. Evaluate the incidence of predation on juvenile salmonids 

emigrating past Woodbridge Dam, and investigate potential 

remedial actions if necessary.

WID, 

EBMUD, 

CDFG, 

USFWS, 

USBR

3406(e)(6) Medium

4. Evaluate the effects of extending the closure of the fishing 

season from 31 December to 31 March (and possibly to 1 

June) to protect juvenile salmonids and adult steelhead and 

prevent anglers from wading on redds.

CDFG Low
78 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Cosumnes River

Action Involved 

parties

Tools Priority

1. Acquire water from willing sellers consistent with 

applicable guidelines or negotiate agreements to reduce 

water diversions or augment instream flows during critical 

periods for salmonids.

Diverters, 

CDFG, 

USFWS, 

USBR

3406(b)(3) High

2. Pursue opportunities to purchase existing water rights 

from willing sellers consistent with applicable guidelines to 

ensure adequate flows for all life stages of salmonids.

CDFG, The 

Nature 

Conservancy 

(TNC), 

USFWS, 

USBR

3406(b)(3) High

•3. Enforce Fish and Game Codes that prohibit 

construction of unlicensed dams.

CDFG Medium

4. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

CDFG, 

CDWR, 

USFWS, 

USBR, 

NMFS, TNC

3406(b)(21) Medium

5. Establish a riparian corridor protection zone. TNC, 

Landowners, 

CDFG

High

6. Rehabilitate damaged areas and remedy incompatible 

land practices to reduce sedimentation and instream water 

temperatures.

TNC, 

Landowners, 

CDFG

High

Evaluation Involved

parties

Tools Priority

1. Determine and evaluate instream flow requirements that Diverters, 3406(e)(6) High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 79

Evaluation Involved

parties

Tools Priority

ensure adequate flows for all life stages of all salmonids. TNC, 

CDFG, 

USFWS, 

USBR

2. Evaluate and facilitate passage of adult and juvenile 

salmonids at existing diversion dams and barriers.

Diverters 

and dam 

builders, 

TNC, 

CDFG, 

USBR, 

USFWS

3406(e)(3) Medium

3. Evaluate the feasibility of restoring and increasing available 

spawning and rearing habitat for salmonids.

TNC, 

CDFG, 

USBR, 

USFWS

3406(e)(6) High
80 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Calaveras River

Action Involved 

parties

Tools Priority

1. Supplement flows with water acquired from willing sellers 

consistent with applicable guidelines or negotiate agreements to 

improve conditions for all life history stages of chinook salmon.

Calaveras 

County 

Water 

District, 

Stockton 

East 

Water 

District 

(SEWD), 

CDFG, 

COE, 

USFWS, 

USBR

3406(b)(3) High

2. Provide flows of suitable water temperatures for all 

salmonid life stages.

CDFG, 

USFWS, 

USBR

3406(b)(3) High

3. Facilitate passage of adult and juvenile salmonids at existing 

diversion dams and barriers.

Diverters, 

CDFG

Medium

4. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

CDFG, 

CDWR, 

USFWS, 

NMFS, 

USBR

3406(b)(21) Medium

Evaluation Involved 

parties

Tools Priority

1. Monitor sport fishing and evaluate the need for regulations to 

protect salmonids.

CDFG Low
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 81

Evaluation Involved 

parties

Tools Priority

2. Evaluate instream flow, water temperature and fish habitat 

use in the Calaveras River to develop a real-time management 

program so that reservoir operations can maintain suitable 

habitat when fish are present.

CDFG, 

Diverters, 

USFWS

High

SAN JOAQUIN BASIN

Merced River

Action Involved 

parties

Tools Priority

•1. Supplement flows provided pursuant to the DavisGrunsky Contract Number D-GGR17 and FERC License 

Number 2179 with water acquired from willing sellers 

consistent with applicable guidelines or negotiate 

agreements as needed to improve conditions for all life 

history stages of chinook salmon.

Merced 

Irrigation 

District 

(MID), 

Diverters, 

CDFG, 

CDWR, 

USFWS, 

USBR

3406(b)(3) High

2. Reduce adverse effects of rapid flow fluctuations. MID, 

CDFG, 

USFWS, 

USBR

High

3. Improve watershed management to restore and protect 

instream and riparian habitat, including consideration of 

restoring and replenishing spawning gravel.

Landowners, 

Merced 

County, 

NRCS, 

CDFG, 

USFWS, 

USBR

High
82 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

4. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

5. Establish a streamwatch program to increase public 

participation in river management.

Public, 

CDFG,

USFWS

Low

Evaluation Involved 

parties

Tools Priority

1. Identify and implement actions to provide suitable water 

temperatures for all life stages of chinook salmon; establish 

maximum temperature objectives of 56°F from October 15 to 

February 15 for incubation and 65°F from April 1 to May 31 

for juvenile emigration.

Dam 

operators, 

CDFG, 

USFWS, 

USBR

3406(g) High

•2. Evaluate and implement actions to reduce predation on 

juvenile chinook salmon, including actions to isolate Aponded@

sections of the river.

CDFG, 

USFWS, 

USBR

3406(e)(6) Medium

3. Evaluate fall pulse flows for attraction and passage benefits 

to chinook salmon and steelhead.

Dam 

operators, 

CDFG, 

USFWS, 

USBR

High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 83

Tuolumne River

Action Involved 

parties

Tools Priority

•1. Implement a flow schedule as specified in the terms of 

the FERC order resulting from the New Don Pedro Project 

(FERC Proceeding P-2299-024). Supplement FERC 

agreement flows with water acquired from willing sellers 

consistent with applicable guidelines or negotiate 

agreements as needed to improve conditions for all life 

history stages of chinook salmon.

City and 

County of 

San 

Francisco, 

Turlock 

Irrigation 

District 

(TID), 

Modesto 

Irrigation 

District 

(MID), 

Lower 

Tuolumne 

River 

Technical 

Advisory 

Committee 

(LTTAC), 

FERC, 

USFWS, 

USBR

3406(b)(3) High
84 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

•2. Improve watershed management and restore and 

protect instream and riparian habitat, including consideration 

of restoring and replenishing spawning gravel and 

performing an integrated evaluation of biological and 

geomorphic processes.

Landowners, 

NRCS, 

CDFG, 

USFWS, 

USBR, 

LTTAC

High

3. Screen all diversions to protect all life history stages of 

anadromous fish.

Diverters, 

LTTAC, 

CDFG, 

CDWR, 

NMFS, 

USFWS, 

USBR

3406(b)(21) Medium

4. Support the Tuolumne River Interpretive Center. CDFG, 

LTTAC

Low

5. Establish a streamwatch program to increase public 

participation in river management.

Public, 

LTTAC, 

CDFG, 

USFWS

Low

6. Coordinate the AFRP with appropriate activities 

supported by the Riparian and Recreation Improvement 

fund that was established by the New Don Pedro 

Settlement Agreement.

LLTAC, 

USFWS, 

USBR

Low

Evaluation Involved 

parties

Tools Priority

1. Identify and implement actions to provide suitable water 

temperatures for all life stages of chinook salmon; establish 

maximum temperature objectives of 56°F from October 15 to 

Dam 

operators, 

CDFG, 

3406(g) High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 85

Evaluation Involved 

parties

Tools Priority

February 15 for incubation and 65°F from April 1 to May 31 

for juvenile emigration.

USFWS, 

USBR, 

LTTAC

•2. Evaluate and implement actions to reduce predation on 

juvenile chinook salmon, including actions to isolate ponded

sections of the river.

TID, MID, 

LTTAC, 

CDFG, 

USFWS, 

USBR

3406(e)(6) Medium

3. Evaluate the effects of flow fluctuations established by the 

guidelines of the FERC Settlement Agreement on spawning, 

incubation, and rearing of chinook salmon, and if substantial 

adverse effects are indicated, modify guidelines to reduce 

effects.

Diverters, 

Hydropower 

operators, 

LTTAC, 

CDFG, 

USFWS, 

USBR

High

4. Evaluate fall pulse flows for attraction and passage benefits 

to chinook salmon and steelhead.

Diverters, 

Hydropower 

operators, 

LTTAC, 

CDFG, 

USFWS, 

USBR

High
86 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Stanislaus River

Action Involved 

parties

Tools Priority

•1. Implement an interim river regulation plan that meets 

the following flow schedule by supplementing the 1987 

agreement between USBR and CDFGa

, through 

reoperation of New Melones Dam, use of (b)(2) water, 

and acquisition of water from willing sellers as needed.

Stanislaus River flow schedules (cfs) by year type Month b

Wet Above

normal

Below

normal

Dry Critical

October 350 350 250 250 200

NovemberMarch400 350 300 275 250

April 1,500 1,500 300/1500c 300/1500d 300/1500e

May 1,500 1,500 1500/300c 1500/300d 1500/300e

June 1,500 800 250 200 200

JulySeptember300 300 250 200 200

Total (taf) 468 410 313 257 247

Baseline 

(taf)

1,015 722 406 242 269

Unimpaired 

(taf)

1,772 1,291 920 631 449

 a

 Existing flow requirements are 98 to 302 taf, based on the 1987 agreement between 

CDFG and USBR (CDFG and USBR 1987); actual schedule is determined on an 

annual basis and depends on available yield, carryover storage, and hydrologic 

conditions.

b

 Year type based on San Joaquin basin 60-20-20 index. Flow schedules are releases 

from Goodwin Dam.

c

 In a below normal water year, April-May flow would be maintained for 45 days at 

1500 cfs and 16 days at 300 cfs.

d

 In a dry water year, April-May flow would be maintained for 30 days at 1500 cfs 

and 31 days at 300 cfs.

e

 In a critical water year, April-May flow would be maintained at 1500 cfs for 30 days 

and at 300 cfs for 31 days.

CDFG, 

USFWS, 

USBR, 

Oakdale 

Irrigation 

District, 

South San 

Joaquin 

Irrigation 

District, 

Stockton East 

Water 

District, 

Central San 

Joaquin 

Water 

Conservation 

District, 

South Delta 

Water 

Agency 

(SDWA), 

COE

3406(b)(1)(B), 

3046(b)(2), 

3406(b)(3)

High

•2. Improve watershed management to restore and 

protect instream and riparian habitat, including 

consideration of restoring and replenishing spawning 

gravel.

Landowners, 

CDFG, 

NRCS, 

COE, 

USFWS, 

USBR

3406(b)(13) High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 87

Action Involved 

parties

Tools Priority

3. Screen all diversions to protect all life history

stages of anadromous fish.

Diverters, 

USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

Evaluation Involved 

parties

Tools Priority

•1. Identify and implement actions to provide suitable water 

temperatures for all life stages of chinook salmon, consistent 

with efforts to maintain adequate flows to provide fish habitat. 

Establish maximum temperature objectives of 56 F from 

October 15 to February 15 for incubation and 65 F from April 

1 to May 31 for juvenile rearing and emigration.

Dam 

operators, 

CDFG, 

USFWS, 

USBR, 

COE

3406(g) High

•2. Evaluate and implement actions to reduce predation on 

juvenile chinook salmon, including actions to isolate ponded

sections of the river.

CDFG, 

USFWS, 

USBR, 

COE

3406(e)(6) Medium

•3. Evaluate and refine a river regulation plan that provides 

adequate flows to protect all life stages of anadromous fish 

based on water storage at New Melones Reservoir, predicted 

hydrologic conditions, and current aquatic habitat conditions.

USFWS, 

USBR, 

CDFG, 

COE

High

4. Develop a carryover storage target for New Melones 

Reservoir to ensure Vernalis flow standards are met during the 

30-day pulse flow period during the third year of a dry or 

critical period. This will protect at least one of three year 

classes of chinook salmon during emigration.

USFWS, 

USBR, 

CDFG, 

SEWD

3406(g) High

°

°
88 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Evaluation Involved 

parties

Tools Priority

5. Evaluate use of the Stanislaus River by American shad and 

consider increasing flows and maintaining mean daily water 

temperatures between 61 F and 65 F from April to June when 

hydrologic conditions are adequate to minimize adverse effects 

to water supply operations and in a manner consistent with 

actions to protect chinook salmon.

Dam 

operators, 

CDFG, 

USFWS, 

USBR

3406(g) High

6. Evaluate fall pulse flows for attraction and passage benefits 

to chinook salmon and steelhead.

USFWS, 

USBR, 

CDFG, 

COE, 

SEWD

° °
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 89

Mainstem San Joaquin River

Action Involved 

parties

Tools Priority

•1. Coordinate with CDFG and others and acquire water 

from willing sellers consistent with applicable guidelines as 

needed to implement a flow schedule that improves 

conditions for all life stages of San Joaquin chinook salmon 

migrating through, or rearing in, the lower San Joaquin River.

River and 

tributary 

water 

managers 

and 

diverters, 

CDFG, 

SWRCB, 

USFWS, 

USBR

3406(b)(1)(B), 

3406(b)(2), 

3406(b)(3)

High

2. Develop an equitable, integrated San Joaquin Basin plan 

that will meet outflow:export objectives identified under 

Sacramento-San Joaquin Delta Operational Target 4 and 

Supplemental Actions Requiring Water 7, 8, and 9.

River and 

tributary 

water 

managers 

and 

diverters, 

CDFG, 

SWRCB, 

CDWR, 

USFWS, 

USBR

High

•3. Reduce or eliminate entrainment of juvenile chinook 

salmon at Banta-Carbona, West Stanislaus, Patterson, and 

El Soyo diversions by implementing the Anadromous Fish 

Screen Program in conjunction with other programs.

Diverters, 

 USFWS, 

USBR, 

NMFS, 

CDFG, 

CDWR

3406(b)(21) Medium

4. Reduce or eliminate entrainment of juvenile chinook 

salmon at smaller riparian pumps and diversions on the 

mainstem San Joaquin River.

Diverters, 

 USFWS, 

USBR, 

NMFS, 

3406(b)(21) Medium
90 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

CDFG, 

CDWR

5. Maintain the 6 mg/L dissolved oxygen standard during 

September through November in the San Joaquin River 

between Turner Cut and Stockton, as described in the 

SWRCB=s 1995 Water Quality Control Plan.

CDFG, 

CDWR, 

COE, 

City of 

Stockton, 

Port of 

Stockton

High

6. Establish a basin-wide conjunctive water use program. River and 

tributary 

water 

managers 

and 

diverters, 

CDFG, 

CDWR, 

USBR, 

USFWS

High

Evaluation Involved 

parties

Tools Priority

1. Identify and implement actions to improve watershed 

management to restore and protect instream and riparian 

habitat.

Landowners, 

CDFG

High

2. Identify and implement actions to maintain suitable water 

temperatures or minimize length of exposure to unsuitable 

water temperatures for all life stages of chinook salmon in the 

San Joaquin River and Delta.

River and 

tributary 

water 

managers and 

diverters, 

CDFG, 

3406(g) High
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 91

Evaluation Involved 

parties

Tools Priority

USFWS, 

USBR

3. Identify and implement actions to reduce predation on 

juvenile chinook salmon.

CDFG, 

USFWS

Medium

4. Identify and attempt to maintain adequate flows for 

migration, spawning, incubation and rearing of white sturgeon 

and green sturgeon from February to May, consistent with 

actions to protect chinook salmon and steelhead and when 

hydrologic conditions are adequate to minimize adverse 

effects to water supply operations.

River and 

tributary 

water 

managers and 

diverters, 

CDFG, 

CDWR

High

5. Identify and attempt to implement actions that will 

maintain mean daily water temperatures between 61°F and 

65°F for at least one month from April 1 to June 30 for 

American shad, consistent with actions to protect chinook 

salmon and steelhead and when hydrologic conditions are 

adequate to minimize adverse effects to water supply 

operations.

CDFG, 

USFWS, 

USBR

3406(g) High

6. Evaluate the potential to develop and implement a strategy 

of coordinating a variety of specific actions, such as 

coincident pulse flows on San Joaquin tributaries, reduced 

Delta exports, hatchery releases, and gravel cleaning to 

stimulate outmigration and reduce predation and entrainment.

River and 

tributary 

water 

managers and 

diverters, 

CDFG, 

USFWS, 

USBR

High

7. Identify, evaluate the need for, and, if needed, attempt to 

maintain adequate flows for migration of steelhead, consistent 

with efforts to maintain adequate flows for chinook salmon.

River and 

tributary 

water 

managers and 

3406(b)(3) High
92 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Evaluation Involved 

parties

Tools Priority

diverters, 

CDFG, 

USFWS, 

USBR

SACRAMENTO-SAN JOAQUIN DELTA

Improvements to aquatic habitat in the Delta are essential to restore the natural production of 

anadromous fish in the Central Valley because habitat in the Delta is highly degraded and all species and 

races of fish use the Delta at some stage in their life history.

Recent actions to improve fish habitat in the Delta are described in the 15 December 1994, Principles 

for Agreement on Bay-Delta Standards between the State of California and the Federal Government 

(Bay-Delta Agreement) and in the State Water Resources Control Board=s May, 1995 Water Quality 

Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (1995 WQCP). The 

AFRP assumes that those actions will continue to be implemented in the future. Should changes occur 

in the 1995 WQCP objectives or the Bay-Delta Agreement, the AFRP will need to determine if new 

restoration actions in the Delta beyond those described below are needed in light of those changes.

Both the Bay-Delta Agreement and 1995 WQCP require operational flexibility of state and federal 

water projects to provide protection for anadromous fish. As described in the Bay-Delta Agreement, 

initial deliberation and operational decisions to achieve this flexibility will be made by the California 

Water Policy Council and Federal Ecosystem Directorate (CALFED) Coordination Group (Ops 

Group) in consultation with water users, environmentalists and fishery representatives. The Ops Group 

develops ways to use the operational flexibility of the State Water Project (SWP) and Central Valley 

Project (CVP) such that species using the estuary receive more protection than they would have 

received by strict adherence to 1995 WQCP standards.

Operational flexibility allows the Ops Group to meet operational targets that contribute to doubling 

natural production of anadromous fish, and the Bay-Delta Agreement=s criterion to maintain water 

quality conditions which, together with other measures in the watershed, would be sufficient to achieve a 

doubling of production of chinook salmon. The operational targets listed in the first table below are the 

AFRP recommendations to the Ops Group. These targets allow variability in the timing and nature of 

operations to meet requirements in the 1995 WQCP.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 93

A second table lists supplemental actions requiring water that may involve changes in operations beyond 

the authority of the Ops Group that further contribute to meeting the AFRP goal. In this table, some 

supplemental actions are identical to operational targets because their full implementation may be 

beyond the authority of the Ops Group. Supplemental actions can be met through a combination of 

project reoperation (Section 3406(b)(1)), management of 800,000 acre-feet of CVP yield (Section 

3406(b)(2)), and acquisition of water from willing sellers (Section 3406(b)(3)). The best combination 

of these three tools for achieving the actions will be determined through the preparation of annual 

implementation plans along with guidance from the long-term water management plan, which will seek to 

maximize the biological benefits of the actions while minimizing their water supply impacts. In some 

years, the three tools may not be sufficient to fully implement all actions, resulting in partial 

implementation of some actions. Sub-priorities are provided as guidance for partial implementation for 

some actions.

These supplemental actions (some in slightly modified form) are being used to develop an 

implementation plan in the form of the CVP operational forecast for water year 1997 and to develop a 

long-term CVP Water Management Plan that integrates these supplemental actions with upstream flow

actions and Delta operational targets.

In addition, these supplemental actions requiring water formed the basis for the nine priorities that were 

provided to the PEIS team for their use in developing alternatives for the PEIS in a letter to interested 

parties dated October 25, 1996 announcing an AFRP workshop on proposed fish flow and habitat 

objectives for selected Central Valley rivers and the Delta.

Supplemental actions not requiring water include screens at diversions and a channel barrier. Some of 

these actions are not under the direct authority of the Ops Group or addressed by the 1995 WQCP, 

however, some actions may be addressed by Category III of the Bay-Delta Agreement.

In developing this Restoration Plan, Interior has made an initial programmatic-level determination of the 

reasonableness of the restoration actions included in the following tables. As USFWS and USBR move 

towards specific plans for implementation based on this Restoration Plan, they will continue to examine 

the reasonableness of a particular mix of restoration actions. The final decision to implement any action 

will be done through the implementation process and described in the implementation plans.

The following operational targets, supplemental actions, and evaluations are intended to be consistent 

with and supportive of the CALFED Bay-Delta process, the Bay-Delta Agreement=s criterion to 

maintain conditions sufficient to achieve a doubling of production of chinook salmon, and with the 

narrative water quality objective in the 1995 WQCP to maintain water quality conditions and other 
94 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

measures sufficient to achieve a doubling of natural production of chinook salmon from the average 

production of 1967-1991, consistent with the provisions of State and federal law.

Operational target Involved 

parties

Tools Priority

•1. Close Delta Cross Channel (DCC) up to 45 days in the 

November through January period, when juvenile salmon 

enter the Delta or flow or turbidity changes trigger salmon 

migration. The DCC gates are to be closed within 24 hours 

when any of the following triggers occur:

1) daily average flow or turbidity of the Sacramento River 

at Freeport increases by 20% from the previous 3 day 

running average;

2) capture of at least one juvenile chinook salmon of 

spring-run size in the Sacramento River tributaries and in 

the Sutter Bypass, or in the Sacramento River at or 

below Knights Landing;

3) capture of at least two juvenile chinook salmon of any 

race in the Sacramento River at or below Knights 

Landing at any Interagency Ecological Program (IEP) 

sampling station in one day.

The gate closure period will be for 10, 15 and 20 

consecutive days in November, December and January, 

respectively, and will remain closed for another 10 

consecutive days if any of the above triggers are met after the 

initial closure for that month.

CALFED 

agencies

WQCP, BayDelta 

Agreement, 

3406(b)(1)(B)

High1

•2. When the DCC is closed during the November through 

January period, limit the average SWP and CVP exports to 

no greater than 35% of Delta inflow if Evaluation 3 

CALFED 

agencies

WQCP, BayDelta 

Agreement, 

High

 1

Although Operational target 1 addresses fish passage, it was assigned high priority because potential to 

increase fish production is great.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 95

Operational target Involved 

parties

Tools Priority

determines that a relatively high ratio of Delta export to inflow 

limits juvenile salmon survival through the Sacramento River 

Delta. Sub-priorities: 1) January, 2) December, 3) 

November.

3406(b)(1)(B)

•3. Maximize DCC closure from May 21 through June 15 

when chinook salmon and other anadromous species are 

abundant in the lower Sacramento River, but keep open 

when the net benefit to striped bass and other sensitive 

species in the lower San Joaquin River is great.

CALFED 

agencies, 

United 

States 

Coast 

Guard, 

Boating 

interests

WQCP, BayDelta 

Agreement, 

3406(b)(1)(B)

High2

•4. Maintain an average export to inflow ratio of no more 

than 45% during February in dry years by increasing the ratio 

to ~55% in early February and decreasing the ratio to ~35% 

in late February, when winter-run chinook salmon smolts are 

present.

CALFED 

agencies

WQCP, BayDelta 

Agreement, 

3406(b)(1)(B)

High

•5. Minimize fish losses and predation at facilities by 

operating state and federal pumps interchangeably when this 

operation achieves a net benefit to anadromous fish 

production.

CALFED 

agencies

WQCP, BayDelta 

Agreement, 

3406(b)(1)(B)

Medium

 2

Although Operational target 3 addresses fish passage, it was assigned high priority because potential to 

increase fish production is great.

Supplemental action requiring water Involved 

parties 

Tools Priority

•6. In conjunction with operation of a barrier at the head of Old 

River and consistent with efforts to conduct evaluations 1 and 2, 

CALFED 

agencies

3406(b)(2), 

3406(b)(3)

High
96 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Supplemental action requiring water Involved 

parties 

Tools Priority

maximize the difference between flows and export rates at levels 

greater than those required under the Delta smelt biological 

opinion during the 30-day April and May pulse flow period.

•7. When a barrier at the head of Old River is not operational, 

limit the combined SWP and CVP exports to 1,500 cfs or 

maintain a Vernalis inflow to total export ratio of 5 to 1 during 

the 30-day April through May pulse flow period.

CALFED 

agencies

3406(b)(2), 

3406(b)(3)

High

•8. Increase the level of protection targeted by the May and 

June X2 requirements to a 1962 level of development (LOD), 

as described below, where the number of days when X2 is 

required at Chipps Island in Table A of the 1995 WQCP is 

shown to the right of the requirements to meet a 1962 LOD and 

where PMI is the previous months eight river index in acre feet.

1962 LOD IN WQCP

PMI MAY JUNE MAY JUNE

1500 0 0 0 0

1750 1 0 0 0

2000 4 0 1 0

2250 13 1 3 0

2500 24 3 11 1

2750 29 7 20 2

3000 30 12 27 4

3250 31 18 29 8

3500 31 23 30 13

3750 31 26 31 18

4000 31 28 31 23

4250 31 29 31 25

4500 31 29 31 27

4750 31 30 31 28

CALFED 

agencies

3406(b)(2), High

•9. During May, maintain at least 13,000 cfs daily flow in the 

Sacramento River at the I Street Bridge and 9,000 cfs at 

Knights Landing to improve transport of eggs and larval striped 

bass and other young anadromous fish and to reduce egg 

settling and mortality at low flows. Sub-priorities: 1) 13,000 cfs 

at I Street Bridge, 2) 9,000 cfs at Knights Landing.

CALFED 

agencies

3406(b)(2), 

3406(b)(3)

High

•10. During the last half of May, ramp (linearly) the total SWP CALFED 3406(b)(2), High

_

<
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 97

Supplemental action requiring water Involved 

parties 

Tools Priority

and CVP export level from what it is at the end of the 30-day 

April and May pulse flow period to that export level proposed 

by the SWP and CVP to meet the requirements of the 1995 

WQCP on June 1.

agencies 3406(b)(3)

•11. Close the DCC during the November through January 

period beyond the 45-day limit defined under Operational 

Target 1 should meeting one of the triggers stipulated in 

Operational Target 1 require additional closure.

CALFED 

agencies

3406(b)(2), 

3406(b)(3), 

High1

•12. Limit the average SWP and CVP exports to no greater 

than 35% of Delta inflow in July. Sub-priorities: 1) July 1 to 

July 14, 2) July 16 to July 31.

CALFED 

agencies

3406(b)(2), 

3406(b)(3)

High

13. Supplement Delta outflow for migration and rearing of 

white sturgeon, green sturgeon, striped bass, and American 

shad by modifying CVP operations and using water available 

under the CVPIA (sections 3406(b)(2) and (3)), consistent with 

actions to protect chinook salmon and steelhead.

CALFED 

agencies

3406(b)(2), 

3406(b)(3)

High

•14. When the DCC is closed during the November through 

January period, limit the average SWP and CVP exports to no 

greater than 35% of Delta inflow if Evaluation 3 determines that 

a relatively high ratio of export to inflow limits survival of 

juvenile chinook salmon migrating through the Sacramento River 

Delta. Sub-priorities: 1) January, 2) December, 3) November.

CALFED

agencies

3406(b)(2),

3406(b)(3)

High

Supplemental action not requiring water Involved 

parties

Tools Priority

•15. Implement actions to reduce losses of juvenile 

anadromous fish resulting from unscreened or inadequately 

screened diversions in the Sacramento-San Joaquin Delta and 

Diverters, 

CDFG, 

CDWR, 

3406(b)(21) Medium

 1

Although Supplemental action 11 addresses fish passage, it was assigned high priority because potential 

to increase fish production is great.
98 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Supplemental action not requiring water Involved 

parties

Tools Priority

Suisun Marsh, if Evaluation 12 determines significant benefits to 

juvenile anadromous fish can be achieved by screening.

USFWS, 

USBR, 

NMFS, 

SWRCB, 

COE

•16. Construct and operate a barrier at the head of Old River 

to improve conditions for chinook salmon migration and 

survival if Evaluation 1 determines that a barrier can be 

operated to improve conditions for salmon with minimal 

adverse effects on other Delta species.

CALFED 

agencies

3406(b)(2), 

3406(b)(3), 

3406(b)(15)

High2

 2

Although Supplemental Action 16 addresses fish passage, it was assigned high priority because potential 

to increase fish production is great.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 99

Evaluation Involved 

parties

Tools Priority

•1. In conjunction with Evaluation 2, evaluate whether a 

temporary rock barrier at the head of Old River can be 

operated during the 30-day April through May pulse flow 

period to improve conditions for chinook salmon migration 

and survival with minimal adverse effects on other Delta 

species, consistent with the COE=s permit (PN 

199600027) to the CDWR and USFWS=s Biological 

Opinion on delta smelt for the Temporary Barriers Project.

IEP 

agencies

3406(b)(15) High1

•2. Evaluate in conjunction with Evaluation 1 the impacts 

of San Joaquin River Delta inflow and SWP and CVP 

export rates on salmon smolt survival through the San 

Joaquin Delta. This evaluation is intended to be consistent 

with the proposed adaptive management plan for the San 

Joaquin River and Delta that is being considered by 

involved parties.

IEP 

agencies

3406(b)(1), 

3406(b)(2), 

3406(b)(3)

High

•3. Evaluate the effect of a low (~35%) versus a high 

(~65%) SWP and CVP export to Delta inflow ratio on the 

survival of coded-wire-tagged, late-fall-run chinook salmon 

smolts migrating through the Delta when the DCC is 

closed.

IEP 

agencies

3406(b)(1), 

3406(b)(2), 

3406(b)(3)

High

•4. Evaluate potential benefits of and opportunities for 

increasing salmonid and other anadromous fish production 

through improved riparian habitats in the Delta.

SWP and 

CVP 

contractors, 

TNC, IEP 

agencies

3406(e)(1) High

•5. Evaluate opportunities to provide modified operations 

and a new or improved control structure for the DCC and 

Georgiana Slough or other methods at those locations to 

assist in the successful migration of anadromous salmonids.

SWP and 

CVP 

contractors, 

IEP 

agencies

3406(b)(14), 

3406(e)(5)

High2

 1

Although Evaluation 1 addresses fish passage, it was assigned high priority because resulting information 

is needed before Supplemental Action 16 can be implemented.
100 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Evaluation Involved 

parties

Tools Priority

•6. Evaluate benefits of and opportunities for additional 

tidal shallow-water habitat as rearing habitat for 

anadromous fish in the Delta.

SWP and 

CVP 

contractors, 

TNC, IEP 

agencies

High

7. Evaluate the benefit of and opportunities for new 

technologies to improve water quality and to guide 

migrating fish.

SWP and 

CVP 

contractors, 

IEP 

agencies

Medium

•8. Evaluate the benefits of short-term pulsed Delta 

inflows (five days or less) on the migration rate and survival 

of anadromous fish.

SWP and 

CVP 

contractors, 

IEP 

agencies

High

•9. Continue to evaluate the effects of Delta hydraulic 

conditions such as net reverse flows on anadromous fish 

migration and distribution.

SWP and 

CVP 

contractors, 

IEP 

agencies

3406(g) High

10. Evaluate the potential effects of reductions in food 

chain organisms in the Delta and Suisun Bay on 

anadromous fish production.

SWP and 

CVP 

contractors, 

IEP 

agencies

3406(g) High

•11. Evaluate whether Delta inflow and export rates and 

other Delta hydrodynamic parameters effect juvenile 

salmon survival when the DCC is closed.

SWP and 

CVP 

contractors, 

IEP 

3406(g) High

 2

Although Evaluation 5 addresses fish passage, it was assigned high priority because the potential to 

increase fish production is great.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 101

Evaluation Involved 

parties

Tools Priority

agencies

12. Evaluate the benefits to juvenile anadromous fish of 

and opportunities for screening diversions and re-locating 

riparian diversions in the Delta and Suisun Marsh.

SWP and 

CVP 

contractors, 

IEP 

agencies

3406(b)(21) Medium

•13. Evaluate the potential effect of Delta export rate 

during the fall on the upstream migration of adult San 

Joaquin chinook salmon.

SWP and 

CVP 

contractors, 

IEP 

agencies

3406(b)(1)(B) High

CENTRAL VALLEY-WIDE

Action Involved 

parties

Tools Priority

•1. Support programs to provide educational outreach and 

local involvement in restoration, including programs like 

Salmonids in the Classroom, Aquatic Wild, and Adopt a 

Watershed and school district environmental camps.

Local 

schools, 

CDFG, 

USFWS, 

NMFS

Low

2. Develop programs to educate the public about anadromous 

fish issues, such as the effects of poaching and environmental 

contaminants, especially contaminants in urban runoff.

CDFG, 

USFWS, 

NMFS, 

Water 

Education 

Foundation, 

California 

Teachers 

Association

Low

3. Reduce toxic chemical and trace element contamination. CDFG, High
102 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Action Involved 

parties

Tools Priority

USFWS, 

SWRCB, 

RWQCBs

•4. Provide additional funding for increased law enforcement to 

reduce illegal take of anadromous fish, stream alteration, and 

water pollution and to ensure adequate protection for juvenile 

fish at pumps and diversions.

CDFG, 

USFWS, 

USBR, 

CDWR

High

Evaluation Involved 

parties

Tools Priority

1. Evaluate the need to revis e harvest regulations to increase 

spawning escapement of naturally produced chinook salmon.

CDFG, 

Pacific 

Fisheries 

Management 

Council 

(PFMC), 

NMFS, 

USFWS

Low

2. Evaluate the potential to modify hatchery procedures to 

benefit native stocks of salmonids.

CDFG, 

CDWR, 

USFWS, 

USBR

3406(e)(2) Low

3. Evaluate and avoid potential competitive displacement of 

naturally produced juvenile salmonids with hatchery-produced 

juveniles by implementing release strategies for hatcheryproduced fish designed to minimize detrimental interactions.

CDFG, 

CDWR, 

USFWS, 

USBR

3406(e)(2) Low

•4. Evaluate and implement specific hatchery spawning 

protocols and genetic evaluation programs to maintain genetic 

diversity in hatchery and natural stocks.

CDFG, 

CDWR, 

USFWS, 

USBR

3406(e)(2) Low

5. Evaluate the transfer of disease between hatchery and CDFG, 3406(e)(2) Low
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 103

Evaluation Involved 

parties

Tools Priority

natural stocks. CDWR, 

USFWS, 

USBR

6. Evaluate effects of trace elements and organic 

contaminants, especially selenium and PCBs, on the health of 

adult white sturgeon and green sturgeon, the viability of their 

gametes, and development of their offspring.

CDFG, 

USFWS

High

•7. Evaluate a program to tag and fin-clip all or a significant 

portion of hatchery-produced fish as a means of collecting 

better information regarding harvest rates on hatchery and 

naturally produced fish and effects of hatchery-produced fish 

on naturally produced fish.

CDFG, 

CDWR, 

USFWS, 

USBR, 

NMFS, 

EBMUD

3406(e)(2) Low

8. Evaluate the direct and indirect effects of contaminants on 

production of anadromous fish.

CDFG, 

USFWS, 

RWQCBs, 

SWRCB

High

9. Evaluate the ability of streams for which target production 

levels exist for chinook salmon but not for steelhead to 

support natural production of steelhead.

CDFG, 

USFWS

3406(e)(6) High

10. Evaluate the effects of exotic species on production of 

anadromous fish.

IEP agencies Low

11. Encourage the restoration of small tributaries by 

evaluating the feasibility of screening or relocating diversions, 

switching to alternative sources of water for upstream 

diversions, restoring and maintaining a protected riparian strip, 

limit excessive erosion, enforcing dumping ordinances, 

removing toxic materials or controlling their source, replacing 

bridge and ford combinations with bridges or larger culverts 

and installing siphons to prevent truncation of small streams at 

irrigation canals.

CDFG, 

USFWS, 

USBR

3406(e)(6) High
104 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

OCEAN

Evaluation Involved 

parties

Tools Priority

1. Evaluate the need to revise harvest regulations on both sport 

and commercial fishers to increase spawning escapement of 

naturally produced chinook salmon.

PFMC, 

CDFG, 

NMFS, 

USFWS

Low

2. Evaluate the effects of sea lion predation on chinook salmon 

production.

PFMC, 

CDFG, 

NMFS, 

USFWS

Low

3. Evaluate the effects of foreign, open-ocean harvest on 

Central Valley chinook salmon and steelhead stocks.

PFMC, 

NMFS, 

CDFG, 

USFWS

Low
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 105

REFERENCES CITED

California Coordinated Resource Management and Planning. 1990. California Coordinated Resource 

Management and Planning Handbook. 18 pp.

California State Water Resources Control Board. 1995. Water quality control plan for the San 

Francisco Bay/Sacramento-San Joaquin Delta estuary. May 1995 (95-1WR). Sacramento, 

CA.

Hilborn, R., and D. Ludwig. 1993. The limits of applied ecological research. Ecological Applications 

3:550-552.

Management Institute for Environment and Business. 1993. Conservation partnerships: a field guide to 

public-private partnering for natural resource conservation. Washington, D.C.; National Fish 

and Wildlife Foundation. 40 pp.

Memorandum of Understanding. 1991. California =s coordinated regional strategy to conserve 

biodiversity: The agreement on biological diversity, September 19, 1991. 6 pp.

Mills, T. J. 1995. Restoring Central Valley streams: A plan for action, status of implementation. 

California Department of Fish and Game, Inland Fisheries Division. Sacramento, CA.

Mills, T. J., and F. Fisher. 1994. Central Valley anadromous sport fish annual run-size, harvest, and 

population estimates, 1967 through 1991. August 1994 draft. California Department of Fish 

and Game, Inland Fisheries Technical Report. Sacramento, CA.

National Marine Fisheries Service. 1994. Listing endangered and threatened species and designating 

critical habitat: Petition to list steelhead throughout its range in Washington, Oregon, California, 

and Idaho. Federal Register 59:27527-27528, May 27, 1994.

National Marine Fisheries Service. 1995. Listing endangered and threatened species and designating 

critical habitat: Petition to list chinook salmon throughout its range in California, Oregon, 

Washington, and Idaho. Federal Register 60:30263-30264, June 8, 1995.

National Marine Fisheries Service. 1996. Endangered and threatened species: Proposed endangered 

status for five ESUs of steelhead and proposed threatened status for five ESUs of steelhead in 

Washington, Oregon, Idaho, and California. Federal Register 61:41541-41561, August 9, 

1996.
106 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Reynolds, F. L., T. J. Mills, R. Benthin, and A. Low. 1993. Restoring Central Valley streams: A plan 

for action. California Department of Fish and Game, Inland Fisheries Division. Sacramento, 

CA.

U.S. Fish and Wildlife Service. 1995. Working paper on restoration needs: Habitat restoration actions 

to double natural production of anadromous fish in the Central Valley of California. Volumes 1-

3. May 9, 1995. Prepared for the U.S. Fish and Wildlife Service under the direction of the 

Anadromous Fish Restoration Program Core Group. Stockton, CA.

U.S. Fish and Wildlife Service. 1996. Sacramento-San Joaquin Delta Native Fishes Recovery Plan. 

U.S. Fish and Wildlife Service, Portland, Oregon.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-1

APPENDICES

A. AFRP Positi on Paper

Presented in its entirety below is the "Position Paper for Development of the Central Valley 

Anadromous Fish Restoration Program". The Position Paper was developed by the AFRP Core 

Group to guide program development. It was released to the public on July 18, 1994 and was slightly 

revised and re-released in Volume 2 of the Working Paper on Restoration Needs (USFWS 1995). 

Only the phone number and address to request copies has been revised since the last release.

POSITION PAPER FOR DEVELOPMENT OF THE CENTRAL VALLEY 

ANADROMOUS FISH RESTORATION PROGRAM

INTRODUCTION

The Plan of Action (POA) for the Central Valley Anadromous Fish Restoration 

Program (Program) identifies the steps necessary to develop the Program (USFWS 

1994). One of the steps included the preparation of a Position Paper to be developed 

by the Core Group. This document is a draft of the Position Paper described in the 

POA.

This Position Paper is a reference document for use by the Core Group and the 

technical teams to guide Program development. Because it was impossible to anticipate 

all issues prior to drafting the Position Paper, this paper will be amended and 

supplements added as needed. To determine if your copy is current and to request 

copies of the Position Paper, contact the Public Information Officer, Central Valley Fish 

and Wildlife Restoration Program, 3310 El Camino Avenue, Sacramento, California 

95821, (916) 979-2760.

The paper is divided into three sections: (1) Program goal and definitions, (2) Intent of 

Title 34, and (3) Implementation criteria. The first section states the Program goal and 

develops general definitions for each of the terms used in the Program goal. The second 

section presents and interprets the intent of Title 34 and reexamines some of the 

definitions presented in the first section. These first two sections lay the foundation for 

the last section.

In the last section, implementation criteria are discussed for the 1967-1991 (baseline) 

period and for the future. Discussions of implementation criteria are separated because 

the two periods require different criteria. As discussed later in this paper, limitations are 

imposed by the type or quantity of data collected during the baseline period. Future 

monitoring programs may be designed to avoid these limitations.
APPENDIX A-2 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

PURPOSE OF POSITION PAPER

The purposes of the Position Paper are two-fold: (1) to explain or clarify the Core 

Group's position on issues related to developing the Program and (2) to document 

reasons used to develop these positions.

PROGRAM GOAL AND RELATED DEFINITIONS

Title 34 requires that "...natural production of anadromous fish in Central Valley rivers 

and streams be sustainable, on a long-term basis, at levels not less than twice the 

average levels attained during the period of 1967-1991..." (Section 3406[b][1]). 

Several terms need to be clearly defined before the program can be designed to meet 

this requirement: natural production, anadromous fish, Central Valley rivers and 

streams, sustainable, long-term basis, and average levels.

Natural Production

Title 34 defines natural production as: "... fish produced to adulthood without direct 

human intervention in the spawning, rearing, or migration processes" (Section 3403[h]). 

 To apply this definition, we must develop an understanding of the meaning of each of 

the components of the definition. Important components that have been identified to 

date are the following: production, adulthood, and direct human intervention.

Production

Ricker (1958) defined production as "the total elaboration of new body substance in a 

stock in a unit of time, irrespective of whether or not it survives to the end of that time." 

Although Ricker's definition includes changes in mass as well as numbers of fish, Title 34 

specifies "... fish produced to adulthood..." and therefore production will refer to 

numbers of fish produced.

Because a fish can only be "...produced to adulthood..." once in its lifetime, an individual 

fish should not be counted twice. In addition, production should be measured over a 

discrete time interval. Because all stocks under consideration are seasonal spawners, a 

direct and simple approach will be to count the first-time spawners each 

spawning season.

Ricker's definition also states that a fish is counted toward production for the time 

period over which production is being measured "...irrespective of whether or not it 

survives to the end of that time". Using Ricker's definition, juvenile fish that did not 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-3

survive to adulthood would be counted. The definition of natural production in Title 34 

specifies "... fish produced to adulthood..." and therefore does not count juvenile fish. 

On the other hand, Title 34 does not discriminate between adult fish that return to 

spawn and those taken in recreational and commercial fisheries. Because Ricker's 

definition includes fish that do not survive to the end of the time period, and because the 

definition of natural production in Title 34 specifies fish produced to adulthood, all 

naturally produced, adult fish shall be counted, including those that are 

harvested prior to spawning.

Including harvested fish is consistent with the definition of production in the California 

Salmon, Steelhead Trout and Anadromous Fisheries Program Act. The California Act 

defines production as "the survival of fish to adulthood as measured by abundance of 

the recreational and commercial catch together with the return of fish to the states 

spawning streams." Because both the Federal and State acts have similar pur poses and 

goals, and because implementation of both acts should be coordinated, it is convenient 

that the definitions of production being implemented for both acts are similar.

Whether or not a fish attains adulthood is key to determining whether or not to count 

that fish toward the production goal. Adulthood is defined below.

Adulthood

Section 3403(h) includes the phrase "...fish produced to adulthood..." as part of the 

definition of natural production. Adulthood is not defined within Title 34. Adulthood is 

generally defined as the state, condition or quality of being fully developed and mature. 

Applying this definition to fish is complicated by the fact that most fish continue to grow 

throughout life (i.e., cessation of growth can't be used to indicate full development) and 

may become sexually mature several times during their lifetime (i.e., although developed 

gonads can be used to indicate maturity, lack of developed gonads cannot be used to 

indicate immaturity). Because the presence or absence of external characters can't 

always be used to identify adult fish, and because sexual maturity (i.e., developed 

gonads) is a transitory state, fishery managers often use size or age criteria to indicate 

maturity.

An adult fish will be defined as one tha t is capable of reproduction. Ability to 

reproduce should be based on some external characteristic, such as size. Because Title 

34 requires that production be compared between baseline and goal periods, the same 

criteria for determination of adulthood will be applied to both periods.

Direct Human Intervention
APPENDIX A-4 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

The definition of natural production precludes "...direct human intervention..." in the 

spawning, rearing, or migration processes of an individual, naturally produced fish. A 

definition of direct human intervention is key to understanding the definition of natural 

production. Humans have pervasively intervened in the structure and function of the 

Sacramento-San Joaquin system. All anadromous fish that spawn in the system have 

been impacted by this intervention. Indeed, Title 34 has as one of its purposes "...to 

address impacts of the Central Valley Project on fish, wildlife, and associated 

habitats..." (Section 3402[b]). But not all human intervention is direct. The word direct 

is an important component of the phrase "...direct human intervention...".

Direct human intervention is any action taken in the absence of intervening 

elements. Any form of intervention that requires handling of fish is direct intervention 

due to a lack of intervening elements. Any action that includes one or more intervening 

elements would be considered indirect intervention.

Hatchery and artificial propagation, including supplementation and out-planting of eggs 

or any other life-stage, requires handling of fish by humans during the spawning and 

rearing processes and therefore are forms of direct intervention. Transporting fish, 

including truck and barge transport, and fish salvage require capture and handling of fish 

during the rearing or migration process and therefore are forms of direct intervention. 

Hatchery and artificial propagation, transport and salvage of fish, or any process that 

requires handling of any life-stage of fish will be considered direct human intervention.

Title 34 clearly states that fish produced with direct human intervention should not be 

included in counts of natural production. In developing the Program, we will avoid 

counting hatchery-produced fish or fish produced with any other form of direct human 

intervention in counts of natural production. The Core Group has determined that there 

will be one exception to this rule: the progeny of naturally spawning fish salvaged at the 

John E. Skinner Delta Fish Protective Facility and the Tracy Fish Protective Facility, if 

they reach adulthood, will be counted as naturally produced.

An example of a form of intervention that does not fit the definition of direct intervention 

is flow manipulation. When we manipulate flow to benefit fish, flow acts as the 

intervening element. Humans directly alter flows and flows alter fish spawning, rearing, 

or migration processes. Therefore, flow manipulation is not a direct but an indirect form 

of intervention. Construction of fish ladders, screens and barriers are forms of indirect 

intervention because each of these structures act as the intervening element. Reservoir 

or flow manipulations (including Delta flows and flows to maintain desired stream 

temperatures), ladders, screens, barriers, and other forms of habitat alteration and 

enhancement activities will not be considered direct human intervention because each of 

these is or has an intervening element and does not require handling of fish.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-5

Because the definition of natural production in Title 34 includes the phrase "...produced 

to adulthood...", fish that are not subject to direct human intervention until after they 

reach adulthood would still be considered naturally produced. For example, a naturally 

produced fish that returned to a hatchery and was spawned in the hatchery would be 

considered naturally produced. Obviously, its progeny would not be considered 

naturally produced because they were produced in a hatchery. Similarly, naturally 

produced adult fish whose migration was subject to direct human intervention would still 

be considered naturally produced, although their progeny would not be considered 

naturally produced.

Anadromous Fish

Title 34 defines anadromous fish as "...those stocks of salmon (including steelhead), 

striped bass, sturgeon, and American shad that ascend the Sacramento and San Joaquin 

rivers and their tributaries and the Sacramento-San Joaquin Delta to reproduce after 

maturing in San Francisco Bay or the Pacific Ocean" (Section 3403[a]). This definition 

identifies five groups or species of fish: salmon, steelhead, striped bass, sturgeon, and 

American shad. The American Fisheries Society recognizes steelhead as the common 

name for the anadromous form of Oncorhynchus mykiss and striped bass and 

American shad as the common names for Morone saxatilis and Alosa sapidissima

(AFS 1991). Clearly, Title 34 includes these species in the definition of anadromous 

fish. The names salmon and sturgeon both include multiple species of fish and the 

meaning of these terms in relation to Program development needs clarification. The 

term "stocks" in the definition of anadromous fish also needs clarification.

Salmon - Salmon is a common name for at least six species of fish. Five species of 

salmon have been observed in the Sacramento River: chinook (O. tshawytscha), coho 

(O. kisutch), sockeye (O. nerka), pink (O. gorbuscha), and chum (O. keta) salmon 

(Moyle 1976, Fry 1973). Chinook salmon are common in the Sacramento-San 

Joaquin system, the other four species are rare. Based on observations of adults during 

1949 through 1958, Hallock and Fry (1967) concluded that sockeye, pink, and chum 

salmon entered the Sacramento River regularly enough to be regarded as very small 

runs, but that coho salmon were so scarce and irregular that they should be regarded as 

strays. Juvenile coho salmon were planted in Mill Creek in 1956, 1957, and 1958, but 

by 1963 coho salmon were almost as scarce as they had been before the introductions 

(Hallock and Fry 1967). During the baseline period, there is no evidence that coho, 

sockeye, pink, or chum salmon maintained self-sustaining spawning runs in the Central 

Valley (Fisher pers. comm.). Because the definition of anadromous fish specifies 

"...salmon... that ascend the Sacramento and San Joaquin rivers...to reproduce..." and 

because chinook salmon is the only salmon known to reproduce in the system on a 
APPENDIX A-6 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

regular basis during the baseline period, the use of the word salmon in the definition will 

be interpreted to mean chinook salmon.

Sturgeon - Two species of sturgeon are found in the Sacramento-San Joaquin system: 

white sturgeon (Acipenser transmontanus) and green sturgeon (A. medirostris) 

(Moyle 1976). Because both species of sturgeon reproduce in the Sacramento-San 

Joaquin system, the word sturgeon will be interpreted to include white and green 

sturgeon.

In summary, the species of anadromous fish identified by Title 34 that reproduce 

in the Sacramento-San Joaquin system include chinook salmon, steelhead, 

striped bass, white sturgeon, green sturgeon, and American shad. The Program 

will be designed to double the natural production of the anadromous forms of these six 

species.

Other anadromous fish - Title 34 does not identify several species of anadromous fish 

that spawn in Central Valley rivers and streams. These include threespine stickleback, 

brown trout, and two species of lamprey and smelt (Fry 1973). The Program will not 

establish restoration goals specific to these species.

Stocks

For purposes of the Program, a stock is defined as a group of individuals which 

are more likely to mate with each other than with individuals not included in the 

group. The term stock describes a fish population that spawns in a particular stream, 

or stream reach, at a particular season and that do not interbreed to a substantial degree 

with any group spawning in a different place, or in the same place at a different time. 

This definition does not rely upon absolute reproductive barriers. In fisheries 

management, stocks are recognized to maintain and improve the genetic basis for 

management.

Several stocks which meet this definition are already recognized. For example, chinook 

salmon are divided into several races based on the season during which they enter the 

rivers to begin their upstream spawning migrations as follows: fall, late-fall, winter, and 

spring runs. Others stocks which might be recognized in the future will likely become 

stocks of special concern.

Good evidence exists for salmon and steelhead that these species return to their natal 

streams to spawn. There is some evidence and little reason not to expect that the same 

relationship holds for some of the other anadromous species. As stated in the POA for 

the Program, the objective of the Program will be to double the natural production of all 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-7

species and races within specific individual streams, and to preserve genetic stocks. If it 

proves unfeasible to double the natural production of a species or race within a specific 

stream, the unmet production increment will be transferred to other individual streams in 

the following order of priority: (1) another stream within the same drainage system, (2) 

another stream within the larger basin, such as the Sacramento River Basin, and (3) any 

stream within the Central Valley.

Central Valley Rivers and Streams

For the purposes of the Program, Central Valley rivers and streams are defined as 

all rivers, streams, creeks, sloughs and other watercourses, regardless of 

volume and frequency of flow, that drain into the Sacramento River basin, the 

San Joaquin River basin downstream of Mendota Pool, or the Sacramento-San 

Joaquin Delta upstream of Chipps Island.

Sustainable

Sustainable means capable of being maintained or kept in existence. In Title 34, 

sustainable refers to natural production, which is defined as "... fish produced to 

adulthood without direct human intervention...." Elimination of direct human intervention 

as a legitimate alternative requires reliance on restoration and maintenance of habitat 

conditions that allow anadromous fish populations to sustain themselves at levels 

consistent with numeric restoration goals. Therefore, in the context of Title 34, 

sustainable is defined as capable of being maintained at target levels without 

direct human intervention in the spawning, rearing or migration processes. 

Production levels specified by numeric goals will be considered sustainable when they 

are maintained under the entire range of conditions resulting from legal human activities, 

as superimposed on natural variability inherent in the system. Human activities shall 

include, but not be limited to, agricultural diversion and discharge, exports, flow 

manipulation, water pollution, dredge and fill, channel modification and damming.

There is an element of time implicit in sustainability. Therefore, if natural production is to 

be sustainable, modifications to system operations as well as improved physical habitat 

and water quality must be provided into the future. Title 34 requires that "...natural 

production...be sustainable, on a long-term basis" and provides for annual funding 

without a specified expiration date. The intent of Title 34 is that numeric restoration 

goals continue to be realized or exceeded in perpetuity.
APPENDIX A-8 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Long-Term Basis

Long-term will encompass at least several generations of fish (not less than 5) 

over a variety of hydrologic conditions (to allow for natural variation in 

production) and will continue indefinitely.

Average Levels

As stated in Title 34, the goal is to sustain natural production "...at levels not less than 

twice the average levels attained during the period of 1967-1991..." To attach numeric 

values to this goal, we need to estimate average levels of production. One problem is 

that average is not a precise statistical term. In statistics, the term average can apply to 

several measures of central tendency (Langley 1971). The most commonly used 

measure of central tendency is the arithmetic mean (Lapin 1975). Consequently, the 

public generally understands average to mean arithmetic mean and it is reasonable to 

assume that this was the intent of the authors of Title 34. Therefore, the definition of 

average will be the arithmetic mean.

INTENT OF TITLE 34

Habitat Restoration

Of the six purposes of Title 34, three are particularly germane to discussion of the intent 

of Title 34 as it relates to the Program. These three purposes are listed below:

(1) to protect, restore, and enhance fish, wildlife, and associated habitats in the 

Central Valley and Trinity River basins of California (3402[a]);

(2) to address impacts of the Central Valley Project on fish, wildlife and associated 

habitats (3402[b]);

(3) to contribute to the State of California's interim and long-term efforts to protect 

the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (3402[e]);

In addition, Section 3406(b)(1)(A) states that the Program "...shall give first priority to 

measures which protect and restore natural channel and riparian habitat values through 

habitat restoration actions, modifications to Central Valley Project operations, and 

implementation of the supporting measures mandated by this subsection..." Because 

Title 34 directs that the Program shall emphasize habitat restoration, emphasis will be 

placed on restoring habitat.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-9

Natural versus Hatchery Production

Title 34 requires that "...natural production of anadromous fish in Central Valley rivers 

and streams be sustainable, on a long-term basis, at levels not less than twice the 

average levels attained during the period of 1967-1991..." (Section 3406[b][1]). The 

requirement that natural production be sustainable on a long-term basis suggests that the 

intent of Title 34 is for the definition of natural production to extend between generations 

of fish. Natural production should be self-sustaining. The Program should not 

depend on hatchery-produced fish to sustain populations of naturally spawning 

fish.

In addition, Title 34 requires investigations of "...opportunities for additional hatchery 

production to mitigate the impacts of water development and operations on, or enhance 

efforts to increase Central Valley fisheries; Provided, That additional hatchery 

production shall only be used to supplement or to re-establish natural production while 

avoiding adverse effects on remaining wild stocks" (Section 3406[e][2]). This section 

provides insight into the intent of Title 34 as it relates to the roles of natural and hatchery 

production and emphasizes avoiding adverse effects of hatchery production on wild 

(naturally produced) stocks. Under Title 34, hatchery production should only be 

used as a last resort to supplement or to re-establish natural production, and 

then only after investigations on the desirability of developing and 

implementing additional hatchery production.

Adverse effects of hatchery production on natural stocks can include reductions in 

population size caused by competition, predation, disease or other factors (Sholes and 

Hallock 1979, Waples 1991). A large potential for negative interaction exists when 

these stocks interbreed (Hindar et al. 1991, Taylor 1991, Waples 1991). The adverse 

effects of interbreeding increase as hatchery-produced fish become more prevalent in 

the naturally spawning population. Interbreeding reduces interpopulation diversity and 

may lead to a reduction in overall productivity and a greater vulnerability to 

environmental change (Waples 1991). Outbreeding depression may also result from 

interbreeding. In addition, large populations of hatchery-produced fish that are 

indistinguishable from naturally produced fish may intensify effects of harvest on naturally 

produced fish (Wright 1993). The simplest way to avoid adverse effects on naturally 

produced stocks is to minimize the opportunities for interaction between naturally and 

hatchery-produced fish. The Program should be designed to avoid adverse 

effects of hatchery production on natural stocks.
APPENDIX A-10 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Harvest

Title 34 does not directly address harvest. Title 34 defines natural production as: "... 

fish produced to adulthood..." (Section 3403[h]) and requires that natural production be 

increased. Inclusion of the term production, and especially production to adulthood, 

suggests that Title 34 does not intend for restriction of harvest to be used as a 

means of achieving Program goals. As stated in the definition of production, 

harvested fish should be included in counts of production. Sound harvest management 

is designed to harvest only excess production, allowing for enough fish to escape 

harvest to maintain production at the highest level the habitat can support.

Title 34 requires that natural production be increased. There are two mechanisms by 

which natural production can be increased: (1)increasing the productivity of the existing 

habitat, and (2) increasing the amount of habitat. These mechanisms are consistent with 

the emphasis Title 34 places on habitat restoration. Doubling produc tivity of existing 

habitat would provide more offspring from the same number of spawners. If existing 

spawning habitat is being fully utilized, then increasing the number of spawners by 

reducing harvest would not increase production. If production of naturally produced 

fish is doubled and escapement is held to present levels, then harvest of naturally 

produced fish could more than double.

The second mechanism, doubling the amount of habitat, would accommodate twice the 

number of spawners. This would also provide twice the number of offspring. Under 

this scenario, harvest of naturally produced fish could double. Under either mechanism, 

barring other harvest restrictions, we would expect at least a doubling of harvest of 

naturally produced fish. To meet the Intent of Title 34, harvest should be maintained 

at levels that allow sufficient numbers of naturally produced fish to spawn to 

meet goals for at least doubling natural production. 

IMPLEMENTATION CRITERIA

As stated earlier, criteria for determination of natural production will conform to the 

definition of natural production and intent of Title 34, including definitions and 

interpretations of intent discussed and refined in this Position Paper. Because 

determination of natural production in the past will require different criteria than in the 

future, criteria for these time periods will be discussed separately.

Criteria for the baseline period

In the past, data collection efforts have not focused on estimating natural production and 

existing data may not provide direct estimates of natural production. In order to 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-11

establish numerical goals for the Program, average levels of natural production must be 

estimated for the baseline period. Estimates will require assessing existing data and 

developing criteria to determine which data are germane. Criteria may not strictly 

conform to the definitions in and intent of Title 34 but are a compromise necessitated by 

a lack of data on natural production.

As explained in the POA, the Core Group and technical teams are responsible for 

developing these criteria. Technical teams are asked to develop initial criteria and 

estimates of average levels of natural production for the baseline period.

Where data are lacking, technical teams will make assumptions to expand existing data, 

or put existing data in perspective. For example, run-size estimates for American shad 

exist for only two years. In addition, young American shad abundance has been 

sampled during the fall emigration each year since 1967, except for 1974 and 1979 

(Mills and Fisher, in preparation). The American shad technical team could look at 

young American shad abundance data to determine if run-size estimates for adults are 

representative of the abundance of shad for the baseline period. This approach has 

assumptions (chief among these is that abundance of young American shad can tell us 

something about average adult run-sizes) which are probably violated to some degree 

and is only presented as an example of what might be considered. Technical teams will 

document options considered for estimating natural production in issue papers that will 

be appended to the Program Plan if not in the text. Data quantity and applicability 

toward estimating natural production varies between species and drainage. Each 

technical team will need to address these issues for each species and drainage 

separately. Criteria for determining natural production during the baseline period will be 

applicable to existing data.

Because there is a relative wealth of data for chinook salmon and because several 

Teams deal with chinook salmon, specific criteria are proposed for them. Most of the 

data necessary to estimate production of each stock of chinook salmon for the baseline 

period are compiled in Mills and Fisher (1994). The proposed procedure for estimating 

yearly production of each race of chinook salmon for each stream during the baseline 

period follows.

In the following explanations and formulas, P is for production, E is for escapement, H 

is for harvest, and h is for the portion of total production not produced naturally. 

Subscripted letters following the normal letters and prior to the first comma represent 

different races of chinook salmon as follows: F for fall, L for late-fall, W for winter, S 

for spring, and C for all races combined. Subscripted letters following the first comma 

represent the following: O for ocean, D for downstream, I for instream, N for natural, H 

for hatchery, and T for total. Subscripted letters following the second comma represent 
APPENDIX A-12 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

the following: CV for Central Valley, SF for San Francisco, M for Monterey, and other 

letter combinations correspond to specific streams (e.g., AM for American River). 

Subscripted letters following a third comma refer only to ocean harvest and are C for 

commercial and R for recreational. In all cases, a subscripted X acts as a "wildcard" 

place holder for an unspecified subscript.

1. A portion of production returns to spawn in each stream, both naturally and in 

the hatchery. Some of these fish are captured before spawning. These fish are 

counted toward production for the stream in which they spawned or were 

harvested according to the following:

a. To determine the total spawning escapement (E X,T,XX) for each race in each individual 

stream, sum the estimated number of each race of chinook salmon returning to spawn 

naturally (EX,N,XX) and in hatcheries (EX,H,XX) for each individual stream.

EX,T,XX = EX,N,XX + EX,H,XX

b. To determine the portion of production for each race returning to each stream (inriver run-size, PX,I,XX), add EX,T,XX to the estimated number of each race of chinook 

salmon harvested in each stream (HX,I,XX). Estimates of HX,I,XX do not exist for all 

streams and all years. Where estimates are not available or are inadequate, best 

professional judgement must be used. Technical Teams should document options 

considered for estimation of HX,I,XX in the Program Plan or in issue papers that will 

be appended to the Program Plan.

PX,I,XX = EX,T,XX + HX,I,XX

c. To determine the total number of each race of chinook salmon returning to the 

Central Valley (PX,I,CV), sum PX,I,XX for all streams in the Central Valley ( PX,I,XX) .

PX,I,CV = PX,I,XX

d. To determine the total number of chinook salmon (all races combined) returning to 

the Central Valley (PC,I,CV), sum PX,I,CV for all races of chinook salmon ( PX,I,CV) .

PC,I,CV = PX,I,CV

2. A portion of production is harvested in the ocean and downstream of areas in rivers where 

the stream responsible for this production is not easily identified. To assign these harvested 

salmon to individual streams, the total number of salmon falling into this category is summed 

and subdivided to race and stream, proportional to the portion of production attributed to 

each race and returning to each stream, according to the following:

<

<

<

<

<

<

<

<
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-13

a. To determine the Central Valley component of ocean harvest (HC,O,CV), sum commercial 

catch at San Francisco (HC,O,SF,C) and Monterey (HC,O,M,C), sum recreational catch at these 

same ports (HC,O,SF,R + HC,O,M,R), and add these together. This estimate of HC,O,CV is 

based on the Central Valley Index (CVI), where harvest of Central Valley stocks equa ls 

landings at major ports south of Point Arena (San Francisco and Monterey). Use of CVI 

to estimate the Central Valley component of ocean harvest assumes that the number of 

Central Valley chinook salmon harvested from ports north of San Francisco is balanced by 

the number of chinook salmon from drainages north of the Central Valley harvested from 

San Francisco and Monterey. To carry HC,O,CV forward in subsequent calculations, assume 

that each chinook salmon harvested in the ocean fishery is equivalent to an adult salmon 

returning to spawn.

HC,O,CV = HC,O,SF,C + HC,O,M,C + HC,O,SF,R + HC,O,M,R

b. To account for that portion of inland harvest that occurs downstream of streams for which 

production is being estimated, estimate portion of inland recreational harvest captured 

downstream of spawning streams (HC,D,CV). Information necessary to estimate HC,D,CV may 

not be available. If an estimate exists, use it. If an estimate of inland harvest for the entire 

Central Valley exists (HX,I,CV), then sum all assignable inland harvest ( HX,I,XX) and 

subtract it from HX,I,CV to determine HC,D,CV. If other options exist, these should be 

explored. HC,D,CV could be assumed to be small and therefore left out of the calculations or 

could be included in HX,I,XX, in which case it would already to assigned to an individual 

stream.

c. To determine ocean and downstream inland harvest for the Central Valley (HC,O+D,CV), 

sum HC,O,CV and HC,D,CV.

HC,O+D,CV = HC,O,CV + HC,D,CV

d. To assign portions of HC,O+D,CV to specific races, subdivide HC,O+D,CV to each race, 

proportional to the portion of production for each race returning to the entire Central 

Valley (PX,I,CV) to the portion of production for all races combined returning to the entire 

Central Valley (PX,I,CV).

HX,O+D,CV = HC,O+D,CV (PX,I,CV/PC,I,CV)

e. To assign portions of HX,O+D,CV to specific streams, subdivide HX,O+D,CV to each stream, 

proportional to the portion of production for that race returning to each stream (PX,I,XX) 

to the portion of production for that race returning to the entire Central Valley (PX,I,CV).

<

<

•
APPENDIX A-14 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

HX,O+D,XX = HX,O+D,CV (PX,I,XX/PX,I,CV)

3. To determine total production for each race and stream (PX,T,XX), sum PX,I,XX and HX,O+D,XX.

PX,T,XX = PX,I,XX + HX,O+D,XX

4. A portion of the total production was not produced naturally (h). For the baseline period, 

only hatchery-produced salmon will be considered to be produced by other than natural 

means. To determine the natural production for each individual stream (PX,N,XX), multiply 

PX,T,XX by (1-h). Technical Teams should document options considered and chosen for 

estimation of h in issue papers that will be appended to the Program Plan or in the text for the 

Program Plan.

PX,N,XX = PX,T,XX (1-h)

Numeric restoration goals for chinook salmon in each stream will be calculated as at least double 

the average of PX,N,XX for each of the years during the baseline period.

Criteria for the future

In the future, opportunities exist to improve estimates of natural production. These range from 

augmenting historic data collection activities with efforts to estimate the proportion of fish that are 

naturally produced, to designing new data collection to better account for natural production. The 

Core Group and technical teams are responsible for designing future monitoring programs.

The Core Group and technical teams have and will identify deficiencies in the baseline data. 

Future monitoring activities will be designed to address and avoid deficienc ies. For example, 

monitoring programs should focus on estimating production, including harvest, on a consistent and 

regular basis, preferably yearly, in all of the streams in the Central Valley.

Monitoring programs should also estimate natural production, requiring some means of separating 

naturally produced fish from fish produced by other than natural means. At the very least, natural 

produc tion must be discernable from hatchery production. Several methods can be used to 

separate naturally produced fish from hatchery-produced fish, including use of scale (Scarnecchia 

and Wagner 1980) or otolith (Paragamian et al. 1992) characteristics and constant fractional 

(Hankin 1982) or complete marking of hatchery-produced fish (Wright 1993), including 

incorporation of genetic markers (Waples 1991), inducement of otolith banding patterns (Volk et 

al. 1990), and more standard methods such as clipping fins. In addition, recommendations for the 

future should include managing naturally and hatchery-produced fish separately.

•

•

•
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-15

In addition, better estimates of harvest of Central Valley salmon in the ocean and of all 

anadromous fish in the Bay, Delta, and in each individual river and stream in the Central Valley 

should be developed. Harvest should be monitored continually.
APPENDIX A-16 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

CITATIONS FOR POSITION PAPER

American Fisheries Society. 1991. Common and scientific names of fishes from the United 

States and Canada. Fifth edition. American Fisheries Society Special Publication 20, 

Bethesda, Maryland. 183 pp.

Fry, D. H., Jr. 1973. Anadromous fishes of California. California Department of Fish and 

Game. 111 pp.

Hallock, R. J., and D. H. Fry, Jr. 1967. Five species of salmon, Oncorhynchus, in the 

Sacramento River, California. California Fish and Game 53:5-22.

Hankin, D. G. 1982. Estimating escapement of Pacific salmon: marking practices to 

discriminate wild and hatchery fish. Transactions of the American Fisheries Society 

111:286-298.

Hindar, K., N. Ryman, and F. Utter. 1991. Genetic effects of cultured fish on natural fish 

populations. Canadian Journal of Fisheries and Aquatic Sciences 48:945-957.

Langley, R. 1971. Practical statistics simply explained. Dover Publications, Inc. New York, 

NY. 399 pp.

Lapin, L. 1975. Statistics: meaning and method. Harcourt Brace Jovanovich, Inc. New York, 

NY. 591 pp.

Miller, B., R. Reisenbichler, P. Wampler, C. Burley, D. Leith, B. Thorson, and P. Brandes. 

1993. Vision action plan on supplementation, Region 1. U.S. Fish and Wildlife Service, 

Region 1. Portland, OR. 12 pp.

Mills, T. J., and F. Fisher. In prep. Central Valley anadromous sport fish annual run-size, 

harvest, and population estimates, 1967 through 1991. Second draft. Inland Fisheries 

Technical Report. California Department of Fish and Game. 62 pp.

Moyle, P. B. 1976. Inland fishes of California. University of California Press. Berkeley, CA. 

405 pp.

Paragamian, V. L., E. C. Bowles, and B. Hoelscher. 1992. Use of daily growth increments on 

otoliths to assess stockings of hatchery-reared kokanees. Transactions of the American 

Fisheries Society 121:785-791.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX A-17

Ricker, W. E. 1958. Handbook of computations for biological statistics of fish populations. 

Bulletin of the Fisheries Research Board of Canada 119. 300 pp.

Scarnecchia, D. L., and H. H. Wagner. 1980. Contribution of wild and hatchery-reared coho 

salmon, Oncorhynchus kisutch, to the Oregon sport fishery. Fishery Bulletin 77:617-623.

Sholes, W. H., and R. J. Hallock. 1979. An evaluation of rearing fall-run chinook salmon, 

Oncorhynchus tshawytscha, to yearlings at Feather River Hatchery, with a comparison of 

returns from hatchery and downstream releases. California Fish and Game 65:239-255.

Sokal, R. R., and F. J. Rohlf. 1969. Biometry. W. H. Freeman and Company, San Francisco, 

CA. 776 pp.

Taylor, E. B. 1991. A review of local adaptation in Salmonidae, with particular reference to 

Pacific and Atlantic salmon. Aquaculture 98:185-207.

U.S. Fish and Wildlife Service. 1994. Central Valley Project Improvement Act - Plan of action 

for the Central Valley Anadromous Fish Restoration Program. U.S. Fish and Wildlife 

Service, 4001 North Wilson Way, Stockton, California 95205. 14 pp.

Volk, E. C., S. L. Schroder, and K. L. Fresh. 1990. Inducement of unique otolith banding 

patterns as a practical means to mass-mark juvenile pacific salmon. Transactions of the 

American Fisheries Society 7:203-215.

Waples, R. S. 1991. Genetic interactions between hatchery and wild salmonids: lessons from 

the Pacific Northwest. Canadian Journal of Fisheries and Aquatic Sciences 48:124-133.

Wright, S. 1993. Fishery management of wild Pacific salmon stocks to prevent extinctions. 

Fisheries (Bethesda) 18(5):3 -4.

Zar, J. H. 1984. Biostatistical Analysis. Second edition. Prentice-Hall, Inc., Englewood Cliffs, 

NJ. 718 pp.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX B-1

B. Production targets for chinook salmon in each stream

Preliminary estimated production targets for chinook salmon. Data for rivers without a race designation 

are for fall-run chinook salmon.

Race and river Production targets

All races combineda 990,000

 Fall run 750,000

 Late-fall run 68,000

 Winter run 110,000

 Spring run 68,000

Sacramento River

Fall run 230,000

Late-fall run 44,000

Winter run 110,000

Spring run 59,000

Clear Creek 7,100

Cow Creek 4,600

Cottonwood Creek 5,900

Battle Creek

Fall run 10,000

Late-fall run 550

Paynes Creek 330

Antelope Creek 720

Mill Creek

Fall run 4,200

Spring run 4,400

Deer Creek

Fall run 1,500

Spring run 6,500

Miscellaneous creeks 1,100

Butte Creek

Fall run 1,500

Spring run 2,000

Big Chico Creek 800

Feather River 170,000

Yuba River 66,000

Bear River 450

American River 160,000

Mokelumne River 9,300

Cosumnes River 3,300

Calaveras River

 Winter run

2,200*

Stanislaus River 22,000

Tuolumne River 38,000

Merced River 18,000

a

Targets for each of the races of chinook salmon may not add up to the target for all races combined due to rounding.

*Production target no longer valid as winter-run is not native production for fall-run chinook salmon yet to be 

determined.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX C -1

C. Contacts and sources of information.

For information on the Anadromous Fish Restoration Program, contact:

Martin A. Kjelson, Program Manager

U.S. Fish and Wildlife Service

Anadromous Fish Restoration Program

Sacramento-San Joaquin Estuary Fishery Resource Office

4001 North Wilson Way

Stockton, CA 95205

(209) 946-6400

E-mail address: martin_kjelson@fws.gov

For information on the Central Valley Fish and Wildlife Restoration Program, including information on 

other sections of the CVPIA that contribute to fish and wildlife restoration, contact:

James J. McKevitt, Program Manager

U.S. Fish and Wildlife Service

Central Valley Fish and Wildlife Restoration Program

3310 El Camino Avenue

Sacramento, CA 95821

(916) 979-2760

E-mail address: jim_mckevitt@fws.gov

For information on the CALFED Bay-Delta Program=s near-term efforts to restore anadromous fish in 

the Central Valley, especially funding for restoration actions, contact:

Cindy Darling or Kate Hansel, Restoration Coordinators

CALFED Bay-Delta Program

Restoration Coordina tion Program

1416 Ninth Street, Suite 1155

Sacramento, CA 95814

(916) 657-2666 or 653-1103

E-mail address: cdarling@water.ca.gov or hanselk@water.ca.gov
APPENDIX C -2 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

For information on the CALFED Bay-Delta Program=s long-term plan for ecosystem restoration, 

contact:

Dick Daniel, Assistant Director or

Terry Mills, Ecosystem Restoration Program Plan Manager

CALFED Bay-Delta Program

Ecosystem Restoration Program Plan

1416 Ninth Street, Suite 1155

Sacramento, CA 95814

(916) 657-2666

E-mail address: ddaniel@water.ca.gov

For information on the California Department of Fish and Game=s efforts to restore anadromous fish in 

the Central Valley, contact:

Alan Baracco

California Department of Fish and Game

Inland Fisheries Division

1416 Ninth Street

Sacramento, CA 95814

(916) 653-4729

Copies of Conservation Partnership: A Field Guide to Public-Private Partnering for Natural Resource 

Conservation may be obtained from:

U.S. Fish and Wildlife Service

Office of Training and Education

4401 North Fairfax Drive

Arlington, VA 22203

(703) 358-1711

or

National Fish and Wildlife Foundation

1120 Connecticut Avenue, NW, Suite 900

Washington, DC 20036

(202) 857-0166
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX C -3

Copies of California Coordinated Resource Management and Planning Handbook may be obtained 

from:

CRMP Coordinator

California Association of Resource Conservation Districts

801 K Street, Suite 1318

Sacramento, CA 95814

(916) 447-7237

FAX (916) 447-2532
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX D-1

D. Template for organization of detailed information on specific actions

The AFRP has developed a draft template containing the following information for each of the actions 

listed in the Restoration Plan.

Watershed or geographic area: Identifies the drainage or geographic area under which the action or 

evaluation description appears in the Restoration Plan. (Where)

Watershed priority: Lists the priority as designated in the Restoration Plan for the watershed or 

geographic area, if applicable.

Action (or evaluation): Includes the text for the action or evaluation as it appears in the Restoration 

Plan, including the number assigned to the action or evaluation. (What)

Location: Identifies the specific location(s), if applicable, of the action or evaluation. Include the stream 

mile(s), city(ies) and county(ies) in which the action or evaluation would be taken. (Where)

AFRP action (or evaluation) priority: Lists the priority relative to other actions and evaluations in the 

drainage, as it appears in the Restoration Plan.

Objective : Briefly states the objective(s) of the action or evaluation. Identifies species or race(s) of 

anadromous fish primarily affected and problem(s) solved by or intended effect(s) of the action or 

evaluation. (Why).

Description: Describes the action or evaluation in detail, including how the action or evaluation will be 

implemented. Cites any literature that may provide further detail. (More detail on what and a 

description of how.)

Background: Describes the existing information leading up to development of the action or evaluation, 

including discussion of alternative actions and of work done to date. Cites any literature that may 

provide further detail. (More detail on why.)

Justification: Describes the reasons for implementing the action or evaluation. Cites any literature that 

may provide further detail. (More detail on why.)

Monitoring needs: Identifies activities, including variables to observe, needed to evaluate the 

effectiveness of the action or to complete the evaluation.

Predicted biological benefits: Identifies anticipated biological benefits, preferably in quantitative 

terms, focusing on anadromous fish and their habitat.
APPENDIX D-2 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Issues: Identifies factors potentially influencing initiation and completion of the action or evaluation. 

These issues may include design constraints, potential impacts of the action or evaluation on the 

economy or on other segments of the ecosystem, ability to evaluate the success of the action or 

evaluation, or the inability of partners to secure funding. This section will also include identification and 

discussion of actions or evaluations that may increase or decrease the effectiveness of the action or 

evaluation described here.

Involved parties: Lists parties involved in implementing the action or evaluation. (Who)

Environmental documentation: Lists environmental documentation and permitting necessary to 

complete the action or evaluation. For example, list should include whether or not an EA and negative 

declaration or FONSI, an EIR, an EIS, or Biological Opinion is required. It will also list any county or 

municipal permits that may be required.

Deliverables: Lists products (e.g., initial design and feasibility reports, environmental documentation, 

progress reports, physical structures, and monitoring reports) that have been or will be completed as 

part of implementation and monitoring.

Schedule: Lists time frame for key events (e.g., start and completion dates for deliverables and other 

major activities necessary for implementation and monitoring) in chart format. Potential for schedule 

revisions should be identified. (When)

Estimated cost to completion: Lists total costs from planning to completion, including permits, 

environmental documentation, and monitoring. Potential for schedule and budget revisions will be 

identified. Both one-time and continuing annual costs will be identified.

Funding: Identifies funding sources (e.g., CVP Restoration Fund, Category III, Four Pumps Mitigation 

Agreement, specific public or private group, or individual) and funds committed each year to 

completion. Sources of both one -time and continuing annual funds will be identified, as available.

Status: Describes stage of development and accomplishments, and future activities and milestones, and 

impediments.

CVPIA implementation tools: Identifies applicable section(s) of the CVPIA.

Action coordinators: Identifies the coordinator(s) designated as an action manager or point of contact 

for each of the involved parties. If a lead coordinator exists, then it will note which coordinator is 

assigned lead. (Who)

Sources of information: Lists literature cited and additional sources of information on the action.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX D-3

Report date : Lists date that the information was last updated.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

E. Summary of information used to prioritize watersheds.

Table E-1. Production target for chinook salmon, presence of CVP flow control structures or facilities, 

and race or species present in each of the watersheds1

 for which actions are listed in the Restoration 

Plan.

River

Chinook 

salmon 

production

target

CVP 

influence

Winter 

run

Spring

run Steelhead

Latefall 

run

San 

Joaquin 

fall run

Fall 

run

Green 

sturgeon

White 

sturgeon

Striped 

bass

American 

shad

Sacramento 

River

990,000 X X X X X X X X X X

Clear Creek 7,100 X X X

Cow Creek 4,600 X2X X

Cottonwood 

Creek

5,900 X X X X

Battle Creek 10,550 X X3 X X X X

Paynes Creek 330 X X

Antelope 

Creek

720 X X X X

Mill Creek 8,600 X X X X

Deer Creek 8,000 X X X X

Misc. creeks 1,100 X X

Butte Creek 3,500 X X X X

Big Chico 

Creek

800 X X X X

Feather River 170,000 X4 X X X X X X

 

 1

The presence of races or species in each of the watersheds is derived from CDFG=s document titled 

Restoring Central Va lley Streams: A Plan for Action, dated November 1993, and authored by F.L. Reynolds, T.J. 

Mills, R. Benthin, and A. Low. Exceptions are footnoted.

2

Although spring-run chinook salmon are sporadically observed in the Cow Creek watershed, there is no 

current potential for sustaining their production because of natural barriers and lack of over-summering holding pool 

habitat.

3

Winter-run chinook salmon on Battle Creek are of hatchery origin.

4

The present Feather River Hatchery spring-run chinook salmon is a combination of fall-run and spring-run 

chinook salmon races (An evaluation of the Feather River Hatchery as mitigation for construction of the California 

State Water Project=s Oroville Dam, Brown and Greene, Environmental Services Office, CDWR, 1995).
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

River

Chinook 

salmon 

production

target

CVP 

influence

Winter 

run

Spring

run Steelhead

Latefall 

run

San 

Joaquin 

fall run

Fall 

run

Green 

sturgeon

White 

sturgeon

Striped 

bass

American 

shad

Yuba River 66,000 X X X X

Bear River 450 X X X X

American 

River

160,000 X X X X X

Mokelumne 

River

9,300 X X X X

Cosumnes 

River

3,300 X

Calaveras 

River

2,200 X X

Merced River 18,000 X X X

Tuolumne 

River

38,000 X5 X X

Stanislaus

River

22,000 X X X X X X

San Joaquin 

River

--- X X ? X X X

SacramentoSan 

 Joaquin 

Delta 

--- X X X X X X X X X X X

 5

Steelhead were observed in the Tuolumne River in 1983 (Bill Loudermilk, CDFG Senior Fishery Biologist, 

personal communication, and In CDFG, Steelhead restoration and management plan for California, D. McEwan and 

T.A. Jackson, 1996).

River

Chinook 

salmon 

production

target

CVP 

influence

Winter 

run

Spring

run Steelhead

Latefall 

run

San 

Joaquin 

fall run

Fall 

run

Green 

sturgeon

White 

sturgeon

Striped 

bass

American 

shad

Sacramento 

River

--- X X X X X X X X X X X

 Joaquin Delta 
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX F-1

F. Projected funding resources.

The CVP Restoration Fund, along with additional agency and other partner funds, if available, will be 

used to implement the AFRP restoration actions. Funds available from the CVP Restoration Fund to 

the AFRP for actions, evaluations, monitoring and assessment during the 1997 federal fiscal year 

(FY97) totaled $10 million, and is expected to continue at about $8 to $10 million for each of the years 

in FY98 to FY2002. Additional Restoration Fund dollars carried over from previous years are also 

available to supplement AFRP funds, if needed. In addition, the Restoration Fund provides sufficient 

flexibility to move funds to areas of greatest need, subject to certain limitations. Specific funding 

allocations and estimates are described each year in annual work plans for the AFRP and in similar 

work plans for each of the other programs conducted pursuant to the CVPIA.
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX G-1

G. List of acronyms and abbreviations.

Acronym or 

abbreviation Description

af acre-feet

AFRP Anadromous Fish Restoration Program, established by Section 3406(b)(1) of 

the CVPIA

AFS American Fisheries Society

(b)(2) water Water managed pursuant to 3406(b)(2), sometimes referred to as the 800,000 

af or dedicated water

Bay-Delta San Francisco Bay and Sacramento-San Joaquin Delta Estuary

BCWC Butte Creek Watershed Conservancy

Bay-Delta Agreement 15 December 1994, Principles of Agreement on Bay-Delta Standards 

between the State of California and the Federal Go vernment

BLM Bureau of Land Management

CALFED A California and federal multi-agency partnership

CALFED agencies California

 California Environmental Protection Agency

 State Water Resources Control Board

 The Resources Agency

 Department of Fish and Game

 Department of Water Resources

Federal

 Department of Commerce

 National Marine Fisheries Service

 Department of the Interior

 Bureau of Reclamation

 Fish and Wildlife Service

 Environmental Protection Agency

CAMP Comprehensive Assessment and Monitoring Program, established by 

Section 3406(b)(16) of the CVPIA

CCRMP California Coordinated Resource Management and Planning

CCWD Calaveras County Water District

CDFG California Department of Fish and Game

CDWR California Department of Water Resources

 
APPENDIX G-2 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Acronym or 

abbreviation Description

CEQA California Environmental Quality Act

CNFH Coleman National Fish Hatchery

COE Corps of Engineers

Core Group AFRP Core Group

CSLC California State Lands Commission

cfs cubic feet per second

CVFWRP Central Valley Fish and Wildlife Restoration Program

CVP Central Valley Project

CVPIA Central Valley Project Improvement Act

DCWC Deer Creek Watershed Conservancy

DCC Delta Cross Channel

Delta Sacramento-San Joaquin Delta

EBMUD East Bay Municipal Utility District

EIR Environmental Impact Report

EIS Environmental Impact Statement

ESA Endangered Species Act

FERC Federal Energy Regulatory Commission

GCID Glenn-Colusa Irrigation District

IEP Interagency Ecological Program for the Sacramento-San Joaquin Estuary

IEP agencies California

 California Environmental Protection Agency

 State Water Resources Control Board

 The Resources Agency

 Department of Fish and Game

 Department of Water Resources

Federal

 Department of Commerce

 National Marine Fisheries Service

 Department of Defense

 Army Corps of Engineers

 Department of the Interior
FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001 APPENDIX G-3

Acronym or 

abbreviation Description

 Bureau of Reclamation

 Fish and Wildlife Service

 Geological Survey

 Environmental Protection Agency

Interior Department of the Interior

maf million acre-feet

MCC Mill Creek Conservancy

MID Modesto Irrigation District

MIEB Management Institute for Environment and Business

MOU Memorandum of Understanding

NEPA National Environmental Protection Act

NMFS National Marine Fisheries Service

NPS National Park Service

NRCS Natural Resources Conservation Service

PCB Polychlorinated biphenyl

PEIS Programmatic Environmental Impact Statement

PFMC Pacific Fishery Management Council

PG&E Pacific Gas and Electric

POA Plan of Action for the Central Valley Anadromous Fish Restoration Program

Position Paper Position Paper for Development of the Central Valley Anadromous Fish 

Restoration Program (Appendix A)

RBDD Red Bluff Diversion Dam

RCD Resource Conservation District

Restoration Fund CVP Restoration Fund, established by Section 3407 of the CVPIA

Restoration Plan AFRP Restoration Plan

RWQCB Regional Water Quality Control Board

SAFCA Sacramento Area Flood Control Association

SB 1086 Senate Bill 1086
APPENDIX G-4 FINAL RESTORATION PLAN FOR THE AFRP: JANUARY 9, 2001

Acronym or 

abbreviation Description

SAWF Sacramento Area Water Forum

Secretary Secretary of the Interior

SEWD Stockton East Water District

SSWD South Sutter Water District

SWP State Water Project

SWRCB State Water Resources Control Board

taf thousand acre-feet

TCCA Tehama -Colusa Canal Authority

TID Turlock Irrigation District

TNC The Nature Conservancy

USBR U.S. Bureau of Reclamation

USEPA U.S. Environmental Protection Agency

USFS U.S. Forest Service

USFWS U.S. Fish and Wildlife Service

USGS U.S. Geological Survey

USRFRHAC Upper Sacramento River Fisheries and Riparian Habitat Advisory Council

WCWD Western Canal Water District

WID Woodbridge Irrigation District

Working Paper Working Paper on Restoration Needs

WQCP Water Quality Control Plan

WRCB Water Resources Control Board

YCWA Yuba County Water Agency