Working Paper 

on Restoration Needs

Habitat Restoration Actions to Double 

Natural Production of Anadromous Fish

in the Central Valley of California

Volume 1
WORKING PAPER ON RESTORATION NEEDS

HABITAT RESTORATION ACTIONS 

TO DOUBLE NATURAL PRODUCTION OF ANADROMOUS FISH

IN THE CENTRAL VALLEY OF CALIFORNIA

Volume 1

Prepared for the U.S. Fish and Wildlife Service

under the direction of the

Anadromous Fish Restoration Program Core Group

May 9, 1995
ORGANIZATION OF THIS WORKING PAPER

This is Volume 1 of three volumes that comprise the Anadromous Fish Restoration Program (AFRP) 

Working Paper on Restoration Needs. The contents of the three volumes are as follows:

Volume 1 describes how the WORKING PAPER was developed, explains the process 

envisioned for completing a final Restoration Plan, and summarizes the production goals, 

limiting factors, and restoration actions sections developed by the AFRP technical teams. 

Interested parties should read the letter from Dale Hall and Wayne White that appears at 

the beginning of Volume 1.

Volume 2 provides descriptions of Central Valley rivers and streams, summarizes 

information on historic and existing conditions for anadromous fish, identifies the problems 

that have led to the decline of anadromous fish populations, and identifies roles and 

responsibilities of state and federal agencies in managing anadromous fish. It also includes 

two key documents that were used by the AFRP Core Group and technical teams to 

develop the WORKING PAPER.

Volume 3 includes the complete production goals, limiting factors, and restoration actions 

sections as submitted by the AFRP technical teams and edited by USFWS staff. Volume 3 

also includes citations for all three volumes of the WORKING PAPER.

To request copies of this Working Paper, call the AFRP=s information line at (800) 742-9474 or (916) 

979-2330 and dial extension 542 after the recorded message begins. You may also obtain copies by 

calling Roger Dunn, CVPIA Public Outreach, at (916) 979-2760 or by sending e-mail requests to 

roger_dunn@fws.gov. The Working Paper is available to be viewed and downloaded on the Internet at 

http://darkstar.dfg.ca.gov/usfws/fws_home.html.

This document should be cited as:

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. Volume 1. May 

9, 1995. Prepared for the U.S. Fish and Wildlife Services under the direction of the Anadromous 

Fish Restoration Program Core Group. Stockton, CA. 
United States Department of the Interior

FISH AND WILDLIFE SERVICE

SACRAMENTO-SAN JOAQUIN ESTUARY FISHERY RESOURCE OFFICE

4001 N. WILSON WAY, STOCKTON, CA 95205-2486

209-946-6400 (VOICE) 209-946-6355 (FAX)

MEMORANDUM April 14, 1995

To: Dale Hall, ARD,

Ecological Services, Portland

Wayne White

State Supervisor-California

From: Core Group Membership, Anadromous Fish Restoration Program (AFRP)

Central Valley Project Improvement Act (CVPIA)

Subject: Transmittal of working paper describing habitat restoration actions to double production of anadromous fish 

in the central valley of California

The attached working paper describes the habitat restoration actions the Core Group believes necessary to at least double the 

production of anadromous fish in the Central Valley, as required by Section 3406(b)(1) of the CVPIA.

We believe that this paper is a necessary technical platform upon which the partic ipating agencies and the public can work 

cooperatively to achieve a sound, reasonable and implementable program.

This paper was developed by eight technical teams composed of experts possessing specific technical and biological 

knowledge of Central Valley drainages and anadromous fish stocks. Revisions by the Core Group and Service staff were 

primarily designed to improve readability and consistency in the document and to assure the restoration actions were justified 

as fully as possible on technical and biological merits.

The paper is the culmination of the initial phase of Program development. Using this working paper as baseline information, 

future efforts will evaluate the implementability and reasonableness of the actions described herein and other actions

suggested by stakeholders and the interested public to finalize and implement the Anadromous Fish Restoration Program by 

October 31, 1995. A Preface to the paper describes the process of program development, and explains that reasonableness 

was not considered in developing the actions needed to double anadromous fish production.

While the Core Group members representing participating state (DFG and DWR) and federal (FWS, USBR, NMFS and 

EPA) agencies believe the paper provides a sound technical background from which to develop the final program, it does not 

mean that there is total agreement on the benefits of restoration actions either alone or in combination. Nor is there a

commitment by any member or agency to implement any of the restoration actions noted herein.

We envision that each core agency will continue to participate in developing a sound and reasonable habitat restoration 

program in cooperation with key stakeholders and the interested public.

Martin A. Kjelson

Program Manager
United States Department of the Interior

FISH AND WILDLIFE SERVICE

911 N. E. 11th Avenue

Portland, Oregon 97232

IN REPLY REFER TO: April 27, 1995

Memorandum

To: Interested Parties

From: Assistant Regional Director, Ecological Services

Region 1, Portland, Oregon 

 State Supervisor, Ecological Services

 Sacramento, California

Subject: The Consideration of "Reasonable Efforts" in Developing the

Anadromous Fish Restoration Program (Section 3406(b)(1) of the

Central Valley Project Improvement Act)

The purpose of this memorandum is to convey the U.S. Fish and Wildlife Service's position 

on the reasonableness of actions presented in the attached Anadromous Fish Restoration 

Program Working Paper (Working Paper) developed by fishery experts from throughout the 

Central Valley.

The Working Paper represents the best available information on the level of restoration 

needed to meet the goal of at least doubling natural production of anadromous fishes. No 

attempt was made by the technical experts to determine if these actions are reasonable or 

desirable based on the potential social or economic impacts. We are providing this 

Working Paper as a starting point so we can understand the biological needs as we 

collectively develop a draft Anadromous Fish Restoration Program (Restoration Program).

As we enter the development phase of the restoration program, the Service is committed to 

working with stakeholders and the interested public to develop a reasonable, 

implementable restoration plan that balances the needs of anadromous fish with those of 

all parties that have an interest in the wise management of California's natural 

resources.

In our review of the Working Paper we have identified habitat restoration actions that we 

believe are unreasonable such as: 1) setting fish flow standards that consistently 

require unimpaired flows; 2) dismantling major water storage reservoirs; and 3) 

restricting total delta exports to low levels for most of the year. During the 

development of the draft Restoration Plan, the Service working with the stakeholders may 

determine other actions to be unreasonable or we may develop additional actions that are 

reasonable.

It is important to emphasize that the Secretary of the Interior's final decision on which 

restoration actions should be implemented will be influenced by a variety of factors. 

These include input and cooperation from the involved public and governmental agencies, 

results of the programmatic environmental impact statement, the benefit per unit cost, 

the monetary resources in the restoration fund and the availability of supplemental water 

for purchase. The fact that actions authorized by the CVPIA are restricted to CVP streams 

and facilities alone and that other restoration measures will require cooperation from 

other federal, state and private entities to be implemented will help assure that the 

final Program will be reasonable.
In summary, this statement is intended to assure all interested parties that the Service 

is committed to developing a plan that is reasonable and will make significant progress 

toward doubling natural production of anadromous fish. The CVPIA, in combination with 

other ongoing restoration activities, offers an unprecedented opportunity to correct the 

fishery, wildlife, and habitat problems we face in the Central Valley. We invite and 

encourage your involvement and cooperation to assure successful development and 

implementation of the Anadromous Fish Restoration Program.
PREFACE i

PREFACE

The Central Valley Project Improvement Act (CVPIA), requires the Secretary of the Interior to develop 

and implement Aa 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]). This program is under development and is known as the Anadromous Fish Restoration 

Program (AFRP).

This working paper is the culmination of the initial phase of development of a final AFRP plan. The paper 

presents a package of habitat restoration actions that, if implemented, would achieve the goal of at least 

doubling natural production. It was developed to provide a platform on which the participating agencies 

and the public will develop actions to include in the final plan. Reasonableness was not considered in 

developing this working paper. For the final plan, reasonable actions will be selected from those described 

in this working paper and additional actions suggested by the public, including stakeholders, other interested 

parties, and public and private agencies.

This preface describes how the working paper was developed, how the final AFRP plan will be developed, 

and the process by which Areasonable efforts@ will be identified and included in the final plan.

The final AFRP plan is scheduled for completion by October 31, 1995. The AFRP is proceeding in three 

general phases: 1) production of the working paper, 2) production of the final AFRP plan, and 3) 

implementation of the plan. 

PRODUCTION OF THE WORKING PAPER 

The first phase covers the past efforts up to the release of this working paper. During this period, a coalition 

of senior fish experts from the U.S. Fish and Wildlife Service, U.S. Bureau of Reclamation, National Marine 

Fisheries Service, U.S. Environmental Protection Agency, California Department of Fish and Game, and 

California Department of Water Resources--the ACore Group@--directed the development of the working 

paper. The Core Group formed eight AFRP technical teams. These teams consisted of experts from state 

and federal agencies, private industry, and academia with specific knowledge of anadromous fish species in 

Central Valley rivers and streams. They developed the restoration actions described in this working paper. 

 The AFRP Core Group and USFWS staff then worked with the technical teams to revise the information 

based on the technical merits of the actions in meeting the restoration goals and to standardize format and 
ii WORKING PAPER ON RESTORATION NEEDS

improve readability. Additional guidelines used to develop this paper are found in the CVPIA, the Plan of 

Action for the Central Valley AFRP, and the Draft Position Paper for Development of the AFRP.

To arrive at the most conservative recommendations needed to double natural production of Central Valley 

anadromous fish stocks, and knowing that reasonableness would be addressed later by a broader group, 

the Core Group directed the technical team members to consider only the scientific basis for their 

recommended actions and to recommend actions whose implementation would ensure that production of 

anadromous fish would at least double.

It was clear early in the process of developing the working paper that predicting the benefits of specific 

restoration actions would be limited by available data. For example, fish population estimates were 

developed during the baseline period for other management purposes, and not for developing restoration 

goals. Despite the limitations, we believe the data, along with management models and the highly respected 

professional opinions of the many involved fishery experts, provide sound technical bases for the actions 

contained in this document.

Overall, the package of actions presented in this paper does not yet represent a fully integrated plan (e.g., 

integration of upstream and Delta actions has not been done in this paper). Most flow recommendations 

have been screened to ensure that they do not exceed unimpaired runoff or limits imposed by reservoir 

storage capacity. In some cases, the flow-carryover storage relationships have been evaluated to balance 

the needs of different fish species or stocks. Coordination with the programmatic environmental impact 

statement (PEIS) team has been helpful to clarify and resolve these issues. Further integration and balancing 

are required to develop a comprehensive program that meets the full intent of the CVPIA.

This working paper gives a clear picture of the types and levels of restoration actions necessary to achieve 

the goal of doubling natural production of Central Valley anadromous fish. By using this working paper as 

baseline information, future efforts, including public participation, will evaluate the reasonableness of actions.

PRODUCTION OF THE FINAL AFRP PLAN

The second phase begins with release of the working paper and will extend to completion of the final AFRP 

plan. In this phase, we will prioritize restoration actions and determine what the interested parties and 

agencies consider reasonable efforts. Determination of reasonableness will rely on public participation and 

on the independent analyses of social, economic, and environmental impacts conducted by the PEIS team. 

Reasonable actions will be selected from actions specified in this working paper and additional actions 

suggested by the public, including stakeholders, other interested parties, and public and private agencies.
PREFACE iii

Priority will primarily be based on benefits, costs, and feasibility of restoration actions. High priority will be 

assigned to actions that have the greatest potential to enhance production of anadromous fish at the least 

cost.

The final AFRP plan will include the habitat restoration actions mandated by the CVPIA in Section 3406 

and under the authority of the Secretary of Interior and additional actions deemed reasonable efforts. We 

believe the mandated actions will improve survival and production of Central Valley anadromous fish but 

will not double production without implementation of additional actions specified in this paper.

IMPLEMENTATION OF THE PLAN

The third phase covers implementation and monitoring of the restoration actions and is discussed in more 

detail under the heading AImplementation Considerations@ in Section I, AIntroduction@. This period will 

extend beyond October 31, 1995. We envision that implementation of the actions authorized by the CVPIA 

will occur in phases due to limitations of time, resources, knowledge, funding, and the need to address many 

complex issues surrounding the implementation of the CVPIA. Phased implementation will provide 

opportunities for the public; private, public, and government agencies; and other interested parties to 

participate throughout the implementation process.

In addition, the Secretary of Interior has limited authority to implement the actions described in this working 

paper. Implementation of a comprehensive program will require the support and participation of the public; 

private, public, and government agencies; and other interested parties who have the authority to implement 

those actions not under authority of the Secretary. Limited authority reinforces the need for public support 

to help ensure that the actions in the final AFRP plan will be reasonable.

As implementation of the restoration actions continues, monitoring plans will be designed to assess the 

biological results and effectiveness of the habitat restoration actions. Results of efforts to monitor the 

effectiveness of the first actions to be implemented may be used to modify actions that will be implemented 

later. To avoid duplication and use available resources wisely, monitoring for the AFRP will be coordinated 

with the Comprehensive Assessment and Monitoring Program 3406 (b)(16) and other efforts to monitor 

anadromous fish in the Central Valley and Bay/Delta.

REQUEST FOR COMMENT AND PARTICIPATION

We request timely, constructive comment on this paper from those representing the many public and private 

interests involved with the CVPIA and the AFRP. Many interested parties have already had the 

opportunity to comment on our Plan of Action, Draft Position Paper, and the California Department of 
iv WORKING PAPER ON RESTORATION NEEDS

Fish and Game's Book of Numbers and to participate in public workshops. Your participation is critical to 

successful development of the final plan. 

We have five requests of each reviewer. First, we ask that you review the working paper for technical 

accuracy. If you observe factual errors, please provide corrections and support for your corrections so that 

we can use that information in the final AFRP plan. Second, you may find that an alternative set of actions 

can achieve the same goals as the package of restoration actions described in this working paper. Again, 

describing such alternatives and the justification to support their validity is important. Third, we are looking 

for opportunities to better integrate the upstream and Delta actions and invite assistance in this complex 

process. Fourth, quantifying the benefits of restoration actions is difficult, both individually and in

combination. If you have additional information on the efficacy of specific actions, we would find that 

information useful. Fifth, while not addressed in this working paper, it is important that you convey to us 

how the implementation of the proposed actions, including criteria for reasonableness, would be most 

effectively addressed to achieve the goals of the CVPIA. Your suggested approaches to this important 

process will help all of us in efficiently planning and developing the final plan.

RESPONSIBILITIES

This working paper and the final AFRP plan are the responsibility of the USFWS as lead agency for the 

AFRP. The USFWS is indebted to the assistance of the technical teams and Core Group members; 

however, this working paper does not necessarily reflect a commitment by any member's agency or 

organization to implement any of the restoration actions noted herein. In that light, the reader should view 

this paper as a reference document whose contents will be modified and improved as we move toward the 

completion of a final, comprehensive restoration plan. Successful completion of the final plan will depend on 

the continued guidance of the Core Group and technical team members, participation of the public and 

interested parties, and support of involved state and federal agencies.
ACKNOWLEDGMENTS i

ACKNOWLEDGMENTS

We thank the following members of the Anadromous Fish Restoration Program's Core Group and 

Technical Teams for their contributions toward completion of this report:

Core Group

Randy Brown..................................................................................................................DWR

Jim Bybee.....................................................................................................................NMFS

Roger Guinee............................................................................................................. USFWS

Susan Hatfield.................................................................................................................. EPA

Marty Kjelson............................................................................................................ USFWS

Ken Lentz......................................................................................................................USBR

Terry Mills.......................................................................................................................DFG

Larry Puckett...................................................................................................................DFG

Jim Smith................................................................................................................... USFWS

Mainstem Sacramento River Salmon and Steelhead Technical Team

Serge Birk .....................................................................................................................USBR

Frank Fisher ....................................................................................................................DFG

Ralph Hinton...................................................................................................................DWR

Rich Johnson.............................................................................................................. USFWS

Keith Marine...............................................................................Vogel Environmental Services

Harry Rectenwald ............................................................................................................DFG

Roger Wolcott..............................................................................................................NMFS

Upper Sacramento River Tributaries Salmon and Steelhead Technical Team

Pat Bigelow............................................................................................................... USFWS

Serge Birk .....................................................................................................................USBR

Stacy Cepello .................................................................................................................DWR

Steve Croci................................................................................................................ USFWS

Ralph Hinton...................................................................................................................DWR

Dave Hoopaugh...............................................................................................................DFG

Spencer Hovekamp .......................................................................................................USBR

Paul Maslin........................................................................... California State University, Chico

Harry Rectenwald ............................................................................................................DFG

Curtis Steitz........................................................................................... Pacific Gas & Electric

Paul Ward .......................................................................................................................DFG
ii WORKING PAPER ON RESTORATION NEEDS

Lower Sacramento River and Delta Tributaries Salmon and Steelhead Technical Team

Dawne Becker.................................................................................................................DFG

Paul Bratovich........................................................................................ Beak Consultants Inc.

Mike Bryan............................................................................................ Beak Consultants Inc.

Dan Castleberry......................................................................................................... USFWS

Roger Guinee............................................................................................................. USFWS

Joe Miyamoto.......................................................................East Bay Municipal Utility District

John Nelson.....................................................................................................................DFG

Kate Puckett..................................................................................................................USBR

Ted Sommer...................................................................................................................DWR

Nick Villa ........................................................................................................................DFG

San Joaquin Basin Salmon and Steelhead Technical Team

Dale Hoffman-Floerke ....................................................................................................DWR

Ken Lentz......................................................................................................................USBR

Bill Loudermilk.................................................................................................................DFG

Carl Mesick....................................................................................... Carl Mesick Consultants

Mindy Nelson..................................................................................... Stanislaus River Council

Gary Taylor............................................................................................................... USFWS

John Wullschleger...................................................................................................... USFWS

Sacramento-San Joaquin Delta Salmon and Steelhead Technical Team

Jim Arthur......................................................................................................................USBR

Pat Brandes............................................................................................................... USFWS

Darryl Hayes...................................................................................................................DWR

Bill Kier...............................................................................................William M. Kier Assoc.

Striped Bass Technical Team

Jim Arthur......................................................................................................................USBR

Loo Botsford..............................................................................University of California, Davis

Chuck Hanson.......................................................................................Hanson Environmental

Dave Kohlhorst................................................................................................................DFG

Larry Stenger.......................................................................Striped Bass Advisory Committee

Don Stevens ....................................................................................................................DFG

American Shad Technical Team

Phil Dunn................................................................................Jones & Stokes Associates, Inc.

Roger Guinee............................................................................................................. USFWS

Mike Meinz .....................................................................................................................DFG

Dick Painter.....................................................................................................................DFG

Ted Sommer...................................................................................................................DWR
ACKNOWLEDGMENTS iii

Lynn Wixom....................................................................................................................DFG

John Wullschleger...................................................................................................... USFWS

Sturgeon Technical Team

Kurt Brown ............................................................................................................... USFWS

Dan Castleberry......................................................................................................... USFWS

Jim De Staso.............................................................................................................. USFWS

Serge Doroshov..........................................................................University of California, Davis

Patrick Foley..............................................................................University of California, Davis

Dave Kohlhorst................................................................................................................DFG

We thank Jones & Stokes Associates, especially Victoria Axiaq, for compiling sections on historic and 

existing conditions, problems, and management factors for Central Valley anadromous fishes and for 

technical editing and formatting the report.

Thanks also to the following biologists and staff at the Sacramento-San Joaquin Estuary Fishery 

Resource Office for their time and energy in reviewing, organizing and compiling this report: Kathy 

Corbin, John Icanberry, Dave Kieckbusch, Yvette Leatherman, Sam Lohr, and Gary Rensink.

Special thanks to the following who improved this document by providing insightful comments and 

criticism: Larry Brown, USGS; Frank Fisher, DFG; Andy Hamilton, USFWS; and Jim McKevitt, 

USFWS.
TABLE OF CONTENTS ix

TABLE OF CONTENTS

VOLUME 1

LETTER FROM THE AFRP CORE GROUP TO WAYNE WHITE

LETTER FROM DALE HALL AND WAYNE WHITE

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

ACKNOWLEDGMENTS ..............................................................................................................v 

SECTION I. INTRODUCTION TO THE WORKING PAPER.......................................... 1-I-1

CENTRAL VALLEY PROJECT IMPROVEMENT ACT............................................. 1-I-1

SECTION 3406............................................................................................................. 1-I-2

IMPLEMENTATION CONSIDERATIONS................................................................. 1-I-4

Prioritizing Actions .............................................................................................. 1-I-4

Tools Available to the Secretary of Interior for Implementing Actions ................... 1-I-4

Tools in the CVPIA ................................................................................ 1-I-4

Tools for use on CVP vs. non-CVP streams............................................ 1-I-6

Cooperation with others.......................................................................... 1-I-7

Schedule for Implementation................................................................................ 1-I-7

Structural modifications ........................................................................... 1-I-7

Water management modifications............................................................. 1-I-8

Operational modifications........................................................................ 1-I-9

EVALUATION OF FLOW NEEDS.............................................................................. 1-I-9

Relations between Flows and Anadromous Fish Populations................................ 1-I-9

Difficulties in Evaluating Flow Needs.................................................................. 1-I-10

Flow evaluation methods....................................................................... 1-I-10

Approaches Taken by Technical Teams............................................................. 1-I-13

Chinook salmon and steelhead............................................................... 1-I-13

Striped bass, American shad, white and green sturgeon.......................... 1-I-14

SECTION II. SUMMARY OF RESTORATION GOALS .................................................1-II-1

SECTION III. SUMMARY OF LIMITING FACTORS...................................................1-III-1

SECTION IV. SUMMARY OF RESTORATION ACTIONS...........................................1-IV-1

INTRODUCTION.......................................................................................................1-IV-1
x WORKING PAPER ON RESTORATION NEEDS

SACRAMENTO RIVER BASIN.................................................................................1-IV-1

Upper Mainstem Sacramento River...................................................................1-IV-1

UPPER SACRAMENTO RIVER TRIBUTARIES.......................................................1-IV-5

Clear Creek......................................................................................................1-IV-5

Cow Creek.......................................................................................................1-IV-6

Bear Creek.......................................................................................................1-IV-6

Cottonwood Creek...........................................................................................1-IV-7

Battle Creek .....................................................................................................1-IV-7

Paynes Creek ...................................................................................................1-IV-9

Antelope Creek ................................................................................................1-IV-9

Elder Creek....................................................................................................1-IV-10

Mill Creek ......................................................................................................1-IV-10

Thomes Creek................................................................................................1-IV-11

Deer Creek.....................................................................................................1-IV-12

Stony Creek ...................................................................................................1-IV-12

Big Chico Creek.............................................................................................1-IV-14

Butte Creek....................................................................................................1-IV-15

Colusa Basin Drain..........................................................................................1-IV-20

Miscellaneous small tributaries.........................................................................1-IV-20

LOWER SACRAMENTO RIVER AND DELTA TRIBUTARIES ............................1-IV-22

Feather River..................................................................................................1-IV-22

Yuba River.....................................................................................................1-IV-26

Bear River......................................................................................................1-IV-29

American River...............................................................................................1-IV-31

Mokelumne River............................................................................................1-IV-33

Cosumnes River..............................................................................................1-IV-36

Calaveras River...............................................................................................1-IV-37

SACRAMENTO-SAN JOAQUIN DELTA...............................................................1-IV-39

SAN JOAQUIN RIVER BASIN ...............................................................................1-IV-43

Lower San Joaquin River Tributaries...............................................................1-IV-43

Merced River......................................................................................1-IV-43

Tuolumne River...................................................................................1-IV-45

Stanislaus River...................................................................................1-IV-47

Lower San Joaquin River....................................................................1-IV-49
TABLE OF CONTENTS xi

VOLUME 2

INTRODUCTION TO VOLUME 2 ........................................................._______lrn

SECTION V. DESCRIPTION OF CENTRAL VALLEY 

 RIVERS AND STREAMS..................................................................................................2-V-1

SACRAMENTO BASIN..............................................................................................2-V-1

Upper Mainstem Sacramento River....................................................................2-V-1

Upper Sacramento River Tributaries...................................................................2-V-1

Clear Creek...........................................................................................2-V-1

Cow Creek............................................................................................2-V-1

Bear Creek ...........................................................................................2-V-2

Cottonwood Creek................................................................................2-V-2

Battle Creek ..........................................................................................2-V-2

Paynes Creek ........................................................................................2-V-3

Antelope Creek .....................................................................................2-V-3

Elder Creek...........................................................................................2-V-3

Mill Creek .............................................................................................2-V-4

Thomes Creek.......................................................................................2-V-4

Deer Creek............................................................................................2-V-4

Stony Creek ..........................................................................................2-V-5

Big Chico Creek....................................................................................2-V-5

Big Chico Creek tributaries -- Mud and Rock Creeks............................2-V-5

Butte Creek...........................................................................................2-V-6

Colusa Basin Drain.................................................................................2-V-6

Miscellaneous small tributaries................................................................2-V-7

North westside tributaries.....................................................................2-V-10

Lower Sacramento River and Delta Tributaries.................................................2-V-11

Feather River.......................................................................................2-V-11

Yuba River..........................................................................................2-V-12

Bear River...........................................................................................2-V-12

American River....................................................................................2-V-12

Mokelumne River.................................................................................2-V-13

Cosumnes River...................................................................................2-V-13

Calaveras River....................................................................................2-V-14

SAN JOAQUIN RIVER BASIN ................................................................................2-V-14

Lower Mainstem San Joaquin River..................................................................2-V-14

Lower San Joaquin River Tributaries................................................................2-V-15
xii WORKING PAPER ON RESTORATION NEEDS

Merced River.......................................................................................2-V-15

Tuolumne River....................................................................................2-V-15

Stanislaus River....................................................................................2-V-16

SACRAMENTO-SAN JOAQUIN DELTA................................................................2-V-16

SECTION VI. CENTRAL VALLEY ANADROMOUS FISHES - HISTORIC AND

 EXISTING CONDITIONS................................................................................................2-VI-1

LIFE HISTORIES........................................................................................................2-VI-1

Chinook Salmon...............................................................................................2-VI-1

Upstream migration and spawning..........................................................2-VI-1

Incubation.............................................................................................2-VI-2

Rearing.................................................................................................2-VI-3

Downstream migration...........................................................................2-VI-3

Ocean life .............................................................................................2-VI-4

Steelhead..........................................................................................................2-VI-4

Upstream migration...............................................................................2-VI-4

Spawning..............................................................................................2-VI-5

Incubation.............................................................................................2-VI-5

Rearing.................................................................................................2-VI-6

Downstream migration...........................................................................2-VI-6

Ocean life .............................................................................................2-VI-6

Striped Bass.....................................................................................................2-VI-6

Upstream migration and spawning..........................................................2-VI-6

Incubation.............................................................................................2-VI-7

Rearing.................................................................................................2-VI-7

Estuarine and ocean migration................................................................2-VI-8

American Shad .................................................................................................2-VI-8

Upstream migration and spawning..........................................................2-VI-9

Incubation...........................................................................................2-VI-10

Rearing...............................................................................................2-VI-10

Downstream migration.........................................................................2-VI-11

Ocean life ...........................................................................................2-VI-11

White Sturgeon...............................................................................................2-VI-11

Upstream migration.............................................................................2-VI-11

Spawning............................................................................................2-VI-12

Incubation...........................................................................................2-VI-13

Rearing...............................................................................................2-VI-13

Downstream, estuarine, and ocean migration........................................2-VI-14

Green Sturgeon...............................................................................................2-VI-15

Upstream migration.............................................................................2-VI-16
TABLE OF CONTENTS xiii

Spawning............................................................................................2-VI-18

Incubation...........................................................................................2-VI-19

Rearing...............................................................................................2-VI-19

Downstream, estuarine, and ocean migration........................................2-VI-19

ABUNDANCE AND DISTRIBUTION (PRE-1967).................................................2-VI-19

Chinook Salmon.............................................................................................2-VI-19

Sacramento River................................................................................2-VI-20

Sacramento River tributaries................................................................2-VI-21

Feather River basin .............................................................................2-VI-21

Eastside tributaries..............................................................................2-VI-21

San Joaquin River...............................................................................2-VI-22

San Joaquin River tributaries................................................................2-VI-22

Steelhead........................................................................................................2-VI-23

Sacramento River................................................................................2-VI-23

Sacramento River tributaries................................................................2-VI-23

Feather and Yuba Rivers.....................................................................2-VI-23

Eastside tributaries..............................................................................2-VI-24

San Joaquin River...............................................................................2-VI-24

San Joaquin River tributaries................................................................2-VI-24

Striped Bass...................................................................................................2-VI-24

American Shad ...............................................................................................2-VI-25

White Sturgeon...............................................................................................2-VI-26

Green Sturgeon...............................................................................................2-VI-29

ABUNDANCE AND DISTRIBUTION (1967-1991)................................................2-VI-29

Chinook Salmon.............................................................................................2-VI-29

Sacramento River................................................................................2-VI-29

Sacramento River tributaries................................................................2-VI-30

Feather River......................................................................................2-VI-31

Eastside tributaries..............................................................................2-VI-31

San Joaquin River and tributaries.........................................................2-VI-31

Steelhead........................................................................................................2-VI-32

Sacramento River................................................................................2-VI-32

Sacramento River tributaries................................................................2-VI-32

Feather River .....................................................................................2-VI-33

Yuba River ........................................................................................2-VI-33

Eastside tributaries..............................................................................2-VI-33

San Joaquin River and tributaries.........................................................2-VI-33

Striped Bass...................................................................................................2-VI-33

American Shad ...............................................................................................2-VI-34

White Sturgeon...............................................................................................2-VI-35
xiv WORKING PAPER ON RESTORATION NEEDS

Green Sturgeon...............................................................................................2-VI-39

ENVIRONMENTAL REQUIREMENTS ..................................................................2-VI-39

Chinook Salmon.............................................................................................2-VI-39

Upstream migration.............................................................................2-VI-39

Spawning............................................................................................2-VI-39

Incubation...........................................................................................2-VI-40

Rearing...............................................................................................2-VI-40

Downstream migration.........................................................................2-VI-41

Ocean life ...........................................................................................2-VI-41

Steelhead........................................................................................................2-VI-42

Upstream migration.............................................................................2-VI-42

Spawning............................................................................................2-VI-42

Incubation...........................................................................................2-VI-43

Rearing...............................................................................................2-VI-43

Juvenile downstream migration.............................................................2-VI-44

Ocean life ...........................................................................................2-VI-44

Striped Bass...................................................................................................2-VI-45

Upstream migration.............................................................................2-VI-45

Spawning............................................................................................2-VI-45

Incubation...........................................................................................2-VI-45

Rearing...............................................................................................2-VI-46

American Shad ...............................................................................................2-VI-46

Upstream migration and spawning........................................................2-VI-46

Incubation...........................................................................................2-VI-47

Rearing...............................................................................................2-VI-47

Downstream migration.........................................................................2-VI-47

White Sturgeon...............................................................................................2-VI-47

Upstream migration.............................................................................2-VI-47

Spawning............................................................................................2-VI-48

Incubation...........................................................................................2-VI-48

Rearing...............................................................................................2-VI-49

Downstream migration.........................................................................2-VI-49

Green Sturgeon...............................................................................................2-VI-50

SECTION VII. PROBLEMS FOR CENTRAL VALLEY ANADROMOUS 

 FISHES ............................................................................................................................. 2-VII-1

CHINOOK SALMON.............................................................................................. 2-VII-1

General Problems............................................................................................ 2-VII-1

Upstream migration............................................................................. 2-VII-1

Spawning............................................................................................ 2-VII-1

Rearing............................................................................................... 2-VII-1
TABLE OF CONTENTS xv

Sacramento River............................................................................................ 2-VII-2

Upstream migration and spawning........................................................ 2-VII-2

Incubation........................................................................................... 2-VII-4

Rearing............................................................................................... 2-VII-5

Downstream migration......................................................................... 2-VII-6

Diversions........................................................................................... 2-VII-7

Predation............................................................................................ 2-VII-9

Yuba River..................................................................................................... 2-VII-9

Downstream migration......................................................................... 2-VII-9

Eastside Tributaries......................................................................................... 2-VII-9

Upstream migration........................................................................... 2-VII-10

Spawning.......................................................................................... 2-VII-10

Incubation......................................................................................... 2-VII-10

Rearing............................................................................................. 2-VII-11

Downstream migration....................................................................... 2-VII-11

San Joaquin River ........................................................................................ 2-VII-12

Upstream migration and spawning...................................................... 2-VII-12

Rearing............................................................................................. 2-VII-12

Downstream migration....................................................................... 2-VII-12

San Joaquin River Tributaries........................................................................ 2-VII-13

Upstream migration and spawning...................................................... 2-VII-13

Rearing............................................................................................. 2-VII-14

Delta/Bay...................................................................................................... 2-VII-14

Upstream migration........................................................................... 2-VII-14

Downstream migration....................................................................... 2-VII-14

Entrainment....................................................................................... 2-VII-15

Water temperature............................................................................ 2-VII-16

Predation.......................................................................................... 2-VII-16

Suisun Marsh Salinity Control Structure............................................. 2-VII-16

STEELHEAD........................................................................................................... 2-VII-16

General Problems.......................................................................................... 2-VII-16

Upstream migration, spawning, and incubation................................... 2-VII-16

Rearing and downstream migration.................................................... 2-VII-16

Sacramento River.......................................................................................... 2-VII-17

Upstream migration and spawning...................................................... 2-VII-17

Downstream migration....................................................................... 2-VII-18

Sacramento River Tributaries......................................................................... 2-VII-18

San Joaquin River and Tributaries.................................................................. 2-VII-18

Delta/Bay...................................................................................................... 2-VII-18

STRIPED BASS ...................................................................................................... 2-VII-21
xvi WORKING PAPER ON RESTORATION NEEDS

General Problems.......................................................................................... 2-VII-21

Stock-recruitment and other life stage relationships............................. 2-VII-21

Decreased fecundity and fertility........................................................ 2-VII-22

Flow and water temperature.............................................................. 2-VII-22

Habitat.............................................................................................. 2-VII-22

Toxic substances............................................................................... 2-VII-22

Competition and predation................................................................ 2-VII-23

Prey availability................................................................................. 2-VII-23

Sacramento River.......................................................................................... 2-VII-24

Flow................................................................................................. 2-VII-24

Toxic substances............................................................................... 2-VII-24

San Joaquin River......................................................................................... 2-VII-25

Delta/Bay...................................................................................................... 2-VII-25

Flow................................................................................................. 2-VII-25

Salinity.............................................................................................. 2-VII-26

Diversions......................................................................................... 2-VII-26

Entrainment....................................................................................... 2-VII-28

Toxic substances............................................................................... 2-VII-30

Habitat.............................................................................................. 2-VII-30

AMERICAN SHAD ................................................................................................ 2-VII-31

General Problems.......................................................................................... 2-VII-31

Flow and water temperature.............................................................. 2-VII-31

Diversions......................................................................................... 2-VII-32

Habitat.............................................................................................. 2-VII-32

Toxic materials.................................................................................. 2-VII-32

Competition and predation................................................................ 2-VII-33

Prey availability................................................................................. 2-VII-33

Sacramento River.......................................................................................... 2-VII-33

San Joaquin River......................................................................................... 2-VII-35

Delta/Bay...................................................................................................... 2-VII-35

Flow................................................................................................. 2-VII-35

Salinity.............................................................................................. 2-VII-36

Entrainment....................................................................................... 2-VII-36

Habitat.............................................................................................. 2-VII-37

Prey availability................................................................................. 2-VII-38

WHITE STURGEON............................................................................................... 2-VII-38

Flows........................................................................................................... 2-VII-38

Diversions..................................................................................................... 2-VII-38

Water Quality............................................................................................... 2-VII-39

Predation...................................................................................................... 2-VII-39

Migration Barriers......................................................................................... 2-VII-39
TABLE OF CONTENTS xvii

GREEN STURGEON.............................................................................................. 2-VII-40

SECTION VIII. MANAGEMENT FACTORS ...............................................................2-VIII-1

AUTHORITIES AND AGENCY RESPONSIBILITIES...........................................2-VIII-1

Federal Role ..................................................................................................2-VIII-1

State Role......................................................................................................2-VIII-5

Local Agency Role.........................................................................................2-VIII-8

Federal Agencies and Statutes........................................................................2-VIII-8

State Agencies and Statutes..........................................................................2-VIII-10

PUBLIC TRUST DOCTRINE................................................................................2-VIII-12

CHINOOK SALMON...........................................................................................2-VIII-14

Harvest........................................................................................................2-VIII-14

Fish Resource Agency Policy/Goals..............................................................2-VIII-15

Classification and management system..............................................2-VIII-15

Salmon and steelhead stream classification system terms....................2-VIII-16

Hatchery/Production Facility Practices..........................................................2-VIII-17

Hatchery production.........................................................................2-VIII-17

Release practices.............................................................................2-VIII-18

Hatchery contribution to ocean fishery..............................................2-VIII-19

Effects of hatchery production on natural production.........................2-VIII-19

STEELHEAD..........................................................................................................2-VIII-19

Harvest........................................................................................................2-VIII-19

Fish Resource Agency Policy/Goals..............................................................2-VIII-20

Hatchery/Production Facility Practices..........................................................2-VIII-20

STRIPED BASS .....................................................................................................2-VIII-22

Harvest........................................................................................................2-VIII-22

Fish Resource Agency Policy/Goals..............................................................2-VIII-22

Hatchery/Production Facility Practices..........................................................2-VIII-27

AMERICAN SHAD ...............................................................................................2-VIII-28

Harvest........................................................................................................2-VIII-28

Fish Resource Agency Policy/Goals..............................................................2-VIII-28

Hatchery/Production Facility Practices..........................................................2-VIII-29

WHITE STURGEON..............................................................................................2-VIII-29

Harvest........................................................................................................2-VIII-29

Fish Resource Agency Policy/Goals..............................................................2-VIII-30

Hatchery/Production Facility Practices..........................................................2-VIII-30

GREEN STURGEON.............................................................................................2-VIII-31

Harvest........................................................................................................2-VIII-31

Fish Resource Agency Policy/Goals..............................................................2-VIII-31
xviii WORKING PAPER ON RESTORATION NEEDS

SECTION IX. KEY AFRP DOCUMENTS.........................................................................2-IX-1

PROCESS OF DEVELOPMENT FOR THE AFRP....................................................2-IX-1

Introduction and Purpose of the Central Valley Anadromous Fish 

 Restoration Program, Plan of Action, May 1994...........................................2-IX-1

Participants.......................................................................................................2-IX-2

General Approach to Development of the AFRP ...............................................2-IX-2

Restoration Goal and Program Evaluation..........................................................2-IX-3

Relationship to Other CVPIA Investigations, the Programmatic EIS, 

 and Other Ongoing Activities.........................................................................2-IX-3

Compliance with the National Environmental Policy Act and the 

 Endangered Species Act ...............................................................................2-IX-4

Public Involvement ............................................................................................2-IX-5

GUIDING PRINCIPLES AND ASSUMPTIONS.......................................................2-IX-5
TABLE OF CONTENTS xix

VOLUME 3

SECTION X. REPORTS FROM THE TECHNICAL TEAMS.........................................3-X-1

INTRODUCTION........................................................................................................3-X-1

A. CHINOOK SALMON AND STEELHEAD.........................................................3-Xa-1

Baseline Natural Production and Goals.............................................................3-Xa-1

Chinook salmon...................................................................................3-Xa-1

Steelhead.............................................................................................3-Xa-3

Upper Mainstem Sacramento River..................................................................3-Xa-3

Limiting factors and potential solutions ..................................................3-Xa-3

Restoration actions.............................................................................3-Xa-13

B. UPPER SACRAMENTO RIVER TRIBUTARIES ................................................3-Xb-1

Clear Creek.....................................................................................................3-Xb-1

Limiting factors and potential solutions ..................................................3-Xb-1

Restoration actions...............................................................................3-Xb-2

Cow Creek....................................................................................................3-Xb-10

Limiting factors and potential solutions ................................................3-Xb-10

Restoration actions.............................................................................3-Xb-12

Bear Creek....................................................................................................3-Xb-14

Limiting factors and potential solutions ................................................3-Xb-14

Restoration actions.............................................................................3-Xb-15

Cottonwood Creek........................................................................................3-Xb-16

Limiting factors and potential solutions ................................................3-Xb-16

Restoration actions.............................................................................3-Xb-17

Battle Creek ..................................................................................................3-Xb-19

Limiting factors and potential solutions ................................................3-Xb-19

Restoration actions.............................................................................3-Xb-21

Paynes Creek ................................................................................................3-Xb-32

Limiting factors and potential solutions ................................................3-Xb-32

Restoration actions.............................................................................3-Xb-32

Antelope Creek .............................................................................................3-Xb-33

Limiting factors and potential solutions ................................................3-Xb-33

Restoration actions.............................................................................3-Xb-34

Elder Creek...................................................................................................3-Xb-35

Limiting factors and potential solutions ................................................3-Xb-35

Restoration actions.............................................................................3-Xb-36

Mill Creek .....................................................................................................3-Xb-38

Limiting factors and potential solutions ................................................3-Xb-38

Restoration actions.............................................................................3-Xb-39
xx WORKING PAPER ON RESTORATION NEEDS

Thomes Creek...............................................................................................3-Xb-43

Limiting factors and potential solutions ................................................3-Xb-43

Restoration actions.............................................................................3-Xb-44

Deer Creek....................................................................................................3-Xb-49

Limiting factors and potential solutions ................................................3-Xb-49

Restoration actions.............................................................................3-Xb-51

Stony Creek ..................................................................................................3-Xb-56

Limiting factors and potential solutions ................................................3-Xb-56

Restoration actions.............................................................................3-Xb-60

Big Chico Creek............................................................................................3-Xb-68

Limiting factors and potential solutions ................................................3-Xb-68

Restoration actions.............................................................................3-Xb-71

Butte Creek...................................................................................................3-Xb-78

Limiting factors and potential solutions ................................................3-Xb-78

Restoration actions.............................................................................3-Xb-82

Colusa Basin drain .......................................................................................3-Xb-111

Limiting factors and potential solutions ..............................................3-Xb-111

Restoration actions...........................................................................3-Xb-112

Miscellaneous small tributaries......................................................................3-Xb-114

Limiting factors and potential solutions ..............................................3-Xb-114

Restoration actions...........................................................................3-Xb-115

C. LOWER SACRAMENTO RIVER AND DELTA TRIBUTARIES........................3-Xc-1

Approach........................................................................................................3-Xc-1

Feather River...................................................................................................3-Xc-2

Limiting factors and potential solutions ..................................................3-Xc-2

Restoration actions...............................................................................3-Xc-5

Yuba River....................................................................................................3-Xc-12

Limiting factors and potential solutions ................................................3-Xc-12

Restoration actions.............................................................................3-Xc-14

Bear River.....................................................................................................3-Xc-30

Limiting factors and potential solutions ................................................3-Xc-30

Restoration actions.............................................................................3-Xc-31

American River..............................................................................................3-Xc-37

Limiting factors and potential solutions ................................................3-Xc-37

Restoration actions.............................................................................3-Xc-40

Mokelumne River...........................................................................................3-Xc-60

Limiting factors and potential solutions ................................................3-Xc-60

Restoration actions.............................................................................3-Xc-64

Cosumnes River.............................................................................................3-Xc-80

Limiting factors and potential solutions ................................................3-Xc-80

Restoration actions.............................................................................3-Xc-80
TABLE OF CONTENTS xxi

Calaveras River..............................................................................................3-Xc-86

Limiting factors and potential solutions ................................................3-Xc-86

Restoration actions.............................................................................3-Xc-88

D. SAN JOAQUIN BASIN.......................................................................................3-Xd-1

Development of Flow Recommendations..........................................................3-Xd-1

Vernalis flow........................................................................................3-Xd-1

Tributary flow recommendations...........................................................3-Xd-3

Merced River...................................................................................................3-Xd-5

Limiting factors and potential solutions ..................................................3-Xd-5

Restoration actions...............................................................................3-Xd-8

Tuolumne River..............................................................................................3-Xd-18

Limiting factors and potential solutions ................................................3-Xd-18

Restoration actions.............................................................................3-Xd-21

Stanislaus River..............................................................................................3-Xd-31

Limiting factors and potential solutions ................................................3-Xd-31

Restoration actions.............................................................................3-Xd-33

Mainstem San Joaquin River...........................................................................3-Xd-42

Limiting factors and potential solutions ................................................3-Xd-42

Restoration actions.............................................................................3-Xd-46

E. SACRAMENTO-SAN JOAQUIN DELTA ..........................................................3-Xe-1

General Approach............................................................................................3-Xe-1

Limiting factors and potential solutions ..............................................................3-Xe-5

Restoration actions.........................................................................................3-Xe-10

F. STRIPED BASS.....................................................................................................3-Xf-1

Baseline Natural Production and Goals..............................................................3-Xf-1

Goals....................................................................................................3-Xf-2

Outflow, export, and stocking considerations.........................................3-Xf-2

Restoration Actions...........................................................................................3-Xf-8

G. AMERICAN SHAD...............................................................................................3-Xg-1

Baseline Period Production and Production Goals.............................................3-Xg-1

Goal....................................................................................................3-Xg-2

Basis for flow recommendations ...........................................................3-Xg-2

Sacramento River Basin - Upper Mainstem Sacramento River..........................3-Xg-3

Limiting factors and potential solutions ..................................................3-Xg-3

Restoration actions...............................................................................3-Xg-4

Lower Sacramento River and Delta Tributaries.................................................3-Xg-6

Limiting factors and potential solutions ..................................................3-Xg-6

Restoration actions...............................................................................3-Xg-6

Feather River...................................................................................................3-Xg-7

Limiting factors and potential solutions ..................................................3-Xg-7
xxii WORKING PAPER ON RESTORATION NEEDS

Restoration actions...............................................................................3-Xg-8

Yuba River......................................................................................................3-Xg-9

Limiting factors and potential solutions ..................................................3-Xg-9

Restoration actions.............................................................................3-Xg-10

American River..............................................................................................3-Xg-12

Limiting factors and potential solutions ................................................3-Xg-12

Restoration actions.............................................................................3-Xg-12

Mokelumne River...........................................................................................3-Xg-13

Limiting factors and potential solutions ................................................3-Xg-13

Restoration actions.............................................................................3-Xg-13

Sacramento-San Joaquin Delta.......................................................................3-Xg-15

Limiting factors and potential solutions ................................................3-Xg-15

Restoration actions.............................................................................3-Xg-16

San Joaquin River..........................................................................................3-Xg-18

Limiting factors and potential solutions ................................................3-Xg-18

Restoration actions.............................................................................3-Xg-19

Lower San Joaquin River Tributaries - Stanislaus River ..................................3-Xg-21

Limiting factors and potential solutions ................................................3-Xg-21

H. WHITE AND GREEN STURGEON.....................................................................3-Xh-1

Baseline Natural Production and Goals.............................................................3-Xh-1

White sturgeon tagging and data analysis...............................................3-Xh-1

Green sturgeon tagging and data analysis...............................................3-Xh-2

Approach........................................................................................................3-Xh-3

Research Needs...............................................................................................3-Xh-5

Sacramento River.............................................................................................3-Xh-5

Limiting factors and potential solutions ..................................................3-Xh-5

Restoration actions...............................................................................3-Xh-7

Feather River.................................................................................................3-Xh-15

Limiting factors and potential solutions ................................................3-Xh-15

Restoration actions.............................................................................3-Xh-16

Bear River.....................................................................................................3-Xh-25

Limiting factors and potential solutions ................................................3-Xh-25

Restoration actions.............................................................................3-Xh-26

San Joaquin River..........................................................................................3-Xh-32

Limiting factors and potential solutions ................................................3-Xh-32

Restoration actions.............................................................................3-Xh-34

Sacramento-San Joaquin Delta.......................................................................3-Xh-43

Limiting factors and potential solutions ................................................3-Xh-43

Restoration actions.............................................................................3-Xh-44

SECTION XI. CITATIONS..................................................................................................3-X-1
TABLE OF CONTENTS xxiii

PRINTED REFERENCES ............................................................................................3-X-1

PERSONAL COMMUNICATIONS .........................................................................3-X-41
SECTION I. INTRODUCTION TO THE WORKING PAPER -

CENTRAL VALLEY PROJECT IMPROVEMENT ACT 1-I-1

SECTION I. INTRODUCTION TO THE WORKING PAPER

CENTRAL VALLEY PROJECT IMPROVEMENT ACT

This Working Paper discusses habitat restoration actions believed necessary to double the natural 

production of chinook salmon, steelhead, striped bass, American shad, and white and green sturgeon in the 

rivers and streams of California's Central Valley. The legal guidelines used to develop this paper can be 

found in the implementing legislation of the Central Valley Project Improvement Act (CVPIA), which is 

described below.

On October 30, 1992, the President signed into law the Reclamation Projects Authorization and 

Adjustment Act of 1992 (Public Law 102-575), including Title XXXIV, the CVPIA. The CVPIA amends 

the authorization of the Department of the Interior's California Central Valley Project (CVP) to include fish 

and wildlife protection, restoration, and mitigation as project purposes having equal priority with irrigation 

and domestic uses and fish and wildlife enhancement as a purpose equal to power generation. The CVPIA 

identifies several specific measures to meet these new purposes and sets a broad goal of sustaining natural 

populations of anadromous fishes produced in Central Valley rivers and streams at double their recent 

average levels. The CVPIA also directs the Secretary of the Interior to operate the CVP consistent with 

these purposes, to meet the federal trust responsibilities to protect the fishery resources of affected federally 

recognized Indian tribes, and to meet all requirements of federal and California law.

The Department of the Interior is developing policies and programs to modify the operations, management, 

and physical facilities of the CVP to comply with the purposes and goals of the CVPIA and the revised 

purposes of the CVP. These policies and programs will define operational criteria and management and 

structural priorities for the CVP. The general purposes of the CVPIA, and of the action proposed by the 

Secretary of the Interior, were identified by Congress in Section 3402:

(a) to protect, restore, and enhance fish, wildlife, and associated habitats in the Central 

Valley and Trinity River basins of California;

(b) to address impacts of the CVP on fish, wildlife, and associated habitats;

(c) to improve the operational flexibility of the CVP;

(d) to increase water-related benefits provided by the CVP to the State of California 

through expanded use of voluntary water transfers and improved water conservation;
1-I-2 WORKING PAPER ON RESTORATION NEEDS

(e) to contribute to the State of California's interim and long-term efforts to protect the San 

Francisco Bay/Sacramento-San Joaquin Delta estuary; and 

(f) to achieve a reasonable balance among competing demands for use of CVP water, 

including the requirements of fish and wildlife, agriculture, municipal and industrial, and 

power contractors.

In addition, the CVPIA includes several specific and general measures, including the requirement to double 

natural production of anadromous fish, that, when implemented, will satisfy the purposes of the CVPIA and 

the revised purposes of the CVP.

These purposes respond to the need to improve the existing water management practices of the CVP. Fish 

and wildlife populations and the condition and extent of their habitats have declined drastically from 

historical levels. Construction and operation of the CVP have contributed to these declines and to the 

decline in water quality and other environmental conditions in the Sacramento-San Joaquin Delta (Delta). In 

recent years, the pattern of demand for water in California has changed; in particular, municipal and 

industrial demand has increased. Under previous laws and existing policies, CVP operations have been 

constrained from fully responding to these changing demands and priorities. As a result, existing operations 

do not display adequate flexibility or reflect a reasonable balance among competing demands. Despite 

these adverse effects, CVP facilities offer tremendous opportunities to restore fish populations and their 

associated habitats in numerous major California waterways. These opportunities are fully embodied in the 

CVPIA.

SECTION 3406

This document was developed under the authority of HR 429, Title 34 - Central Valley Project 

Improvement Act, and specifically Section 3406(b)(1):

FISH AND WILDLIFE RESTORATION ACTIVITIES - The Secretary, immediately 

upon enactment of this title, shall operate the Central Valley Project to meet all obligations 

under state and federal law, including but not limited to the federal Endangered Species 

Act, 16 U.S. ' 1531, et seq., and all decisions of the California State Water Resources 

Control Board establishing conditions on applicable licenses and permits for the project. 

The Secretary, in consultation with other State and Federal agencies, Indian tribes, and 

affected interests, is further authorized and directed to:

(1) develop 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-
SECTION 1. INTRODUCTION -

SECTION 3406 1-1-3

1991; Provided, That this goal shall not apply to the San Joaquin River between Friant 

Dam and the Mendota Pool, for which a separate program is authorized under subsection 

3406(c) of this title; Provided further, That the programs and activities authorized by this 

section shall, when fully implemented, be deemed to meet the mitigation, protection, 

restoration, and enhancement purposes established by subsection 3406(a) of this title; And 

provided further, That in the course of developing and implementing this program the 

Secretary shall make all reasonable efforts consistent with the requirements of this section 

to address other identified adverse environmental impacts of the Central Valley Project not 

specifically enumerated in this section.

(A) This 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; 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.

(B) As needed to achieve the goals of this program, the Secretary is authorized and 

directed to modify Central Valley Project operations to provide flows of suitable 

quality, quantity, and timing to protect all life stages of anadromous fish, except that 

such flows shall be provided from the quantity of water dedicated to fish, wildlife, 

and habitat restoration purposes under paragraph (2) of this subsection; from the 

water supplies acquired pursuant to paragraph (3) of this subsection; and from 

other sources which do not conflict with fulfillment of the Secretary's remaining 

contractual obligations to provide Central Valley Project water for other authorized 

purposes. Instream flow needs for all Central Valley Project controlled streams 

and rivers shall be determined by the Secretary based on recommendations of the 

U.S. Fish and Wildlife Service after consultation with the California Department of 

Fish and Game.

(C) The Secretary shall cooperate with the State of California to ensure that, to the 

greatest degree practicable, the specific quantities of yield dedicated to and 

managed for fish and wildlife purposes under this title are credited against any 

additional obligations of the Central Valley Project which may be imposed by the 

State of California following enactment of this title, including but not limited to 

increased flow and reduced export obligations which may be imposed by the 

California State Water Resources Control Board in implementing San Francisco 

Bay/Sacramento-San Joaquin Delta Estuary standards pursuant to the review 

ordered by the California Court of Appeals in U.S. v. State Water Resources 
1-I-4 WORKING PAPER ON RESTORATION NEEDS

Control Board, 182 Cal.App.3rd 82 (1986), and that, to the greatest degree 

practicable, the programs and plans required by this title are developed and 

implemented in a way that avoids inconsistent or duplicative obligations from being 

imposed upon Central Valley Project water and power contractors.

(D) Costs associated with this paragraph shall be reimbursable pursuant to existing 

statutory and regulatory procedures.

IMPLEMENTATION CONSIDERATIONS

Three aspects of implementation are considered here: 1) prioritizing actions, 2) tools available to the 

Secretary of Interior for implementing actions, and 3) schedule for implementation. The implementation 

process provides an opportunity to ensure that the restoration actions taken are reasonable.

Prioritizing Actions

Setting priorities for actions will require public participation. Most prioritization should occur before the 

AFRP plan is completed. To set priorities for actions, criteria for assigning priority to actions must be 

developed. These criteria should assign high priority to actions that are likely to provide the greatest benefit 

to production of anadromous fish, especially those actions that protect and restore natural channel and 

riparian habitat values. Other criteria may include assigning high priority to actions that improve the habitat 

of species that are endangered, threatened, or of special concern; that improve production of multiple 

species; that can be implemented rapidly; that and the Secretary has authority or cooperation from others to 

implement. Actions that are not considered Areasonable efforts@ should not be assigned high priority.

Because not all actions can be implemented simultaneously, an attempt will be made to implement highpriority items first. Monitoring the success of implemented actions will provide information that will help 

reevaluate priorities for remaining actions. The implementation schedule should be flexible so that unique 

opportunities to implement actions can be taken advantage of, even if these actions are not the highest 

priority actions. Because implementation will continue well past the date the AFRP plan is completed, and 

because public participation will be necessary to implement many actions needed to double production of 

anadromous fish, participation will continue throughout the implementation process.
SECTION 1. INTRODUCTION -

SECTION 3406 1-1-5

Tools Available to the Secretary of Interior for Implementing Actions

Tools in the CVPIA - The USFWS anticipates that the tools available to the Secretary of the Interior for 

achieving the goals of the AFRP include implementing all sections of the CVPIA. Sections 3406(b)(2) 

through (21) of the CVPIA authorize and direct the Secretary of Interior to take specific actions. These 

actions have been categorized as structural modifications, water management modifications, and operational 

modifications. Two elements do not fit these categories: element (b)(16), the comprehensive monitoring 

program, and element (b)(19), a reevaluation of carryover storage criteria. A brief description of the 

elements in each of the three categories is listed below. Further details are provided in the CVPIA.

Structural modifications -

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

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

Trap.

3406(b)(12) - 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 Delta Cross Channel and Georgiana Slough.

3406(b)(15) - Install barrier at head of Old River.

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

District Diversion Dam.

3406(b)(20) - Mitigate for the Glenn-Colusa Irrigation District=s Hamilton City Pumping Plant.

3406(b)(21) - Adequately screen diversions.
1-I-6 WORKING PAPER ON RESTORATION NEEDS

Water management modifications -

3406(b)(1)(B) - Modify CVP operations.

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

purposes.

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

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

3406(b)(12) - Provide increased flows in Clear Creek.

3406(b)(18) - Restore striped bass fishery in Bay/Delta.

Operational modifications -

3406(b)(1)(B) - Modify CVP operations.

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

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

3406(b)(7) - Meet diversion limits that apply to the CVP.

3406(b)(9) - Eliminate fish losses due to flow fluctuations of CVP.

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

3406(b)(14) - Improve operations at Delta Cross Channel and Georgiana Slough.

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

District Diversion Dam.

3406(b)(20) - Mitigate for GCID=s Hamilton City Pumping Plant.
SECTION I. INTRODUCTION -

IMPLEMENTATION CONSIDERATIONS 1-1-7

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.

Tools for use on CVP vs. non-CVP streams - Tools available to the Secretary to implement actions on 

streams 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 

and use of the 800,000 acre-feet are limited to CVP-controlled streams. The CVP-controlled streams 

include the Sacramento, American, Stanislaus, and San Joaquin rivers (although restoration of anadromous 

fish habitat on the San Joaquin River is limited to that section downstream of Mendota Pool). There are a 

number of entities involved or affected by the management of water supplies on these rivers.

Non-CVP controlled streams include Battle, Mill, Deer, Butte, Stony, Elder, and Thomas creeks and 

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

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

municipalities and industry manage facilities and flows on these streams. The CVPIA does not provide the 

Secretary with the direct authority to implement actions on these streams.

Cooperation with others - To implement actions on streams or at facilities where the Secretary does not 

have authority, the Secretary will need the cooperation of the entities with the authority to implement the 

actions. These entities include SWRCB, the Federal Energy Regulation Commission (FERC), and others 

that may or do establish diversion restrictions and minimum flow requirements. Other regulatory processes 

under DFG, EPA, NMFS, the Corps, and other state, federal, county, and local agencies have significant 

potential to influence the implementation of specific restoration actions in the AFRP. Efficient and timely 

coordination and strong cooperative efforts with these organizations are essential to implement a

comprehensive AFRP.

In addition, the "Principles for Agreement on Bay/Delta Standards between the State of California and the 

Federal Government", signed on December 15, 1994, has potential to supplement restoration actions in the 

CVPIA. Category III of the agreement provides for private funding of nonflow actions to improve fish 

protection. This element of the agreement is to be implemented immediately (1995) and the development of 

specific actions is currently in progress. Other ongoing restoration or mitigation efforts include the four 

pumps agreement (DWR and DFG 1986) and DFG efforts described in ARestoring Central Valley Streams: 

A Plan for Action@ (Reynolds et al. 1993) and the subsequent implementation report (DFG 1995). All of 

these activities contribute to restoration of anadromous fish habitat in the Central Valley and each of them is 

implementing actions described in the Working Paper. The challenge for the AFRP is to assist and augment 

these activities.

Schedule for Implementation
1-I-8 WORKING PAPER ON RESTORATION NEEDS

Limitations due to time restrictions, lack of money in the restoration fund, legal and administrative 

constraints, and the need to balance actions to meet other goals of the CVPIA, among others, will require 

that actions be implemented in phases. Given these limitations, it is difficult to predict how rapidly we can 

proceed with implementing actions.

The first restoration actions to be implemented are envisioned to be a combination of those mandated in the 

CVPIA and other non-CVP actions. Actions requiring structural, water management, and operational 

modifications are discussed below. For each of these categories, actions for which tools are provided in the 

CVPIA are discussed first, and actions for which tools other than those provided directly by the CVPIA 

(those actions that would need to be implemented through other authorities) are discussed second.

Structural modifications - Of the sections of the CVPIA categorized above as structural modifications, 

most could be implemented soon if given a high priority for use of restoration funds. Several have already 

been implemented, at least in part, or are being designed. These include mitigating for the Tracy fish facilities 

(b)(4); constructing the temperature control device at Shasta Dam (b)(6); minimizing fish passage problems 

at RBDD (b)(10); implementing CNFH Plan (b)(11); replenishing gravel below CVP reservoirs (b)(13); 

installing a (sound) barrier at Georgiana Slough (b)(14); installing a (temporary) barrier at the head of Old 

River (b)(15); and mitigating for GCID=s Hamilton City Pumping Plant (b)(20). Replenishing gravel below 

CVP reservoirs (b)(13) will be a continuous process and will take time to significantly restore habitat.

As noted earlier, a major potential to implement structural modifications in the near term may be provided 

through coordination with the actions carried out under Category III of the principles for agreement on 

Bay/Delta standards.

Water management modifications- Modifications to CVP operations to provide flows of suitable quality, 

quantity, and timing to protect all life stages of anadromous fish (b)(1)(B) are currently being implemented 

although there is potential for improvement with further effort and evaluation of the benefits achieved. These 

modifications affect CVP-controlled streams and the Delta.

Management of the 800,000 af for fishery and habitat restoration (b)(2) has been ongoing since 1993. This 

element has been affected by the Bay/Delta Framework Agreement, in that the CVP obligation for Delta 

flow needs is provided from the 800,000 af. Hence, the remaining portion of the 800,000 af of CVP yield 

will be available for the needs of the AFRP. The Bay/Delta agreement is to be in effect for the next 3 years.

Some amount of the restoration fund is available to acquire supplemental water supplies (b)(3) for use by 

the AFRP. This element stipulates the need to define how the Secretary intends to use CVP operational 

modifications; water banking, conservation, transfer, conjunctive use, and land fallowing. Land fallowing 

includes purchase and lease of agricultural lands and acquisition of associated water and water rights 

options. The acquisition of supplemental water would be effective in the Delta and would provide added 

tributary flows in both CVP and non-CVP Central Valley streams. Success of water acquisition in the near 
SECTION I. INTRODUCTION -

IMPLEMENTATION CONSIDERATIONS 1-1-9

term will be influenced by the availability of restoration funds and the willingness of sellers to provide water 

for fishery purposes. Acquisition of supplemental water supplies brings in the major stakeholders in the 

water user community. Success in gaining supplemental water supplies for fishery restoration will depend on 

how well all parties can work together and cooperate.

Other actions from the CVPIA relate to flow standards required to be met by the CVP (b)(7) and pulse 

flows to increase migratory fish survival (b)(8). Both are ongoing under the Bay/Delta agreement, which 

requires the CVP and SWP to meet flow standards, export-to-inflow ratios, pulse flows, and Delta Cross 

Channel operational criteria. These actions are designed to provide fish protection sufficient for currently 

listed threatened and endangered species and to avoid additional listings.

Finally, there are ongoing regulatory processes by FERC and the SWRCB that may establish new minimum 

flow mitigation requirements for the Yuba, Mokelumne, and Tuolumne rivers in the near future. These 

processes provide improved tributary flows and Delta inflow, further aiding implementation of the 

restoration actions.

Operational modifications - Most of the operation modification elements of the CVPIA

(b)(1[B],4,5,7,9,10,14,17 and 20) are currently being implemented to some extent although there is 

potential for improvements with further effort and evaluation of the benefits achieved. There is also potential 

for operational modifications on non-CVP streams that would provide benefits to anadromous fish.

EVALUATION OF FLOW NEEDS

To aid the reader in appreciating the complexity of defining flow needs for anadromous fish restoration, we 

have provided discussion of several key aspects of this issue.

Relations between Flows and Anadromous Fish Populations

The assumption that there is a relationship between river flow and anadromous fish populations may have 

initially stemmed from the observation that large rivers maintained large runs of fish, medium-sized rivers 

held medium-sized runs, and small streams produced relatively few fish, even in very wet years. A 

common-sense explanation is that there is relationship between the size of a river and the number of fish it 

will support and the size of a river and the amount of water running through it.

If the CVP is viewed as an experiment testing this assumption, various examples of the relationships 

between flow and fish can be observed. Flow and temperature changes after the construction of Shasta 

Dam created cold water habitat for a large population of winter-run chinook salmon in the 1950s and 

1960s. This population subsequently declined as flow and flow-related conditions changed and, perhaps, 

as changing operations in the Delta reduced survival there. New Melones Dam on the Stanislaus River 
1-I-10 WORKING PAPER ON RESTORATION NEEDS

created conditions under which salmon populations were strong in wet years when flow patterns 

approximated a natural state and neared extinction under dry conditions when a greater proportion of 

unimpaired winter and spring runoff was retained in reservoirs. 

Extirpation of anadromous fish from much of the mainstem San Joaquin River after the severe reduction in 

flow that followed the completion of Friant Dam provides additional evidence of the relationship between 

the size of the river and water flow and fish populations. Systemwide, except on the American and Feather 

rivers where the success of natural populations is very difficult to gauge because of the presence of large 

hatcheries, strong evidence suggests that reducing winter and spring flows tends to reduce populations of 

anadromous fish that rear and migrate in winter and spring. In addition to the effects of hatchery production, 

factors that confound the precise determination of optimum fish flows include differences in life history 

requirements, water quality problems, land use impacts, altered river and floodplain morphology, and 

obstruction of access to historical spawning reaches. 

Difficulties in Evaluating Flow Needs

The value of a restoration action depends on how effectively it addresses the factors that are actually limiting 

to the population of a target species. For example, the value of a mechanical device designed to allow the 

release of warmer reservoir water to draw fish to spawning areas and the later release of cool water to 

improve egg survival would be diminished if fish were not drawn to spawning areas by warmer water or if 

overall productivity were primarily controlled by conditions in the estuary.

Identifying the flows needed to restore fish production in regulated streams is controversial because 

modifying flow regimes to meet the needs of fish may undermine the objectives of the groups who benefit 

from the existing management scheme. In the Central Valley, the primary objectives of water managers are 

typically flood control and water storage for later agricultural and urban uses. Consequently, rationales for 

changing flow patterns are often intensively debated among stakeholders, and close attention is applied to 

the biological judgments underlying them. Because they are perceived as being less costly, nonflow 

alternatives are seldom subjected to the same level of scrutiny. However, the degree of uncertainty 

associated with the benefits of actions such as gravel supplementation and screening is equal to or greater 

than that associated with modification of flow. For any restoration measure, the key decision is this: does it 

target a problem that is actually limiting to the target species? Intuitively, the benefits of screening 

agricultural diversions to prevent entrainment of juvenile fish appear obvious; however, there would be little 

value in spending limited funds on screening if fish excluded from upstream diversions were subsequently lost 

in the Delta as a result of direct and indirect effects of exports at the state and federal water projects. 

Similarly, there would be little value in increasing the quantity of available spawning gravel if the problem that 

actually limits juvenile production is lack of adequate rearing habitat. 

Similar problems surround the evaluation of restoration proposals to improve fish habitat by changing flow 

regimes. As with most other restoration measures, improvements in fish production resulting from modified 

flow regimes cannot be quantitatively predicted at this time. CVPIA includes provisions intended to 
SECTION I. INTRODUCTION -

EVALUATION OF FLOW NEEDS 1-1-11

overcome this deficiency, notably Section 3406(b)(16), which requires development of a comprehensive 

program to assess the biological results and effectiveness of restoration actions, and Section 3406(g), which 

requires development of biological and water system models to improve scientific understanding of various 

elements of the Central Valley ecosystem. 

Flow evaluation methods - One of the tools available for evaluating fishery flows is the Instream Flow 

Incremental Methodology (IFIM) developed by USFWS's Instream Flow Group, now the River Systems 

Management Section of the National Biological Service Mid-continent Ecological Sciences Center. IFIM 

provides a means of estimating the amounts of fish habitat available at various flows, commonly through 

PHABSIM, a series of computer programs simulating river hydraulics and fish habitat. Because available 

habitat can be presented over a range of flows, the methodology provides a means of evaluating tradeoffs 

between fish habitat and water supply.

The IFIM process for determining relationships between stream flow and habitat is at base simple and 

direct, consisting of three steps:

1. Observe fish in streams and measure the physical characteristics of the habitat they use.

2. Measure or estimate the amount of similar habitat available in a stream at various flows.

3. Compare the habitat available in the river under various flows to the habitat used by fish. 

The flow that provides the greatest amount of habitat, modified by macrohabitat constraints 

such as temperature and water quality, is the optimum flow for a given life stage. This 

information may then be used in any variety of ways to develop a larger view of the overall 

biological effect of flows. 

The primary physical microhabitat variable addressed through currently applied IFIM methods is water 

velocity, because the area of river with usable velocity defines the area where fish can live. Substrate 

quality, an essential element of salmonid spawning habitat, is also usually characterized in a Central Valley 

IFIM habitat study. Depth is always included in flow studies because it is needed for velocity estimation at 

unmeasured flows, and because fish need a certain depth of water to swim and breathe. Other variables 

thought to be important to fish, such as cover and food production, can be included in IFIM microhabitat 

estimates, but this has not been seriously attempted in any Central Valley study, possibly because evidence 

of their relationship to long-term flows above a minimal level is inconclusive or difficult to obtain.

For Central Valley chinook salmon and steelhead, important flow-dependent life stages include adult 

spawning, egg incubation, and juvenile rearing and migration. Because habitat needs change as fish grow 

from fry to smolts, rearing fish are usually divided into two categories, fry and juveniles above about 50 

millimeters (mm) long. Steelhead trout are generally divided into adult, fry, and juvenile life-stages. Useful 
1-I-12 WORKING PAPER ON RESTORATION NEEDS

IFIM habitat criteria for shad, striped bass, and sturgeon have not been developed in California and 

probably will not be, given the difficulty of observing these fish in the open water or depths they inhabit.

IFIM techniques are often viewed as limited or deficient in estimating necessary fishery flows. Various 

criticisms are that PHABSIM processes posit an unreal relationship between habitat and fish production, 

they do not adequately account for cover or other variables sometimes thought to be flow related, or the 

relationship between where a fish lives and why it lives there is unclear. Whatever the merit of these 

criticisms, four main problems are faced by IFIM users in California: 

1. No system of estimating proper fishery flows, including IFIM, has been verified by 

quantification of the relationships between fish habitat and fish production. A 10-year study 

is underway, however, to test the IFIM and determine whether changes in aquatic habitat 

caused by changes in the flow produce predictable changes in fish populations (Studley et 

al. 1993). To achieve this, it will be necessary to determine the numerical relationships 

between various life stages of fish with different or even conflicting habitat requirements, 

which has not been attempted in any Central Valley flow study. Such information is 

expected to be developed under Sections 3406(b)(16) and 3406(g) of the CVPIA, and 

various specific data needs are described in sections of this report.

2. Because young salmonids are small and comparatively weak, they need low velocities to 

survive in rivers. Chinook salmon ranging from about 33 to 50 mm long, for example, are 

most commonly found in still water near stream edges. Absolute areas of this slow water 

habitat generally increase with decreasing flow, so it is usually possible to interpret flow 

study results as showing that decreasing flow increases rearing habitat and that maximum fry 

habitat is provided by no flow at all, when the river becomes a series of still pools. This 

ignores the importance of flows for food transport, temperature moderation, and habitat 

diversity, but finding the point on a flow-versus-habitat curve where food transport and 

habitat diversity become of overriding importance is a matter of interpretation. Because of 

this, IFIM studies have sometimes become more a focus of debate than a means of 

resolution, with high-flow proponents rejecting estimated rearing flows and out-of-stream 

water users defending them.

3. Some Central Valley rivers have had average natural rearing flows reduced an order of 

magnitude or more so that the flows available for IFIM studies barely approach the lower 

limit of natural conditions. Most information available on anadromous fish and habitat 

condition in California is based on study of drastically altered streams, and little is known 

about the amounts of habitat that unimpaired flows provided. Doubling production implies 

a return to some approximation of preproject habitat conditions, but flows at preproject 

rearing-season levels have not been studied on any Central Valley stream. Flow studies 

have largely evaluated habitat in streams that are being operated like canals. To cite one 

example, available sampling techniques restricted the Yuba River flow study of 1991 to 
SECTION I. INTRODUCTION -

EVALUATION OF FLOW NEEDS 1-1-13

measurement of a high flow of 1,035 cubic feet per second (cfs) in reaches where average 

natural rearing-season flows were well over 6,000 cfs. The resulting habitat estimates have 

been the basis for flow recommendations but may not include the flows that exploit the full 

habitat potential of the river.

4. Problems with IFIM methods are most pronounced for early life stages. Juvenile salmonids 

are small, mobile, and difficult to statistically enumerate in all but the smallest streams; direct 

knowledge of their behavior and habits in Central Valley streams is sparse, and commonly 

supplemented with inferences from studies of tagged hatchery fish or fragmentary capture 

records of variable quality. Consequently, flow studies and flow recommendations have 

been oriented toward spawning, which is relatively easily quantified; lack of data has 

sometimes limited consideration of juvenile life stages to providing flows for temperature 

control or to releasing brief flow pulses that may improve survival during migration.

IFIM has been widely applied, despite its imperfections, partly because no more technically sound yet 

feasible method is widely available. Some alternatives include rarely used IFIM precursors such as the 

USFS sag-tape and the PG&E-Waters method; arbitrary setting of flows at a statistical level of unimpaired 

flow; and, where sufficient flow and population records exist, analysis of historical trends such as the 

regressions used for San Joaquin tributary streams in this report. 

A final and pervasive alternative method of flow evaluation is consideration of available biological data to 

develop a qualitatively derived flow schedule or to support and modify a flow schedule developed by largely 

intuitive processes. Most Central Valley flow recommendations, including those in this paper, use this 

method to some extent and are based substantially on professional judgment. A brief summary of the 

technical team approach by river system follows.

Approaches Taken by Technical Teams

With these complications in mind and with the legislated goal of determining conditions that would result in a 

doubling of natural production of anadromous fish, the AFRP technical teams have taken various 

approaches to developing draft flow recommendations. 

Chinook salmon and steelhead - Mainstem Sacramento River recommendations have been constrained by 

two factors. Several distinct stocks of salmon, each with different habitat requirements, exist in the river; 

one of these species has been listed under the federal Endangered Species Act and must be given priority. 

The Sacramento River recommendations therefore call for operations that maintain a storage pool that will 

enable the delivery of cool water from Shasta Reservoir through spring and summer, when winter-run 

chinook salmon are in the river. Within this pattern, there has been an attempt to optimize fall- and late fallrun salmon spawning flows and to reduce fluctuations that could affect spawning and rearing success during 

winter. Although an IFIM study has been conducted on Clear Creek and a Mill Creek IFIM study is in 
1-I-14 WORKING PAPER ON RESTORATION NEEDS

progress, flow recommendations for the other tributaries to the upper Sacramento River are based largely 

on professional judgment and observation of fish population response to existing and historical flow. In 

several cases, recommendations are to restore minimal flow levels to reaches that would otherwise be 

entirely dewatered during periods of the year that are critical for salmon or steelhead. Authors have 

recommended that existing knowledge be improved by conducting IFIM studies on most of the important 

tributaries. 

Flow recommendations for spawning and rearing in most of the lower Sacramento tributaries rely, at least in 

part, on conclusions drawn from IFIM studies. However, on the Feather, Yuba, Bear, American, and 

Mokelumne rivers, flows derived through IFIM have been modified to varying degrees based on knowledge 

of species= environmental requirements, additional observational data, professional judgment, carryover 

storage, and other water management imperatives such as flood control. IFIM studies have not been 

conducted on the Bear or Cosumnes rivers. On the former, fish flows were derived from knowledge of 

salmon requirements and a flow simulation model; on the latter, flow recommendations reflect the average 

conditions during baseline period years when production goals (as indicated by escapement) were actually 

met. Calaveras River flow recommendations are based on a USFWS IFIM study that sought to identify 

flow needs for a race of winter-run salmon.

Recommendations for the mainstem San Joaquin River are based on a regression of chinook salmon 

escapement on Vernalis flow and combined state and federal exports during April, May, and June in the 

year of outmigration. Allocation of total basin outflow between the tributaries and mainstem river was based 

on the by-year type percentages contributed to total San Joaquin Basin unimpaired runoff from 1922 to 

1990. IFIM-based flow recommendations were applied to tributaries in dry year types when unimpaired 

flow in the reaches that are currently accessible to salmon and steelhead were inadequate for late rearing, 

spawning, and incubation. On the Merced River, where no IFIM study has been conducted, IFIM flows 

from a similarly sized drainage were used as a surrogate. DFG has plans to conduct an IFIM study on the 

Merced River in the near future.

Striped bass, American shad, white and green sturgeon - There are no studies that specifically identify 

flow requirements for striped bass, American shad, white sturgeon, or green sturgeon. Flow

recommendations for striped bass are based on a modification of an existing DFG model that predicts the 

adult population based on Delta outflow, exports/diversions, and stocking rates. Recommendations for 

shad and both species of sturgeon reflect average flow during those baseline period years when data 

indicate that the production goals were actually met. For shad, April-May Delta outflow was related to 

abundance of juveniles in the DFG fall midwater trawl and was allocated to individual stream on the basis of 

percent contribution to unimpaired runoff. For sturgeon, flow to production estimates were identified on a 

river-by-river basis. 
SECTION II. SUMMARY OF RESTORATION GOALS 1-II-1

SECTION II. SUMMARY OF RESTORATION GOALS

Restoration goals for four races of chinook salmon, steelhead, striped bass, American shad, and white and 

green sturgeon are presented in the following table. The Core Group defined the restoration goal for 

anadromous fish to be equal to at least twice the mean estimated natural production for the baseline period 

(1967-1991). It defined natural production during the baseline period to be that portion of production not 

produced in hatcheries and defined production to be the number of fish that recruit to adulthood in a given 

year, including newly recruited fish that are harvested. 

Volume 3, Section X, AReports from the Technical Teams,@ provides the details and methods for estimating 

restoration goals. In Section Xa and appendices A and B, production goal numbers for salmon and 

steelhead are broken down by stream and race. Methods for adult striped bass are discussed in Section 

Xf; for American shad in Section Xg; and for white and green sturgeon in Section Xh. Because there are no 

data to estimate the adult component of the American shad population for any years except 1976 and 1977, 

young-of-the-year abundance in the California Department of Fish and Game fall midwater trawl was used 

to estimate our numeric restoration goal.

AFRP goals for anadromous fish production

in Central Valley rivers and streams.

Species Goal

Chinook salmon, all races 990,000 

Fall run 750,000 

Late fall run 68,000 

Winter run 110,000 

Spring run 68,000 

Steelhead 13,000 

Striped bass 2,500,000 

American shad 4,300a

White sturgeon 11,000 
1-II-2 WORKING PAPER ON RESTORATION NEEDS

Species Goal

Green sturgeon 2,000 

a The goal for American shad is expressed as the juvenile index as derived from the DFG fall midwater 

trawl.
SECTION III. SUMMARY OF LIMITING FACTORS 1-III-1

SECTION III. SUMMARY OF LIMITING FACTORS

Following are general categories of factors that were identified by the AFRP technical teams as limiting 

natural production of anadromous fish in Central Valley streams. Not all of these problems affect all 

species, life stages, or streams. The order in which these items appear in the list is a rough indication of how 

often they were identified as a problem by the technical teams. For example, inadequate flow was identified 

as a problem for virtually all species and streams. For more detailed information on the specific factors that 

affect particular species and streams, readers should refer to the appropriate sections in Volume 3 of this 

Working Paper. 

1. Inadequate timing and/or magnitude of flow to provide suitable conditions for one or more 

life stage

2. Water temperatures that regularly exceed tolerances of one or more life stage

3. Loss of natural stream habitat

a. Loss of spawning gravel; lack of spawning gravel recruitment

b. Sedimentation resulting from riparian and upland land use impacts

c. Loss of bank and riparian cover

d. Loss of floodplain and other low-velocity stream habitat

4. Obstacles to fish passage

5. Entrainment of juveniles at riparian and Delta diversions

6. Direct and indirect impacts of Central Valley Project and State Water Project Delta 

pumping operations

7. Effects of point and nonpoint source discharge of organic pollutants, pesticides, and 

miscellaneous toxic chemicals

8. Legal and illegal harvest of adult fish
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

INTRODUCTION and SACRAMENTO RIVER BASIN 1-IV-1

SECTION IV. SUMMARY OF RESTORATION ACTIONS

INTRODUCTION

Section IV summarizes the restoration actions that appear in their complete and original form in Volume 3. 

For purposes of the summary, organization and presentation has been changed by combining actions for all 

six anadromous fish species for each river or stream. Information for actions that do not involve 

modification of flow is limited to a brief, descriptive title, a statement of the objective with respect to 

improving conditions for anadromous fish, and a list of the species and races for which the action was 

proposed. Flow requirements for all six species are combined into tables by river, or, where the technical 

teams have made recommendations for multiple points on a single river, by flow station. Where flow needs 

for two or more species overlap within a river, or at a flow station, the flows presented in the table are those 

that would provide the greatest overall benefits for anadromous fish. Water year types are based on the 

Sacramento River Index and San Joaquin Basin 60-20-20 Index except as otherwise noted. Interested 

parties who wish to read more detailed descriptions of restoration actions, or would like to review the 

supporting technical information, can order copies of Volume 3 from the USFWS by calling 1-800-742-

9474 or 1-916-979-2330 and dialing 542 after the recorded message begins. Copies may also be 

obtained by calling Roger Dunn, CVPIA Public Outreach, at 1-916-979-2760 or by sending e-mail 

requests to roger_dunn@fws.gov.

SACRAMENTO RIVER BASIN

Upper Mainstem Sacramento River

1. Develop and implement an integrated river regulation plan that balances carryover storage 

needs with instream flow needs based on runoff and storage conditions: Actively regulate river flows 

and reservoir storage in the upper Sacramento River system to provide necessary habitat for the production 

of all races of chinook salmon and the anadromous fish they coexist with, consistent with sound ecological 

management principles. 
1-IV-2 WORKING PAPER ON RESTORATION NEEDS

Minimum recommended Sacramento River flows (cfs) 

at Keswick Dam (RM 302), for the period October 1 to April 30a.

Carryover 

storage 

Keswick Dam 

release

Carryover 

storage

Keswick Dam 

release

1.9 3,250 2.5 4,250

2.0 3,250 2.6 4,500

2.1 3,250 2.7 4,750

2.2 3,500 2.8 5,000

2.3 3,750 2.9 5,250

2.4 4,000 3.0 5,500

a Based on October 1 carryover storage (maf) 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 to 3.2 maf 

for temperature control.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

2. Implement the Grimes flow schedule: Provide minimum or greater flows to ensure suitable 

conditions for adult American shad and white and green sturgeon to migrate upstream, spawn, and allow 

progeny to survive.

Sacramento River flows (cfs) at Grimes (RM 125)

Month

Wet 

Above

normal

Below 

normal Dry Critical

February-March 17,700a17,700a-- -- --

April-May 19,800b17,700a13,200c9,300c5,400c

a

Flows needed for white and green sturgeon spawning. Flows of 15,200 cfs needed for American shad 

spawning during April-May of above-normal water years. 

b

Flows needed for American shad spawning. Flows of 17,700 cfs needed for white and green sturgeon 

spawning.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

INTRODUCTION and SACRAMENTO RIVER BASIN 1-IV-3

c

Flows required for American shad spawning.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; American shad; white and 

green sturgeon

3. Maintain mean monthly flows of 31,000 cfs at Verona from February to May in wet and abovenormal years: Provide minimum or greater flows to ensure suitable conditions for adult white and green 

sturgeon to migrate upstream, spawn, and allow progeny to survive.

Species: White and green sturgeon

4. Develop a flow regime that imitates natural flow changes and avoids dewatering redds or 

isolating or stranding juveniles on monthly and daily rates of change: Prevent redd dewatering or 

stranding or isolating adults and juveniles.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

5. Complete an integrated instream flow study (IFIM) to refine a river regulation program that 

actively balances fishery habitat with the flow regime, including needs for adequate temperature, 

flushing flows, outmigration, channel maintenance, attraction flows, and maintenance of a riparian 

corridor: Regulate CVP releases to provide adequate spawning and rearing habitat for salmon and 

steelhead and to minimize flow fluctuations to avoid dewatering redds and stranding or isolating adult and 

juvenile fish.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

6. Manage flow to restore riparian vegetation: Consider all features of how flow influences 

ecosystem.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

7. Maintain water temperatures at or below 56°F from Keswick Dam to Bend Bridge except in 

extreme water years: Develop a water management plan that will ensure USBR's ability to provide cold 

water during critical months and budget cold water reserves in reservoirs to maximize survival during critical 

months.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; American shad; white and 

green sturgeon
1-IV-4 WORKING PAPER ON RESTORATION NEEDS

8. Raise RBDD gates for a minimum period from September 15 to June 30: Provide unimpeded 

adult and juvenile passage past RBDD and decrease juvenile mortality associated with predators.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; white and green sturgeon

9. Complete the process to find final solutions to passage problems at RBDD and improve 

passage conditions beyond opening the dam gates longer than 8 months: Provide unimpeded adult 

and juvenile passage and decrease juvenile mortality associated with predators.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; white and green sturgeon

10. Implement structural and operational modifications at ACID to eliminate stranding, toxic 

discharges, improve screens, and eliminate passage problems for chinook salmon and steelhead: 

Provide safe passage for adult and juvenile salmon past ACID.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

11. Construct escape channel from stilling basin to the Sacramento River at Keswick Dam:

Avoid entrapment of salmonid adults at Keswick Dam stilling basin.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

12. Implement structural and operational modifications to eliminate entrainment at water 

diversions: Increase survival of outmigrating anadromous fish stocks by reducing entrainment through 

correcting unscreened or inadequately screened water diversions.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; white and green sturgeon

13. Implement structural and operational modifications to eliminate impingement and

entrainment of juvenile salmon at GCID water diversion: Correct problems at the GCID water 

diversion.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; white and green sturgeon

14. Complete EPA Superfund cleanup of Iron Mountain Mine by 1996: Remedy water quality 

problems associated with Iron Mountain Mine and other toxic discharges.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; white and green sturgeon

15. Avoid potential competitive displacement of wild, naturally produced juveniles with hatcheryreleased juveniles by stabilizing hatchery production levels and implementing release strategies 
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SACRAMENTO RIVER BASIN 1-IV-5

designed to minimize detrimental interactions: Evaluate competitive displacement between hatchery 

and natural stocks.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

16. Implement specific hatchery spawning protocols and genetic evaluation programs to maintain 

genetic diversity in hatchery and wild stocks: Maintain genetic diversity in hatchery stocks.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

17. Evaluate transfer of disease between hatchery and natural stocks: Evaluate disease relations 

between hatchery and natural stocks.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

18. Create a 50,000-acre meander belt from Red Bluff to Chico Landing to provide gravel 

recruitment, large woody debris, moderate air temperatures, and nutrient input to the lotic 

system: Restore and preserve riparian forests.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

19. Devise alternative methods other than the Gradient Restoration Facility to increase head 

differential for the Glenn-Colusa Irrigation District diversion: Facilitate sturgeon passage past 

GCID.

Species: White and green sturgeon

UPPER SACRAMENTO RIVER TRIBUTARIES

Clear Creek

1. Release 200 cfs of water from Whiskeytown Dam to Clear Creek from October to April and 

150 cfs the remainder of the year with variable spring-time releases depending on water year 

type: Provide adequate instream flows, suitable water temperatures, and channel maintenance flows for all 

life stages of salmon and steelhead. 

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead
1-IV-6 WORKING PAPER ON RESTORATION NEEDS

2. Maintain water temperatures at or below 65°F during periods of juvenile rearing, at or below 

60°F during adult holding and prespawn, and at or below 56°F during egg incubation: Increase 

salmonid production by providing optimum water temperatures at all critical life stages, especially for springrun chinook salmon and steelhead. 

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

3. Restrict gravel mining and restore degraded channel: Eliminate the severe adverse effects of 

gravel mining.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

4. Provide effective fish passage above Saeltzer Dam: Provide salmon with access to habitat above 

 McCormick-Saeltzer Dam.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

5. Prevent habitat degradation due to sedimentation and urbanization: Develop erosion and stream 

corridor protection programs.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

6. Restore gravel and spawning habitat: Compensate for lost spawning gravel recruitment and 

spawning areas blocked by Whiskeytown Dam.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

Cow Creek

1. Work with water right holders to obtain an agreement for adequate flows for fall-run salmon 

migration and spawning and juvenile steelhead: Provide suitable passage and early spawning flows 

(particularly in dry years) for fall-run chinook salmon adults and adequate flows for juvenile steelhead 

rearing.

Species: Fall-run chinook salmon; steelhead

2. Effectively screen agricultural diversions: Prevent loss of juvenile steelhead due to entrainment.

Species: Steelhead
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-7

3. Improve passage at agricultural diversion dams: Improve passage for adult steelhead and increase 

steelhead spawning and rearing habitat.

Species: Steelhead

Bear Creek

1. Restore instream flows: Provide adequate instream flows to permit safe passage of juvenile and adult 

salmon and steelhead at key times of the year.

Species: Fall-run chinook salmon; steelhead

2. Build and operate fish screens on all unscreened diversions: Prevent losses of migrating juvenile 

fall-run salmon and steelhead into agricultural diversions.

Species: Fall-run chinook salmon; steelhead

Cottonwood Creek

1. Protect and enhance spawning gravel: Increase spawning opportunities.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

2. Eliminate attraction flows in Crowley Gulch: Eliminate stranding mortalities.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

3. Improve land use practices: Reduce water temperatures to improve holding, spawning, and rearing 

habitat and reduce siltation and sedimentation of existing spawning gravel.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

Battle Creek

1. Treat CNFH water supply: Eliminate the potential for waterborne disease to adversely affect hatchery 

production.

Species: Fall- and late fall-run chinook salmon; steelhead

2. Allow passage above the CNFH weir: Increase available habitat for all salmonid runs and life stages.
1-IV-8 WORKING PAPER ON RESTORATION NEEDS

Species: Fall- and late fall-run chinook salmon; steelhead

3. Increase bypass flows at PG&E's hydropower diversions according to the following table: 

Provide streamflow of sufficient quantity and quality to provide adequate holding, spawning, and rearing 

habitat.

Diversion Months Flow (cfs)

Keswick All year 30

September-November 40

January-April 40

North Battle Creek Feeder

May-August 30

Eagle Canyon May-November 30

December-April 50

Wildcat May-November 30

December-April 50

South May-November 20

December-April 30

Inskip May-November 30

December-April 40

Coleman September-April 50

May-August 30

The following interim flows will be implemented during the initial phase. Optimum flows, which are listed in 

the table above, will not be required until the spring-run population numbers are sufficient to utilize all 

available habitat.

1. Eagle Canyon Dam- release 40 cfs at Eagle Canyon Dam from September 1 to April 1, 

and 30 cfs for the remainder of the year.

2. Coleman Diversion - release 50 cfs from Coleman Diversion from October 1 to 

February 1 and 30 cfs for the remainder of the year.

3. Wildcat Diversion- close Wildcat Diversion to allow all the spring-water to remain in the 

creek and avoid entraining juvenile outmigrants in the power canal.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-9

4. Coleman Forebay - deliver canal water to Coleman Hatchery through a bypass pipe.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

4. Construct rack to prevent adult salmon from entering Gover diversion: Prevent loss of spawning 

adult fall-run chinook.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

5. Screen Orwick diversion: Prevent straying of spawning adult fall-run chinook salmon and prevent 

entrainment of juvenile salmonids.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

6. Screen tailrace of Coleman Powerhouse: Prevent straying of spawning adult chinook salmon and 

steelhead.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

7. Construct fish screens at the following PG&E water diversions: Wildcat, Eagle Canyon (only if 

barrier described in Action 9 is modified), Coleman, North Battle Creek Feeder, Inskip, and 

South: Minimize loss of both adult and juvenile salmonids.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

8. Evaluate effectiveness of fish ladders at PG&E diversions: Ensure that fish passage is occurring.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

9. Improve fish passage in Eagle Canyon: Facilitate movement of adult salmon and steelhead to 

habitat in North Battle Creek and above upper Eagle Canyon.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

10. Examine feasibility of establishing a spawning population of winter-run chinook salmon:

Increase genetic diversity and current habitat of the endangered Sacramento River winter-run chinook 

salmon.

Species: Winter-run chinook salmon
1-IV-10 WORKING PAPER ON RESTORATION NEEDS

Paynes Creek

1. Restore adequate instream flows: Provide minimum instream flows to improve spawning, rearing, 

and migration opportunities.

Species: Fall-run chinook salmon

2. Restore spawning gravel: Increase spawning potential. 

Species: Fall-run chinook salmon

Antelope Creek

1. Restore instream flows: Provide adequate instream flows to permit safe passage of adult salmon at 

key times of the year.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

2. Create defined stream channel: Reduce infiltration losses and maintain flows to the Sacramento 

River.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

Elder Creek

1. Construct a fish passage structure over Corning Canal Siphon: Improve fish passage for chinook 

salmon and steelhead.

Species: Fall-run chinook salmon; steelhead

2. Adopt an erosion control ordinance to minimize sediment input into Elder Creek: Reduce 

sediment input into Elder Creek.

Species: Fall-run chinook salmon; steelhead

Mill Creek

1. Improve transportation flows in the valley reach of Mill Creek: Ensure that upstream migrating 

spring-run chinook and downstream migrating spring and late fall-run chinook and steelhead migrate safely 

through the lower portion of Mill Creek. Increased flows in fall will also improve spawning conditions for 

fall-run chinook salmon.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-11

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

2. Remove Clough Dam: Provide unimpaired passage where an existing structure presently obstructs 

migrating adults under certain flow conditions.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

3. Protect and restore anadromous salmonid fisheries habitat and preserve the long-term 

productivity of the upper Mill Creek aquatic ecosystem through cooperative watershed

management: Identification of restoration priorities and protection of Mill Creek's aquatic ecosystem 

through cooperative land use management in the upper watershed.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

4. Improve salmon spawning areas in lower Mill Creek: Increase available spawning habitat at 

selected sites in lower Deer Creek to accommodate increased runs of fall- and late fall-run chinook salmon.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

5. Maintain and restore riparian habitat along lower reaches of Mill Creek: Help maintain cool 

water temperatures.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

Thomes Creek

1. Modify gravel mining methods: Improve land use practices.

Species: Fall- and spring-run chinook salmon; steelhead

2. Modify timber harvest practices: Improve land use practices.

Species: Fall- and spring-run chinook salmon; steelhead

3. Modify grazing practices: Improve land use practices.

Species: Fall- and spring-run chinook salmon; steelhead

4. Stabilize areas of high erosion: Reduce impacts of previous land use practices and improve habitat.
1-IV-12 WORKING PAPER ON RESTORATION NEEDS

Species: Fall- and spring-run chinook salmon; steelhead

5. Replace Corning Canal Siphon: Improve fish passage.

Species: Fall- and spring-run chinook salmon; steelhead

6. Minimize diversion barriers usage: Improve fish passage.

Species: Fall- and spring-run chinook salmon; steelhead

7. Develop a release strategy for TCC into Thomes Creek between October and May. Until a 

strategy is developed, flows of 50 cfs should be released from TCC into Thomes Creek: Improve 

fish flows in Thomes Creek to ensure survival of all salmonid life stages.

Species: Fall-run chinook salmon; steelhead

8. Conduct regular water quality monitoring: Provide suitable water quality.

Species: Fall-run chinook salmon

Deer Creek

1. Improve transportation flows in the valley reach of Deer Creek: Ensure that upstream migrating 

spring-run chinook salmon and downstream migrating juvenile spring- and late fall-run chinook and 

steelhead can migrate safely through the lower 10 miles and pass over three diversion dams in lower Deer 

Creek. Also, provide improved flows for adult fall-run salmon.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

2. Protect and restore chinook salmon and steelhead habitat and preserve the long-term 

productivity of the upper Deer Creek aquatic ecosystem through cooperative watershed

management: Reduce the effects of land use practices.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

3. Improve salmon spawning areas in lower Deer Creek: Increase available spawning habitat at 

selected sites in lower Deer Creek to accommodate increased runs of fall- and possibly late fall-run chinook 

salmon.

Species: Fall- and late fall-run chinook salmon
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-13

4. Maintain and restore riparian habitat along lower reaches of Deer Creek: Help maintain low 

water temperatures.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

5. Conduct flood management activities: Carry out required flood management activities with 

minimum damage to the fishery resources and riparian habitat in the lower 5 miles of Deer Creek.

Species: Fall-, late fall-, and spring-run chinook salmon; steelhead

Stony Creek

1. Install siphon under Stony Creek for GCID canal: Provide passage for all life stages and prevent 

entrainment of juvenile salmonids.

Species: Fall- and late fall-run chinook salmon

2. Develop water management release strategy for Black Butte Dam: Provide adequate flows.

Species: Fall- and late fall-run chinook salmon

3. Comply with RBDD mitigation by providing flows between 100 cfs and 500 cfs of water per 

day to Stony Creek via TCC: Provide adequate flows.

Species: Fall- and late fall-run chinook salmon

4. Modify gravel extraction permits: Provide suitable spawning habitat.

Species: Fall- and late fall-run chinook salmon

5. Add spawning gravel to Stony Creek: Provide suitable spawning habitat.

Species: Fall- and late fall-run chinook salmon

6. Develop a distinct creek channel: Provide suitable spawning habitat.

Species: Fall- and late fall-run chinook salmon

7. Develop plan to establish a riparian corridor: Provide suitable water temperatures.
1-IV-14 WORKING PAPER ON RESTORATION NEEDS

Species: Fall- and late fall-run chinook salmon

8. Discontinue diversions to the TCC: Alleviate passage problems, ensure adequate flows, and 

prevent entrainment.

Species: Fall- and late fall-run chinook salmon

9. Correct problems associated with North Diversion Dam: Provide fish passage for all life stages, 

provide adequate flows past dam, and prevent entrainment.

Species: Fall- and late fall-run chinook salmon

10. Develop plan to assess water quality: Ensure adequate water quality for all life stages.

Species: Fall- and late fall-run chinook salmon

11. Conduct Instream Flow Incremental Methodology (IFIM): Determine preferred water flows for 

all life stages.

Species: Fall- and late fall-run chinook salmon

Big Chico Creek

1. Substitute an alternative source of irrigation water for that currently supplied by the M&T 

Ranch Pumps: Prevent loss of juvenile salmonids and permit sufficient attraction flows for adults.

Species: Fall-, late fall-, and spring-run chinook salmon

2. Repair Iron Canyon fish ladder: Facilitate movement of adult spring-run chinook and steelhead to 

favorable summer holding habitat.

Species: Fall-, late fall-, and spring-run chinook salmon

3. Split low flow between Big Chico Creek and Lindo Channel: Minimize trapping and subsequent 

loss of both adult and juvenile salmonids from periodic dewatering of Lindo Channel.

Species: Fall-, late fall-, and spring-run chinook salmon

4. Replace spawning gravel in the channels modified for flood control: Improve spawning habitat for 

fall- and late fall-run chinook.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-15

Species: Fall- and late fall-run chinook salmon; steelhead

5. Repair the Lindo Channel weir and fishway: Facilitate upstream passage of spring chinook and 

steelhead from Lindo Channel.

Species: Fall-, late fall-, and spring-run chinook salmon

6. Improve cleaning procedure at One-Mile Pool: Reduce siltation of downstream spawning and 

rearing habitat.

Species: Fall-, late fall-, and spring-run chinook salmon

7. Preserve primary summer holding areas for spring-run chinook salmon: Obtain title or 

conservation easement on land adjacent to primary summer holding pools for spring-run chinook. This is 

especially important considering the marginal summer temperatures and possibility of residential

development in those areas. Additional disturbance would cause significant mortality.

Species: Fall-, late fall-, and spring-run chinook salmon

8. Revegetate denuded stream reaches, restore and maintain a protected riparian strip: Expand 

the usable habitat and provide habitat diversity, cover from predators, and shade to keep the water cooler 

in late spring.

Species: Fall-, late fall-, and spring-run chinook salmon

9. Replace gravel in the flood-diversion reach of Mud Creek: Expand the usable habitat and provide 

habitat diversity for rearing salmon and their prey.

Species: Fall-, late fall-, and spring-run chinook salmon

Butte Creek

1(a). Obtain rights to approximately 105 cfs of water from Parrott-Phelan diversion: Provide 

adequate instream flows for all life stages of salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

1(b). Maintain a minimum 40 cfs instream flow below Centerville Diversion Dam: Provide suitable 

holding, spawning, and rearing habitat.
1-IV-16 WORKING PAPER ON RESTORATION NEEDS

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

1(c). Purchase existing water rights from diverters: Ensure adequate instream flows.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

2(a). Build new high-volume fish ladder at Durham Mutual Dam: Provide adequate passage for 

adult salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

2(b). Install fish screens on both diversions at Durham Mutual Dam: Prevent entrainment of 

juvenile salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

3(a)(1). Develop and construct Western Canal Siphon: Eliminate adult passage and juvenile 

entrainment problems associated with five dams and obtain additional instream flows.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

3(a)(2). Investigate the possibility of consolidation or replacement of additional diversions below 

the Western Canal Siphon Project: Eliminate adult passage and juvenile entrainment problems and 

potentially obtain additional instream flows.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

3(a)(3). Acquire water rights as part of the Western Canal Siphon Project: Obtain adequate 

instream flows.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

3(b)(1). Adjudicate water rights and provide watermaster service or equivalent for entire creek: 

Ensure adequate instream flows.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

3(b)(2). Remove Western Canal Dam and replace with siphon: Expedite adult passage, eliminate 

straying of adults, and prevent entrainment of juveniles.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-17

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

3(b)(3). Establish operational criteria for Sanborn Slough Bifurcation: Provide better passage for 

adult salmonids and prevent entrainment of juveniles.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

3(b)(4). Develop operational criteria for, and potential modification to, Butte Slough outfall: 

Provide sufficient attraction and passage flows for adults and outmigration flows for juveniles.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(a)(1). Build new high-volume fish ladder at Adams Dam: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(a)(2). Install fish screens on both diversions at Adams Dam: Prevent entrainment of juvenile 

salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(a)(3). Build new high-volume fish ladder at Gorrill Dam: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(a)(4). Install fish screens on diversions at McGowan Dam: Prevent entrainment of juvenile 

salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(a)(5). Install fish screens on three diversions at McPherrin Dam: Prevent entrainment of juvenile 

salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(b)(1). Install fish screens on both diversions at Western Canal Dam: Prevent entrainment of 

juvenile salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead
1-IV-18 WORKING PAPER ON RESTORATION NEEDS

4(b)(2). Build new high-volume fish ladder at Western Canal Dam: Improve adult fish salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(b)(3). Install fish screens on both diversions at Gorrill Dam: Prevent entrainment of juvenile 

salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(b)(4). Build new high-volume fish ladder at McPherrin Dam: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

4(c)(1). Build new high-volume fish ladder at McGowan Dam: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(a)(1). Build new high-volume fish ladder at East-West Diversion Weir: Improve adult fish 

passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(a)(2). Establish operational criteria for the East and West Barrows: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(a)(3). Establish operational criteria for Sutter Bypass Weir #2: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(a)(4). Establish operational criteria for Nelson Slough: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(a)(5). Establish operational criteria for Sutter Bypass Weir #1: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(a)(6). Install fish screens at Sanborn Slough Bifurcation: Prevent entrainment of juvenile salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-19

5(a)(7). Install fish screens at White Mallard Dam: Prevent entrainment of juvenile salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(a)(8). Screen diversions within Sutter Bypass where necessary: Prevent entrainment of juvenile 

salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(b)(1). Install culvert and riser at White Mallard Duck Club outfall: Prevent straying of adult 

salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(b)(2). Rebuild and maintain existing culvert and riser at Drumheller Slough outfall: Prevent 

straying of adult salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(b)(3). Establish operational criteria for Sutter Bypass Weir #5: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

5(b)(4). Establish operational criteria for Sutter Bypass Weir #3: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

6(a)(1). Initiate legal action on diverters who are violating water right allocations: Ensure sufficient 

instream flows.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

6(a)(2). Install high-volume fish ladder on Sutter Bypass Weir #2: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

6(a)(3). Install high-volume fish ladder on Sutter Bypass Weir #1: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead
1-IV-20 WORKING PAPER ON RESTORATION NEEDS

6(a)(4). Install fish screens on Little Dry Creek pumps: Prevent entrainment of juvenile salmonids.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

6(a)(5). Increase law enforcement of fishing regulations: Eliminate or reduce poaching.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

6(b)(1). Install high-volume fish ladder on Sutter Bypass Weir #5: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

6(b)(2). Install high-volume fish ladder on Sutter Bypass Weir #3: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

7(a)(1). Install high-volume fish ladder at White Mallard Dam: Improve adult fish passage.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

7(a)(2). Develop and enforce land use plans that create buffer zones between the creek and 

development: Protect existing salmonid habitat from further human development.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

7(a)(3). Develop a watershed management program: Protect existing salmonid habitat while 

providing for human use of the resources.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

7(b). Enhance fish passage at natural barrier below Centerville Diversion Dam: Increase the 

amount of available salmonid habitat.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead

8(a). Enhance fish passage at PG&E diversion dams: Increase the amount of available salmonid 

habitat.

Species: Fall- and spring-run chinook salmon; possibly late fall-run chinook salmon and steelhead
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-21

Colusa Basin Drain

1. Develop defined migrational routes: Provide direct access to Westside Tributaries

Species: Fall-run chinook salmon

2. Develop defined migrational flows: Provide direct access to Westside Tributaries

Species: Fall-run chinook salmon

3. Reduce water temperatures: Enhance survival in Colusa Drain and Westside Tributaries

Species: Fall-run chinook salmon

Miscellaneous small tributaries

Sacramento River tributaries that typically can provide rearing habitat only for salmonids:

Name USGS Quad

Side of

River

Streams known to support juvenile rearing

Pine Ord Ferry east

Toomes Vina east

Dye Los Molinos east

Oat Los Molinos west

Coyote Gerber west

Reeds Red Bluff East west

Brewery Red Bluff East west

Dibble Red Bluff East west

Inks Bend east

Anderson Ball's Ferry west

Olney Enterprise west

Streams presumed to support juvenile rearing

Burch Foster Island west

Jewett Vina west
1-IV-22 WORKING PAPER ON RESTORATION NEEDS

Name USGS Quad

Side of

River

McLure Vina west

Red Bank Red Bluff East west

Salt Red Bluff East east

Ash Ball=s Ferry east

Stillwater Ball=s Ferry east

Churn Cottonwood east

Sulfur Redding* east

Streams with potential to support juvenile rearing

Seven Mile Red Bluff East east

Frasier Bend west

Spring Bend west

Clover Cottonwood east

Middle Redding* west

Salt Redding* west

Jenny Redding* west

Rock Redding* west

a

 Indicates 15-minute topographic quadrangle map.

1. Revegetate denuded stream reaches and restore and maintain a protected riparian strip in all 

tributaries: Expand the usable rearing habitat and provide habitat diversity, cover from predators, and 

shade to keep the water cooler in late spring.

Species: Chinook salmon, runs unknown; steelhead

2. Move pumps to the Sacramento River, where sufficient bypass flow exists, to avoid

entrainment of juvenile salmonids (screen pumps): Reduce loss of juveniles to agricultural diversion.

Species: Chinook salmon, runs unknown; steelhead 

3. Find alternative sources of water for upstream diversions: Prevent early dewatering of stream 

reaches used for rearing.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-23

Species: Chinook salmon, runs unknown; steelhead

4. Survey tributaries for toxic materials, follow with cleanup projects as needed; expand 

enforcement of dumping ordinance: Remove hazards and potential hazards such as car batteries, oil 

filters, and animal carcasses from streams. Prevent further use of streams for dumps.

Species: Chinook salmon, runs unknown; steelhead 

5. Replace bridge/ford combinations with bridges or large culverts: Expand the usable habitat in 

some tributaries.

Species: Chinook salmon, runs unknown; steelhead

6. Provide siphons to get "beheaded" tributaries streams past irrigation canals: Expand the 

usable habitat.

Species: Chinook salmon, runs unknown; steelhead

LOWER SACRAMENTO RIVER AND DELTA TRIBUTARIES

Feather River

1. Increase flows in the low-flow channel: Enhance and maintain spawning and rearing habitat.

Feather River flows (cfs) in the low-flow channel

Schedule AaSchedule Bb

Month

Wet

Above 

normal

Below 

normal Dry Critical All year 

September-May 2,500 2,500 2,500 1,700 1,700 800

June-August 1,100 1,100 1,100 800 800 800

a

Schedules A and B are based on two different modeling scenarios presented in a draft IFIM report 

(Sommer 1994). The modeling scenarios differed in assumptions about depths preferred by spawning 
1-IV-24 WORKING PAPER ON RESTORATION NEEDS

chinook salmon. Schedule A is recommended for adoption and evaluation. If Schedule A results in 

reduced in spawning habitat, Schedule B flows (or flows derived from subsequent analyses) should be 

adopted. Flows in warmer months may be contingent on completion of the temperature model. 

Temperature model likely to require higher flows than specified to supply cold water downstream of 

Thermalito outlet for spring-run chinook salmon.

Species: Fall- and spring-run chinook salmon; steelhead

2. Consider providing experimental pulse flows: Stimulate outmigration of juvenile chinook salmon.

Species: Fall- and spring-run chinook salmon; steelhead

3. Consider providing experimental high-turbidity pulses: Stimulate outmigration of juvenile chinook 

salmon.

Species: Fall- and spring-run chinook salmon; steelhead

4. Restore gravel and create spawning habitat: Reduce armoring; increase spawning habitat.

Species: Fall- and spring-run chinook salmon; steelhead

5. Replenish gravel: Reduce spawning habitat degradation.

Species: Fall- and spring-run chinook salmon; steelhead

6. Complete temperature model: Develop a temperature model as a tool for river management.

Species: Fall- and spring-run chinook salmon; steelhead; possibly striped bass; American shad; white and 

green sturgeon

7. Conduct studies on the hatchery program: Determine distribution of Feather River Fish Hatchery 

chinook salmon in Central Valley stocks and determine genetic integrity of Feather River spring-run chinook 

salmon.

Species: Fall- and spring-run chinook salmon

8. Implement the Gridley flow schedule: Enhance and maintain spawning and rearing habitat for 

chinook salmon, steelhead, American shad, and white and green sturgeon.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

UPPER SACRAMENTO RIVER TRIBUTARIES 1-IV-25

Feather River flows (cfs) at Gridleya

Month

Wet

Above 

normal

Below

normal Dry Critical

October-January 2,500b2,500b2,500b1,700b1,700b

February-March 7,000c7,000c2,500 1,700b1,700b

April-May 7,000d7,000d3,000 2,100 2,100 

June-August 1,000 1,000 1,000 1,000 1,000 

September 2,500e2,500e2,500e1,400e1,400e

a

Flows proposed on interim basis until completion of DWR=s instream flow study. Flows may be further 

modified for sturgeon reproduction.

b

Flows needed for spawning and incubation of salmonids. Initial results from a DWR/DFG instream flow 

study indicate that spawning habitat in this reach would be maximized in the 750 to 2,750 cfs range 

(Sommer 1994).

c

Flows needed for white and green sturgeon spawning. Flows needed for spawning and incubation of 

salmonids are 2,500 cfs in wet and above-normal years.

d

Flows needed for white and green sturgeon spawning. Flows needed for spawning and incubation of 

salmonids are 3,000 cfs in wet and above-normal years.

e

Flows contingent on completion of the temperature model. Temperature model likely to require flows to 

come from upstream of Thermalito outlet to meet temperature needs downstream.

Species: Fall- and spring-run chinook salmon; steelhead; white and green sturgeon

9. Implement the Nicolaus flow schedule: Provide adequate flows for spawning and progeny survival 

for American shad and white and green sturgeon.
1-IV-26 WORKING PAPER ON RESTORATION NEEDS

Feather River flows (cfs) at Nicolaus

Month

Wet

Above 

normal

Below 

normal Dry Critical

February-March 11,500a

April-May 15,700b12,100b10,500b7,400b4,300b

a

Flows needed for white and green sturgeon spawning.

b

Flows needed for American shad spawning. Flows needed for sturgeon spawning are 11,500 cfs in wet 

and above-normal years. 

Species: American shad; white and green sturgeon

10. Maintain mean daily water temperatures below 63°F at Gridley and below 68°F throughout 

the Feather River between February and June for sturgeon spawning; maintain mean daily water 

temperatures between 61°F and 65°F for at least 1 month between April 1 and June 30 for 

American shad: Improve American shad and white and green sturgeon spawning success and egg survival 

by managing pumpback operations at Thermalito Reservoir.

Species: American shad; white and green sturgeon

11. Remove physical and water quality barriers that impede access to spawning habitat: Identify 

potential physical and water quality barriers, and determine extent of problem. Once barriers are identified, 

remove or facilitate passage around these barriers.

Species: White and green sturgeon

12. Reduce sturgeon entrainment: Identify extent of sturgeon entrainment. Increase survival of 

sturgeon larvae and juveniles by reducing or eliminating entrainment.

Species: White and green sturgeon

13. Determine effects of poaching and fishing on spawning stock size: Increase size of spawning 

stock if significantly reduced by fishing or poaching.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

LOWER SACRAMENTO RIVER AND DELTA TRIBUTARIES 1-IV-27

Species: White and green sturgeon

14. Improve water quality: Improve survival and condition of sturgeon.

Species: White and green sturgeon

15. Identify availability of suitable sturgeon spawning habitat: Identify potential sturgeon spawning 

sites and evaluate availability of such sites to adults. Take corrective actions if suitable spawning habitat is 

limiting.

Species: White and green sturgeon

Yuba River

1. Implement the Marysville flow schedule: Optimize migration, spawning, incubation, rearing, and 

outmigration conditions in the lower Yuba River for chinook salmon and American shad. 

Yuba River flows (cfs) at Marysville 

Month Wet 

Above 

normal

Below 

normal Dry Critical

October-March 700a700a700a700a700a

April-May 9,200b7,000b6,100b4,300b2,500b

June 1,500c1,500c1,500c1,500c1,500c

July-September 450d450d450d450d450d

a

Flows needed for spawning, incubation, and rearing of chinook salmon and steelhead.

b

Flows needed for American shad spawning. Flows needed for rearing and outmigration of chinook 

salmon and steelhead spawning were 1,000 cfs in April and 2,000 cfs in May for all water year types.

c

Flows needed for rearing and outmigration of chinook salmon and steelhead and spawning of steelhead. 
1-IV-28 WORKING PAPER ON RESTORATION NEEDS

d

Flows needed for steelhead rearing.

Species: Fall-run chinook salmon; steelhead; American shad

2. Evaluate the effectiveness of pulse flows for facilitating successful juvenile salmon

outmigration: Optimize outmigration success when water is in short supply (e.g., dry and critically dry 

water years).

Species: Fall-run chinook salmon; steelhead

3. Reduce and control instream flow ramping rates: Reduce hazards posed to juvenile salmonids 

when flow rates change rapidly.

Species: Fall-run chinook salmon; steelhead

4. Maintain adequate instream flows for temperature control: Enhance spawning, incubation, 

rearing, and outmigration conditions.

Species: Fall-run chinook salmon; steelhead; American shad

5. Evaluate and modify (if found to be effective) the water release outlets at Englebright Dam: 

Assess whether enhancement of control, via shutter configuration, over temperature of water released 

downstream, and management of the cold water pools, is warranted.

Species: Fall-run chinook salmon; steelhead

6. Improve efficiency of screening devices at Hallwood-Cordua, Brophy-South Yuba, and Browns 

Valley water diversions: Reduce entrainment and related losses. 

Species: Fall-run chinook salmon; steelhead

7. Improve efficiency of fish bypasses at Hallwood-Cordua, Brophy-South Yuba, and Browns 

Valley water diversions: Reduce entrainment and related losses. 

Species: Fall-run chinook salmon; steelhead

8. Exclude piscivores from areas around Hallwood-Cordua, Brophy-South Yuba, and Browns 

Valley water diversions: Reduce predation losses of juvenile salmonids.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

 SACRAMENTO-SAN JOAQUIN DELTA 1-IV-29

Species: Fall-run chinook salmon; steelhead

9. Maintain a minimum flow of 175 cfs through the critical Simpson Lane reach during the 

spawning period in dry and critical years: Facilitate passage of spawning adults through the critically 

shallow portions of the Simpson Lane reach.

Species: Fall-run chinook salmon; steelhead

10. Modify fish ladders at Daguerre Point Dam: Facilitate passage of spawning adults.

Species: Fall-run chinook salmon; steelhead

11. Maintain appropriate flows through ladders at Daguerre Point Dam during the spawning 

season: Facilitate passage of spawning adults.

Species: Fall-run chinook salmon; steelhead 

12. Purchase streambank conservation easements: Improve habitat and instream cover.

Species: Fall-run chinook salmon; steelhead

13. Terminate program to remove woody debris from stream channel: Provide instream cover for 

juvenile salmonids, especially upstream of Daguerre Point Dam.

Species: Fall-run chinook salmon; steelhead

14. Place large woody debris in stream channel: Provide instream cover for juvenile salmonids.

Species: Fall-run chinook salmon; steelhead

15. Impose stricter harvest regulations on commercial fishers: Increase spawning escapement of 

naturally produced chinook salmon.

Species: Fall-run chinook salmon; steelhead

16. Conduct weekly on-river patrols in areas where poaching is a concern: Increase spawning 

escapement.

Species: Fall-run chinook salmon; steelhead
1-IV-30 WORKING PAPER ON RESTORATION NEEDS

17. Modify the dam face of the Daguerre Point Dam: Reduce juvenile mortality from predation as 

outmigrants pass over the dam.

Species: Fall-run chinook salmon; steelhead

18. Maintain mean daily water temperatures between 61°F and 65°F for at least 1 month between 

April 1 and June 30 at Marysville: Improve American shad spawning success and egg survival using 

multilevel outlets.

Species: American shad

Bear River

1. Implement the Wheatland flow schedule: Provide a sufficient amount of water at preferred 

temperatures for migration, holding, spawning, incubation, rearing, and outmigration of chinook salmon and 

spawning of white and green sturgeon.

Bear River flows (cfs) at Wheatlanda

Month

Wet

Above 

normal

Below 

normal

October 1-14 100b100b100b 

October 15-December 31 250b250b250b 

January 250c250c250c 

February-March 900d900d250c,d

April-May 900d900d250c 

June 250e250e250e 

July-September 10f10f10f 

a

Salmonid flows apply for wet to below-normal years. Sturgeon flows are for above-normal and wet 

year types.

b

Flows needed for spawning, incubation, and rearing of chinook salmon and steelhead.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

 SACRAMENTO-SAN JOAQUIN DELTA 1-IV-31

c

Flows needed for spawning, incubation, rearing and outmigration of chinook salmon and steelhead. 

Physical habitat needs alone (depth, velocity, and substrate in PHABSIM analyses) suggest that chinook 

salmon require at least 190 cfs from January to March and 100 cfs from April to June.

d

Flows needed for white and green sturgeon spawning. Flows needed for spawning, incubation, and 

rearing (February-March) and rearing and outmigration (April-May) of chinook salmon and steelhead 

were 250 cfs in February through May. 

e

Flows needed for rearing and outmigration of chinook salmon and steelhead.

f

Flows will need to be higher to address temperature requirements of steelhead.

Species: Fall-run chinook salmon; steelhead; white and green sturgeon

2. Conduct an IFIM study to determine instream flow and temperature requirements for all life 

stages of salmon and steelhead: Ensure that the available water is utilized to its fullest potential to benefit 

all life stages of salmon and steelhead.

Species: Fall-run chinook salmon; steelhead

3. Implement the Wheatland and Highway 70 water temperature standards: Protect all life stages 

of juvenile salmonids and white and green sturgeon. Develop operational criteria for Camp Far West and 

other upstream reservoirs to improve temperature conditions in the lower Bear River.

Bear River water temperatures (°C)a at Wheatland and 

Highway 70 bridges (temperatures in parentheses are °F).

Month Wheatland Highway 70

October 1-14 15.6 (60) 15.6 (60)

October 15-December 31 14.4 (58) 13.9 (57)

January-March 13.3b (56) 13.9b (57)

April-June 15.6b (60) 15.6b (60)

July-September 18.3 (65) 18.3 (65)

a Recommended mean daily temperatures to be maintained during wet, above-normal, and below-normal 

water years. 
1-IV-32 WORKING PAPER ON RESTORATION NEEDS

b Water temperatures maintained at or below 63°F for white and green sturgeon spawning, from just 

downstream of Camp Far West Reservoir to confluence with the Feather River, between February and 

May in wet and above-normal years.

Species: Fall-run chinook salmon; steelhead; white and green sturgeon

4. Effectively screen all diversions: Reduce loss of production to entrainment.

Species: Fall-run chinook salmon; steelhead; white and green sturgeon

5. Monitor water quality particularly at agricultural return outfalls: Ensure that suitable water 

quality exists for all life stages of salmonids. Take appropriate action to correct water quality problems.

Species: Fall-run chinook salmon; steelhead; white and green sturgeon

6. Negotiate removal or modification of the culvert crossing at Patterson Sand & Gravel and 

other physical and chemical barriers impeding anadromous fish migration: Provide uninhibited 

passage for all life stages of anadromous fish. 

Species: Fall-run chinook salmon; steelhead; white and green sturgeon

7. Investigate the extent that poaching and/or fishing reduces adult spawning stock: Increase 

production by decreasing adult mortality associated with poaching and fishing.

Species: White and green sturgeon

American River

1. Implement the H Street Bridge flow schedule: Optimize migration, spawning, incubation, rearing, 

and outmigration conditions in the lower American River for chinook salmon, steelhead, and American shad.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

 SACRAMENTO-SAN JOAQUIN DELTA 1-IV-33

American River flows (cfs) at H Street Bridge

Month

Wet

Above 

normal

Below

normal Drya Criticala

Critical

relaxationb

Octoberc 2,500 2,000 2,000 1,750 1,750 800

November-Februaryc2,500 2,000 2,000 1,750 1,750 1,200

Marchd3,000 3,000 3,000 2,000 2,000 1,500

April-Maye11,200 8,600 7,400 5,300 3,100 1,500

June 4,500d3,000d3,000d2,000d2,000d500f

Julyf2,500 2,500 2,500 1,500 1,500 500

Augustf2,500 2,000 2,000 1,000 1,000 500

Septemberf2,500 1,500 1,500 500 500 500

a The dry and critical flow regimes can accommodate all but the most severe drought conditions. 

b The "critical relaxation" flow regime is intended for application to only the most severe drought years.

c

Flows needed for chinook salmon spawning and incubation.

d

Flows needed for salmonid rearing and outmigration.

e

Flows needed for American shad spawning. Refer to flows in March for salmonid requirements.

f

Flows for steelhead rearing.

Species: Fall-run chinook salmon; steelhead; American shad
1-IV-34 WORKING PAPER ON RESTORATION NEEDS

2. Develop water allocation guidelines: Provide, through planning, a reasonable way to divide limited 

water resources among all appropriate users, including fish.

Species: Fall-run chinook salmon; steelhead

3. Evaluate the effectiveness of pulse flows for facilitating successful juvenile salmonid

outmigration: Optimize outmigration success when water is in short supply (e.g., dry and critically dry 

years).

Species: Fall-run chinook salmon; steelhead

4. Reduce and control instream flow ramping rates and flow fluctuation: Reduce hazards posed to 

juvenile salmonids when flow rates change quickly.

Species: Fall-run chinook salmon; steelhead

5. Reconfigure Folsom Dam (penstock inlet ports) "shutters": Enhance control over temperature of 

water released downstream and allow improved management of Folsom Reservoir's cold water pool.

Species: Fall-run chinook salmon; steelhead

6. Replenish spawning gravel and/or restore existing spawning grounds: Enhancement of 

spawning habitat.

Species: Fall-run chinook salmon; steelhead

7. Improve the fish screen at Fairbairn Water Treatment Plant: Reduce entrainment losses. 

Species: Fall-run chinook salmon; steelhead

8. Modify timing and rate of water diverted from the river annually: Reduce entrainment losses. 

Focus effort toward minimizing the impacts of diversions during periods when juvenile salmonids migrate 

(e.g., April through June).

Species: Fall-run chinook salmon; steelhead

9. Develop a riparian corridor management plan: Improve and protect riparian habitat and instream 

cover.

Species: Fall-run chinook salmon; steelhead
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

 SACRAMENTO-SAN JOAQUIN DELTA 1-IV-35

10. Terminate current programs that remove woody debris from the river channel: Provide 

instream cover for juvenile salmonids. 

Species: Fall-run chinook salmon; steelhead

11. Impose stricter harvest regulations on both sport and commercial harvesters: Increase 

spawning escapement of naturally produced chinook salmon.

Species: Fall-run chinook salmon; steelhead

12. Conduct weekly on-river patrols in areas where poaching is a concern: Increase spawning 

escapement.

Species: Fall-run chinook salmon; steelhead

13. Change hatchery procedures to benefit native stocks: Rebuild native stocks.

Species: Fall-run chinook salmon; steelhead

Mokelumne River

1. Implement the Woodbridge Dam flow schedule: Increase escapement and survival of salmonids 

and American shad in the lower Mokelumne River.

Mokelumne River flowsa (cfs) just downstream 

of Woodbridge Dam

Month

Wet

Above 

normal

Below

normal Dry Critical 

Octoberb300c300c300c200c200c

November-Decemberb350c300c300c200c200c

Januaryb400d300d300d200c200c

Februaryb450d350d350d200d200d

March 550d350

d

350d250d250d

April-May 3,700e2,900e2,500e1,800e1,000e
1-IV-36 WORKING PAPER ON RESTORATION NEEDS

Mokelumne River flowsa (cfs) just downstream 

of Woodbridge Dam

Month

Wet

Above 

normal

Below

normal Dry Critical 

June 950d500d500d150d150d

July 250d100d100d60f60f

August-September 60f60f60f60f60f

a Daily flow fluctuations shall not exceed 10% of the average flow within any 24-hour period, and weekly 

fluctuations shall not exceed 20% of the average flow within any 7-day period. Flows should not be 

reduced by more than 300 cfs during any 6-day period.

b

Should flows exceed 400 cfs for any 7-day period during the peak spawning season (OctoberDecember), flows shall not be reduced below 400 cfs for the duration of the spawning/incubation period 

(October-February).

c

Flows needed for chinook salmon spawning and incubation.

d

Flows needed for chinook salmon rearing and outmigration.

e

Flows needed for American shad spawning. Flows needed for salmon in April are 700 cfs (wet years), 

600 cfs (above- and below-normal years) and 350 cfs (dry and critical years). Flows needed for 

salmon in May are 1,250 cfs (wet years), 900 cfs (above- and below-normal years) and 400 cfs (dry 

and critical years).

f Based on report of an instream barrier near Thornton that will prevent or impair the upstream migration 

of adult chinook salmon at flows less than 60 cfs (DFG 1991).

Species: Fall-run chinook salmon; steelhead; American shad

2. Provide flows maximizing suitable chinook salmon spawning habitat: Improve quantity of 

spawning habitat. 

Species: Fall-run chinook salmon; steelhead
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

 SACRAMENTO-SAN JOAQUIN DELTA 1-IV-37

3. Replenish gravels suitable for salmonid spawning habitat: Improve quantity and quality of habitat.

Species: Fall-run chinook salmon; steelhead

4. Cleanse spawning gravels of fine sediments: Improve the quality of spawning habitat.

Species: Fall-run chinook salmon; steelhead

5. Prevent sedimentation of spawning gravel: Improve the quality of spawning habitat. 

Species: Fall-run chinook salmon; steelhead

6. Restrict flow fluctuations and reductions: Prevent redd dewatering and stranding of juvenile 

salmonids.

Species: Fall-run chinook salmon; steelhead

7. Remove Woodbridge Dam or delay installing dam flashboards until July: Reduce losses of 

salmon smolts to predation.

Species: Fall-run chinook salmon; steelhead

8. Reduce or eliminate mortality and delays of juvenile salmonids associated with passage past 

the Woodbridge Irrigation District diversion and Woodbridge Dam: Improve survival of juvenile 

salmonids past the Woodbridge Irrigation District diversion and Woodbridge Dam.

Species: Fall-run chinook salmon; steelhead

9. Eliminate barriers to efficient and timely migration of adult salmonids: Improve passage 

conditions at Woodbridge Dam for adult salmonid migration.

Species: Fall-run chinook salmon; steelhead and American shad

10. Screen all diversion in the lower Mokelumne River to DFG standards: Prevent entrainment or 

loss of juvenile salmonids.

Species: Fall-run chinook salmon; steelhead; American shad
1-IV-38 WORKING PAPER ON RESTORATION NEEDS

11. Maintain suitable water temperatures for all salmonid life stages: Provide for timely migrations 

and increased survival of adult and juvenile salmonids.

Species: Fall-run chinook salmon; steelhead

12. Enhance and maintain riparian corridor: Improve streambank and channel rearing for juvenile 

salmonids.

Species: Fall-run chinook salmon; steelhead

13. Set and enforce water quality standards: Provide optimal water quality for all life stages of 

salmonid.

Species: Fall-run chinook salmon; steelhead

14. Eliminate adverse effects of poaching and angling on salmonid production: Protect adult 

salmonid production.

Species: Fall-run chinook salmon; steelhead

15. Evaluate the feasibility of increasing available rearing habitat: Maximize suitable rearing 

habitat.

Species: Fall-run chinook salmon; steelhead

Cosumnes River

1. Determine and set instream flow requirements: Ensure adequate flows for all life stages of 

salmonids.

Species: Fall-run chinook salmon; possibly steelhead

2. Restrict water diversions during critical periods for salmonids: Ensure adequate instream flows 

for all life stages and provide better passage for adults and juveniles.

Species: Fall-run chinook salmon; possibly steelhead

3. Purchase existing water rights: Ensure adequate flows for all life stages of salmonids.

Species: Fall-run chinook salmon; possibly steelhead
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-39

 4. Evaluate diversion dams and barriers for fish passage problems: Ensure passage problems for 

adult and juvenile salmonids.

Species: Fall-run chinook salmon; possibly steelhead

5. Remedy passage problems identified in Action 4: Ensure of passage adult and juvenile salmonids.

Species: Fall-run chinook salmon; possibly steelhead

6. Enforce Fish and Game Codes that prohibit construction of unlicensed dams: Ensure 

unimpeded passage of adult and juvenile salmonids.

Species: Fall-run chinook salmon; possibly steelhead

7. Effectively screen all diversions: Prevent loss of juvenile salmonids to entrainment.

Species: Fall-run chinook salmon; possibly steelhead

8. Establish riparian corridor protection zone: Preserve existing salmonid habitat from incompatible 

land use and moderate water temperature.

Species: Fall-run chinook salmon; possibly steelhead

9. Rehabilitate damaged areas: Remedy incompatible land use practices that have increased 

sedimentation of the river and elevate water temperatures.

Species: Fall-run chinook salmon; possibly steelhead

Calaveras River

1. Implement the Calaveras flow schedule: Optimize migration, spawning, incubation, rearing, and 

outmigration conditions for chinook salmon.

Calaveras River flows (cfs)a 

Month

Wet

Above 

normal

Below

normal Dry Critical

February 19-29 225b70 70 50 50 
1-IV-40 WORKING PAPER ON RESTORATION NEEDS

Calaveras River flows (cfs)a 

Month

Wet

Above 

normal

Below

normal Dry Critical

March 1-20 225b225b225b225b225b

March 21-30 225b225b225b120c120c

March 31-September 15 200c160c160c120c120c

September 16-October 31 100d100d100d100d100d

November 1-February 18 70e70e70e50e50e

a

Flows for spawning and incubation, rearing, and temperature control are needed only to Bellota because 

most fish remain above where the majority of diversions occur. However, 50 to 70 cfs left instream to 

tidewater would help maintain the overall health of the river system. Flows are proposed on an interim 

basis until more complete instream flow studies are conducted.

b

Flows of 225 cfs are needed for attraction and passage of adults and smolts. Flows are required to 

mouth of San Joaquin River.

c

Flows needed for spawning and incubation.

d

Flows needed for juvenile rearing, including temperature protection. 

e

Flows needed for juvenile rearing.

Species: Winter-run chinook salmon

2. Manage water temperatures for all salmonid life stages, including spawning, incubation, 

rearing, juvenile outmigration, and adult migration: Provide suitable water temperatures for salmonid 

survival.

Species: Winter-run chinook salmon

3. Remove migration barriers affecting salmonids: Improve upstream and downstream migration.

Species: Winter-run chinook salmon
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-41

4. Evaluate screening needs and install screens as needed on existing diversions that may affect 

juvenile outmigrants: Protect outmigrants.

Species: Winter-run chinook salmon

5. Monitor sport fishing and regulations: Protect chinook and other salmonids.

SACRAMENTO-SAN JOAQUIN DELTA

1. Provide protection for juvenile salmonids migrating through the Delta from November 1 

through June 30, equivalent to protection provided by restricting exports to minimal levels: 

Increase survival in Delta for all juvenile salmonid life stages (and potentially adults) affected by CVP and 

SWP exports. This includes juveniles migrating through the Delta using the mainstem rivers, as well as 

juveniles diverted into the central and southern portions of the Delta and juveniles emigrating from the San 

Joaquin Basin.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; striped bass 

2. Establish a moratorium on net increases in Delta diversions and withdrawals at the Contra 

Costa Canal: Reduce direct and indirect losses of striped bass resulting from the operation of the pumps 

and diversions.

Species: Striped bass

3. Close the DCC gates from 1 October through 30 June: Increase the survival of juvenile fish 

migrating down the mainstem Sacramento River by reducing the number diverted into the central and 

southern Delta.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; American shad

4. Maintain positive QWEST flows, or an equivalent measure of net seaward flows at Jersey 

Point, of 1,000 cfs in critical and dry years, 2,000 cfs in below- and above-normal years, and 3,000 

cfs in wet years from October 1 through June 30: Increase survival of smolts migrating down the 

mainstem rivers, decrease the number of smolts diverted into the central Delta, increase the survival of 

smolts diverted into the central Delta, and provide attraction flows for the San Joaquin Basin adults 

(October-December).

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; striped bass; American shad; 

white and green sturgeon
1-IV-42 WORKING PAPER ON RESTORATION NEEDS

5. Increase mean monthly flow at Vernalis to 4,500 cfs, 6,000 cfs, 8,000 cfs, 12,000 cfs, and 

21,000 cfs in critical, dry, below-normal, above-normal, and wet year types (60-20-20) during 

smolt migration period: Increase the survival of smolts migrating through the Delta originating from the 

San Joaquin Basin.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead

6. Implement the Delta outflow schedule: Increase production of striped bass, American shad; white 

and green sturgeon

Delta outflow (cfs) measured at Chipps Islanda

Month

Wet

Above

normal

Below

normal Dry Critical

October 11,500 7,500 6,500 7,500 7,000 

November 29,500 24,000 13,000 13,500 8,000 

December 80,500 36,000 24,500 19,500 12,500 

January 100,500 85,500 36,500 20,000 18,000 

February 103,000 85,500 57,500 40,000 18,000 

March 101,000 89,500 51,000 50,500 24,500 

April 99,200b76,100b68,000d49,500d 27,100 f

May 99,500c77,500c66,100e46,600e 27,100 f

June 67,500 44,500 36,000 24,000 16,500 

July 27,000 16,000 12,000 8,500 6,000 

August 11,000 7,000 6,000 5,000 3,500 

September 8,000 6,500 5,500 4,500 3,500 

a

Flows needed for striped bass except where noted.

b

Flows needed for American shad. Flows needed for striped bass are 96,500 cfs and 73,000 cfs in wet 

and above-normal years, respectively. Flows needed for white and green sturgeon are 25,000 cfs; with 

minimum daily outflows not less than 20,000 cfs and 15,000 cfs in April and May, respectively. 
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-43

c

Flows needed for striped bass. Flows needed for American shad are 99,200 cfs and 76,100 cfs in wet 

and above-normal water years, respectively. Flows needed for white and green sturgeon are 25,000 cfs 

with minimum daily outflows not less than 20,000 cfs and 15,000 cfs in April and May, respectively. 

d

Flows needed for striped bass. Flows needed for American shad are 66,100 cfs and 46,500 cfs in 

below-normal and dry water years.

e

Flows needed for American shad. Flows of 65,500 cfs, 46,500 cfs needed for striped bass in belownormal and dry water years, respectively.

f

Flows needed for American shad. Flows needed for striped bass are 25,500 cfs and 27,000 cfs in April 

and May, respectively.

Species: Fall-, late fall-, winter-, and spring-run chinook salmon; steelhead; striped bass; American shad; 

white and green sturgeon

7. Reduce predation at and near the SWP and CVP pumps: Improve survival of striped bass eggs, 

larvae, and juveniles entrained by the SWP and CVP pumps.

Species: Striped bass

8. Improve CVP and SWP salvage operations: Improve survival of eggs, larvae, and juveniles.

Species: Striped bass; white and green sturgeon

9. Minimize loss and/or entrainment of eggs, larvae, and juveniles at the Contra Costa Canal 

diversion: Improve survival of eggs, larvae, and juveniles as they enter historical nursery areas.

Species: Striped bass; white and green sturgeon

10. Minimize loss and/or entrainment of eggs, larvae, and juveniles at the PG&E power 

generating plants: Improve survival of eggs, larvae, and juveniles as they enter historical nursery areas.

Species: Striped bass; white and green sturgeon

11. Eliminate, relocate, or reduce Sherman and Twitchell Island diversions: Improve survival of 

eggs, larvae, and juveniles as they enter historical nursery areas.

Species: Striped bass; white and green sturgeon
1-IV-44 WORKING PAPER ON RESTORATION NEEDS

12. Minimize loss and/or entrainment of eggs, larvae, and juveniles at private agricultural 

diversions: Improve survival of eggs, larvae, and juveniles as they enter historical nursery areas.

Species: Striped bass; white and green sturgeon

13. Support measures to prevent development of a water quality barrier to adult striped bass 

migration in the San Joaquin River near Stockton: Ensure access to spawning areas in the San 

Joaquin River upstream of Stockton.

Species: Striped bass

14. Reduce toxic chemical and trace metal pollution: Provide better water quality for all life stages of 

anadromous fish.

Species: Striped bass; white and green sturgeon

15. Eliminate or reduce dredging and dredge spoil contribution to water pollution: Provide better 

water quality for all life stages of anadromous fish.

Species: Striped bass; white and green sturgeon

16. Reduce or eliminate unnecessary landfill projects: Reduce or eliminate habitat loss due to filling of 

Bay and Delta tidelands.

Species: Striped bass

17. Reduce or eliminate illegal take and poaching: Reduce impacts of illegal fishing on striped bass 

populations.

Species: Striped bass

18. Reduce or eliminate the annual summer die-off of adult striped bass: Reduce mortality of adult 

striped bass.

Species: Striped bass

19. Minimize incidental take of adult striped bass by commercial bay shrimp fishery: Increase

young-of-the-year striped bass survival.

Species: Striped bass
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-45

20. Reduce or eliminate introduction of exotic aquatic organisms: Reduce impacts that exotic 

species have on striped bass and their food supply.

Species: Striped bass

SAN JOAQUIN RIVER BASIN

 

Lower San Joaquin River Tributaries

Merced River -

1. Implement the Merced River flow schedule: Manage flows to benefit all life stages of chinook 

salmon.

Merced River flows (cfs) at Crocker-Hoffman Diversion to confluence with 

the San Joaquin River (flows rounded to nearest 50 cfs)

Month Weta

Above

normal

Below 

normal

 

Dry Critical

October 350b300b300b250b250b

November 350b350b300b300b250b

December 600c550c300b300b250b

January 1,100c600c300b300g250g

February 1,450c1,050c500g300g250g

March 1,500c1,050c600g450g400g

April 1,800d1,350d1,150d950d750d

May 2,950d2,300d1,750d1,200d850d

June 2,850d1,450d1,150d650d450d

July 1,150e400e250 200f200f

August 350f300f25f200f200f

September 350f300f25f200f200f
1-IV-46 WORKING PAPER ON RESTORATION NEEDS

a Year types based on San Joaquin Basin 60-20-20 Index.

b Based on IFIM spawning flow recommendations for similar size drainages (Reynolds 1993) and the 

assumption that greater than historical flows are needed to compensate for elimination of access to 

upstream habitat. 

c Based on historical (1922-1991) percent monthly contribution to total annual unimpaired runoff for the 

Stanislaus River basin and the assumption that flow should not be reduced between spawning and 

outmigration to prevent redd dewatering or stranding of rearing juveniles.

d Based on Vernalis flow requirement and historical (1922-1990) percent monthly contribution to total 

annual unimpaired runoff.

e Based on historical (1922-1990) percent monthly contribution to total annual unimpaired runoff.

f Based on IFIM recommendations for similar size drainages ( Reynolds 1993) and the assumption that 

greater than historical flows are needed to compensate for elimination of access to upstream habitat.

g Based on IFIM flow recommendations for similar size drainages and the assumption that flow should not 

be reduced between spawning and outmigration to prevent redd dewatering or stranding of rearing 

juveniles.

Species: Fall-run chinook salmon

2. Adjust flow schedule to maintain water temperatures at 56°F between October 15 and 

February 15, and at 65°F between April 1 and May 31: Maintain water temperature within ranges 

suitable for chinook salmon spawning, incubation, rearing, and outmigration.

Species: Fall-run chinook salmon

3. Reduce impacts of rapid flow fluctuations: Increase hatching success and juvenile survival by 

reducing ramping rates and eliminating flow fluctuation during key periods.

Species: Fall-run chinook salmon

4. Restore and protect instream and riparian habitat: Ensure the long-term sustainability of physical, 

chemical, and biological conditions needed to meet production goals for chinook salmon through restoration 

and protection of stream ecosystem.

Species: Fall-run chinook salmon
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-47

5. Install and maintain fish protection devices at riparian pumps and diversion: Reduce or 

eliminate loss of juvenile chinook salmon due to entrainment by pumps and diversions.

Species: Fall-run chinook salmon

6. Provide additional law enforcement: Increase spawning success, reduce entrainment, and prevent 

additional destruction of stream habitat.

Species: Fall-run chinook salmon

7. Provide fish passage around reservoirs: Increase production and minimize impacts on water 

interests by providing access to additional spawning/rearing habitat upstream of reservoirs.

Species: Fall-run chinook salmon; steelhead

Tuolumne River -

1. Implement the Tuolumne River flow schedule: Manage flows to benefit all life stages of chinook 

salmon.

Tuolumne River flows (cfs) at LaGrange Dam to confluence 

with the San Joaquin River (flows rounded to nearest 50 cfs)

Month Weta

Above

normal

Below 

normal Dry Critical

October 750b300b300b200b150b

November 1250c800c350b300b150b

December 1,400c1,050c350b350b200c

January 1,700c1,150c500c400b250c

February 2,100c1700c950c700c500c

March 2,300c1,700c1,300c1,000c900c

April 2,950d2,450d2,350d1,900d1,500d

May 5,150d4,200d3,350d2,500d1,850d

June 5,000d3,250d2,600d1,550d1,000d

July 2,150e900e650e250e200e
1-IV-48 WORKING PAPER ON RESTORATION NEEDS

Tuolumne River flows (cfs) at LaGrange Dam to confluence 

with the San Joaquin River (flows rounded to nearest 50 cfs)

Month Weta

Above

normal

Below 

normal Dry Critical

August 450e200e100f100f50f

September 350f150f150f100f50f

a Year type based on San Joaquin Basin 60-20-20 Index.

b Based on USFWS IFIM flow recommendations (USFWS unpublished data) and the assumption that 

greater than historical flows are needed to compensate for elimination of access to upstream habitat. 

c Based on historical (1922-1990) percent monthly contribution to total annual unimpaired runoff for the 

Tuolumne River Basin and the assumption that flow should not be reduced between spawning and 

outmigration to prevent redd dewatering or stranding of rearing juveniles.

d Based on Vernalis flow requirement and historical (1922-1990) percent monthly contribution to total 

annual unimpaired runoff.

e Based on historical (1922-1990) percent monthly distribution of total annual unimpaired runoff.

f

Flow based on USFWS IFIM recommendations.

Species: Fall-run chinook salmon

2. Adjust flow schedule to maintain water temperatures at 56°F between October 15 and 

February 15 and at 65°F between April 1 and May 31: Maintain water temperature within ranges 

suitable for chinook salmon spawning, incubation, rearing, and outmigration.

Species: Fall-run chinook salmon

3. Reduce impacts of rapid flow fluctuations: Increase hatching success and juvenile survival by 

reducing ramping rates and eliminating flow fluctuation during key periods.

Species: Fall-run chinook salmon
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-49

4. Restore and protect instream and riparian habitat: Ensure the sustainability of physical, chemical, 

and biological conditions needed to meet production goals for chinook salmon through restoration and 

protection of the stream ecosystem.

Species: Fall-run chinook salmon

5. Install and maintain fish protection devices at riparian pumps and diversions: Prevent or 

eliminate loss of juvenile chinook salmon due to entrainment.

Species: Fall-run chinook salmon

6. Provide additional law enforcement for illegal take of salmon, stream alteration, and water 

pollution and to ensure adequate protection for juvenile salmon at pumps and diversions: Increase 

spawning success, reduce entrainment, improve water quality, and prevent additional destruction of stream 

habitat.

Species: Fall-run chinook salmon

7. Provide fish passage around reservoirs: Increase production and minimize impacts on water 

impacts by providing access to additional spawning/rearing habitat upstream of reservoirs.

Species: Fall-run chinook salmon

Stanislaus River -

1. Implement the Stanislaus River flow schedule: Manage flows to benefit all life stages of chinook 

salmon.

Stanislaus River flows (cfs) from Goodwin Dam to confluence 

with the San Joaquin River (flows rounded to nearest 50 cfs)

Month Weta

Above

normal

Below 

normal Dry Critical

October 350b350b300b250b250b

November 400b350b300b300b250b

December 850c650c300b300b250b

January 1,150c800c300d300d250d
1-IV-50 WORKING PAPER ON RESTORATION NEEDS

Stanislaus River flows (cfs) from Goodwin Dam to confluence 

with the San Joaquin River (flows rounded to nearest 50 cfs)

Month Weta

Above

normal

Below 

normal Dry Critical

February 1,450c1,150c700c450d300d

March 1,550c1,150c850c650c550c

April-May 5,600e4,300e3,800e2,700e1,500e

June 2,650f1,600f1,300f700f450f

July 900g400g350h200h250h

August 350h300h250h200h200h

September 350h300h250h200h200h

a Year types based on San Joaquin Basin 60-20-20 Index.

b

Flow based on IFIM Recommendations and the assumption that greater than historical flows are needed 

to compensate for elimination of access to upstream spawning habitat. 

c Based on historical (1922-1990) percent monthly contribution to total annual unimpaired runoff for the 

Stanislaus River basin and the assumption that flow should not be reduced between spawning and 

outmigration to prevent redd dewatering or stranding of rearing juveniles.

d Based on USFWS IFIM spawning flow recommendations and the assumption that flow should not be 

reduced between spawning and outmigration to prevent redd dewatering and stranding of rearing 

juveniles.

e

Flows needed for American shad spawning. Flows needed for salmon during April are 2,100 cfs, 1,800 

cfs, 1,750 cfs, 1,250 cfs, and 950 cfs in wet, above-normal, below-normal, dry, and critical water years. 

 Flows needed for salmon during May are 3,500 cfs, 2,750 cfs, 2,050 cfs, 1,400 cfs, and 900 cfs in 

wet, above-normal, below-normal, dry, and critical water years. Stanislaus River contribution to 

Vernalis flow standard. Based on historical monthly contribution of the Stanislaus River to total 

unimpaired runoff for the San Joaquin River Basin, 1922-1990.

f

Stanislaus River contribution to Vernalis flow standard. Based on historical monthly contribution of the 

Stanislaus River to total unimpaired runoff for the San Joaquin River Basin, 1922-1990.
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-51

g Based on historical (1922-1990) percent monthly contribution to total annual unimpaired runoff for the 

Stanislaus River basin.

h Based on USFWS IFIM flow and assumption that greater than unimpaired flow is needed to 

compensate for eliminations of access to upstream habitat.

Species: Fall-run chinook salmon

2. Operate New Melones, Tulloch, and Goodwin reservoirs to maintain water temperatures at 

56°F between October 15 and February 15 and at 65°F between April 1 and May 31: Maintain 

water temperature within ranges suitable for chinook salmon spawning, incubation, rearing, and 

outmigration.

Species: Fall-run chinook salmon

3. Restore and protect instream and riparian habitat: Ensure the long-term sustainability of physical, 

chemical, and biological conditions needed to meet production goals for chinook salmon through restoration 

and protection of the stream ecosystem.

Species: Fall-run chinook salmon

4. Reduce impacts of rapid flow fluctuations: Increase hatching success and juvenile survival by 

reducing flow fluctuation rates resulting from peaking power and other reservoir operations.

Species: Fall-run chinook salmon

5. Install and maintain fish protection devices at riparian pumps and diversions: Reduce or 

eliminate loss juvenile chinook salmon due to entrainment by pumps and diversions.

Species: Fall-run chinook salmon

6. Provide additional law enforcement for illegal take of salmon, stream alterations, water 

pollution and to ensure adequate screening of pumps and diversions: Increase spawning success, 

reduce entrainment, improve water quality, and prevent additional destruction of stream habitat.

Species: Fall-run chinook salmon

7. Remove or modify of Old Melones Dam: Reduce fall water temperatures in the Stanislaus River. 

Species: Fall-run chinook salmon
1-IV-52 WORKING PAPER ON RESTORATION NEEDS

8. Provide fish passage around reservoirs: Increase production and minimize impacts of anadromous 

fish restoration on water interests by providing access to additional spawning and rearing habitat upstream 

of reservoirs.

Species: Fall-run chinook salmon; steelhead

Lower San Joaquin River

1. Implement the Stevinson flow schedule: Manage flows to benefit all life stages of chinook salmon. 

San Joaquin flows (cfs)a at Stevinson (flows rounded to nearest 50 cfs)

Month

Wetb

Above 

normal

Below 

normal Dry Critical

April 5,150 2,650 2,050 1,750 1,250

May 7,000 4,450 3,050 2,300 1,600

June 6,800 3,450 2,600 1,700 1,050

a

San Joaquin contribution to Vernalis flow standard. Based on Vernalis flow standards and the historical 

percent contribution of the San Joaquin River to total unimpaired San Joaquin Basin runoff.

b Year types based on San Joaquin Basin 60-20-20 Index.

Species: Fall-run chinook salmon

2. Provide mean monthly flows of at least 7,000 cfs at Newman between February and May in 

wet and above-normal water years: Increase sturgeon production by providing adequate flows for 

upstream migration, spawning, and progeny survival.

Species: White and green sturgeon

3. Implement the Vernalis flow schedule: Manage flows to benefit all life stages of chinook salmon, 

American shad, and white and green sturgeon. 
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-53

San Joaquin River flows (cfs) at Vernalis

Month

Weta

Above

normal

Below

normal Dry Critical 

October 1,450b950b900b700b650b

November 2,000b1,500b950b900b650b

December 2,850b2,250b950b950b700b

January 3,950b2,550b1,100b1,000b750b

February 14,000c 14,000c2,150b1,450b1,050b

March 14,000c14,000c2,750b2,100b1,850b

April 28,400d21,800d18,900d13,500d7,800d

May 28,400d21,800d18,900d13,500d7,800d

June 17,300e9,750e7,650e4,600e2,950e

July 4,200d1,700d1,250d650d650d

August 1,150d800d600d500d450d

September 1,050d750d650d500d450d

a Year types based on San Joaquin Basin 60-20-20 Index.

b

Sum of flow from the Stanislaus, Tuolumne, and Merced rivers.

c

Flows needed for sturgeon spawning. Flows needed for salmon in February are 5,000 cfs (wet years) 

and 3,900 cfs (above-normal years). Flows needed for salmon in March are 5,350 cfs (wet years) and 

3,900 (above-normal years) in March. Salmon flows are sum of flows from the Stanislaus, Tuolumne, 

and Merced rivers. 

d

Flows needed for American shad spawning. Flows needed for salmon in April are 12,000 cfs (wet 

years), 8,250 cfs (above-normal years), 7,300 cfs (below-normal years), 5,850 cfs (dry years), and 

4,450 cfs (critical years). Flows needed for salmon in May are 18,600 cfs (wet years), 13,700 cfs 

(above-normal years), 10,200 cfs (below-normal years), 7,400 cfs (dry years), and 5,200 cfs (critical 
1-IV-54 WORKING PAPER ON RESTORATION NEEDS

years). See footnote e for explanation on flow derivation. Flows needed for white and green sturgeon 

spawning are 14,000 cfs in wet and above-normal water years.

e

Flow required to meet salmon production goals based on regression relationship:

ES,T = (1.820QV)-(0.051XF,S)-18,417.3 (Carl Mesick Consultants 1994)

Where, for a given year class, ES,T is the sum of escapement into the Stanislaus and Tuolumne rivers as 

2- and 3-year-old fish, QV is average San Joaquin River flow (cfs) at Vernalis from April 1 through June 

30 in the year of outmigration, and XF,S is total combined monthly exports (af) for the federal (CVP) and 

state (SWP) water projects, from April 1 through June 30 in the year of outmigration. Flow is allocated 

between April, May, and June on the basis of historical occurrence of unimpaired runoff.

Species: Fall-run chinook salmon; American shad; white and green sturgeon

4. Install and maintain fish protection devices at Banta-Carbona, West Stanislaus, Patterson, and 

El Soyo diversions: Reduce or eliminate loss of juvenile chinook salmon resulting from entrainment by the 

four largest diversions on the San Joaquin River.

Species: Fall-run chinook salmon; depending on mesh aperture could have benefits for striped bass, 

American shad, juvenile white and green sturgeon

5. Install and maintain fish protection devices at small agricultural diversions: Increase survival of 

juvenile salmon by reducing or eliminating entrainment.

Species: Fall-run chinook salmon; depending on mesh aperture could have benefits for striped bass, 

American shad, juvenile white and green sturgeon 

6. Continue prohibition on sport harvest of chinook salmon in the San Joaquin Basin upstream of 

Mossdale; extend closure on the mainstem San Joaquin River downstream to Chipps Island: 

Increase spawning success by preventing harvest of salmon escaping into San Joaquin River tributaries.

Species: Fall-run chinook salmon

7. Prohibit dredging of Stockton ship channel during critical periods: Prevent dissolved oxygen 

stage during periods when adult or juvenile salmon are migrating through the lower San Joaquin River and 

Delta.

Species: Fall-run chinook salmon
SECTION IV. SUMMARY OF RESTORATION ACTIONS -

SAN JOAQUIN RIVER BASIN 1-IV-55

8. Operate head of Old River barrier to protect migrating adults and juveniles: Improve water 

quality for migrating adults, reduce entrainment of outmigrating smolts.

Species: Fall-run chinook salmon; white and green sturgeon

9. Modify reservoir operation to maintain mainstem San Joaquin River water temperatures at 

56°F between October 15 and February 15 and at 65°F between April 1 and May 31 for chinook 

salmon; maintain water temperatures between 61°F and 65°F for 1 month between April 1 and 

June 30 for American shad; and maintain water temperatures below 63°F in spawning areas and 

below 68°F throughout the San Joaquin River in wet and above-normal water years between 

February and May for white and green sturgeon: Prevent delays in adult migration and associated 

higher rates of egg mortality and increase survival of outmigrating juveniles by reducing stress and mortality 

associated with high water temperatures. Water temperatures also provide for sturgeon migration, final 

stages of sexual maturation, spawning, and progeny survival.

Species: Fall-run chinook salmon; American shad; white and green sturgeon

10. Establish a basinwide Conjunctive Water Use Program: Obtain adequate water to meet 

anadromous fish-flow requirements while minimizing impacts on other water users.

Species: Fall-run chinook salmon

11. Reduce predator populations: Increase survival of juvenile salmon by reducing predator 

populations.

Species: Fall-run chinook salmon

12. Remove barriers to sturgeon migration: Remove barriers that prevent or slow the migration of 

sturgeon to areas where sturgeon spawn. 

Species: White and green sturgeon

13. Adopt gear restrictions eliminating illegal harvest of white and green sturgeon: Increase size 

of spawning stock.

Species: White and green sturgeon 

14. Improve water quality: Improve survival and condition of sturgeon.

Species: White and green sturgeon