Department of the Interior

U.S. Bureau of Reclamation

U.S. Fish and Wildlife Service

Central Valley Project 

Improvement Act

Public Law 102-575

ANNUAL REPORT

Fiscal Year 2007
TABLE OF CONTENTS i 

I. INTRODUCTION .............................................................................. 1

II. EXECUTIVE SUMMARY.................................................................11

III. 2007 PROGRAMMED ACTIVITIES AND ACCOMPLISHMENTS . 15

3406:

(b)(1) Anadromous Fish Restoration Program .............................................................. 15 

(b)(1) “other” Habitat Restoration Program ............................................................................... 21

(b)(1) “other” & (b)(23) Trinity River Restoration Program........................................................................ 26

(b)(23)

(b)(1)(B) Modifi ed CVP Operations .................................................................................... 29

(b)(2) Dedicated 800,000 acre-feet Project Yield ......................................................... 32

(b)(3) & (g) Water Acquisition Program – Instream Water ..................................................... 35

(b)(4) Tracy (Jones) Pumping Plant Program ................................................................ 37

(b)(5) Contra Costa Canal Pumping Plant ..................................................................... 40

(b)(9) & (b)(19) Flow Fluctuations and Reservoir Storage ............................................................ 42

(b)(10) Red Bluff Diversion Dam ..................................................................................... 44

(b)(11) Coleman National Fish Hatchery ........................................................................ 47

(b)(12) Clear Creek Restoration Program ....................................................................... 50

(b)(13) Spawning Gravel Program ................................................................................... 53

(b)(15) Head of Old River Barrier .................................................................................... 56

(b)(16) Comprehensive Assessment and Monitoring Program ....................................... 58

(b)(20) Glenn-Colusa Irrigation District Program ............................................................ 61

(b)(21) Anadromous Fish Screen Program ..................................................................... 63 

(c)(1) San Joaquin River Comprehensive Plan ............................................................. 66

(d)(1), (2) & (5) Introduction to the Refuge Water Supply Program .............................................. 68

(b)(3) & (d)(2) Water Acquisition Program – Refuge Water ........................................................ 72

(d)(5) Refuge Facilities Construction Program and San Joaquin Basin Action Plan 

 Lands Program ...........................................................................................................74

(d)(1), (2) & (5) Refuge Water Conveyance (Wheeling) ............................................................... 76

(g) Ecological/Water Systems Operations Models .................................................. 78

3408:

(h) Land Retirement Program ................................................................................... 81

Appendices

Appendix A Glossary of Terms ................................................................................................ 85

Contents
ii CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2007 ANNUAL REPORT

List of Figures

Introduction 

Figure 1 Central Valley Project System .................................................................................... 2

Figure 2 Central Valley Refuges Receiving CVPIA Water Supplies ......................................... 5

Figure 3 Total CVPIA Obligations by Action Category and Fund Source (1993-2007) ............ 8

(b)(1) “other” 

Figure 4 Habitat Restoration Program Project Locations (1996-2007) ................................... 22

(b)(1) “other” & (b)(23)

Figure 5 Trinity River Restoration Program Map .................................................................... 26

(b)(2) 

Figure 6 Average Annual (b)(2) Water Use in thousand acre-feet (TAF) (2002-2005) ........... 32 

(b)(4) 

Figure 7 Tracy (Jones) Pumping Plant .................................................................................... 37

(b)(5) 

Figure 8 Contra Costa Canal Pumping Plant .......................................................................... 40

(b)(10) 

Figure 9 Red Bluff Diversion Dam .......................................................................................... 44 

Figure 10 Spawning Returns, Winter-Run Chinook, Sacramento River (1967-2006) ............... 46 

(b)(11) 

Figure 11 Coleman Fish Hatchery ............................................................................................ 47 

(b)(12) 

Figure 12 Gravel Injection and Channel Restoration Sites ....................................................... 50 

Figure 13 Fall-Run Chinook Salmon Escapement, Clear Creek (2007) ................................... 51 

Figure 14 Adult Spring-Run Chinook Salmon Population, Clear Creek (2001-2007) ............... 51 

Figure 15 Juvenile Fall-Run Chinook Salmon Produced/Adult Female, 

 Clear Creek (1998-2005) .......................................................................................... 51

Figure 16 Clear Creek Channel Restoration Project Phases ................................................... 52

(b)(13) 

Figure 17 Gravel Placement Sites ............................................................................................ 53

(b)(16) 

Figure 18 Estimated Total Natural Chinook Production, Central Valley (1992-2007) ............... 59 

(b)(20) 

Figure 19 Glenn-Colusa Irrigation District Pumping Plant ........................................................ 61

(b)(21) 

Figure 20 CVPIA Fish Screens Constructed (1992-2007) ........................................................ 65

(d) Introduction 

Figure 21 Central Valley Refuges Receiving CVPIA Water Supplies ....................................... 68

(h) 

Figure 22 Land Retirement Program Sites ............................................................................... 81
TABLE OF CONTENTS iii 

List of Tables

Introduction 

Table 1 FY 2007 Funding Obligations by Provision................................................................. 7

(b)(1) 

Table 2 Summary of Final Restoration Plan Actions and Evaluations Addressed 

 (1995-2007) ...........................................................................................................................16

Table 3 Chinook salmon AFRP production, Central Valley (1992-2006) ............................... 20 

Table 4 Chinook salmon AFRP production, in Battle, Butte, and Clear creeks and 

 Mokelumne River (1992-2006)...................................................................................... 20

(b)(1) “other” 

Table 5 Acres of Habitat Protected and Restored Per Year (1996-2007) ............................. 23

Table 6 Recipients of FY 2007 HRP Funds ........................................................................... 24

(b)(1) “other” & (b)(23)

Table 7 Target Natural Escapement, Trinity River ................................................................. 27

(b)(1)(B) 

Table 8 IFIM Studies Completed and Planned as of 2007 .................................................... 31

(b)(2) 

Table 9 Allocation vs. Use of (b)(2) Water (2001-2007) ......................................................... 33

Table 10 FY 2007 Use of (b)(2) Water ..................................................................................... 34 

(b)(3) 

Table 11 Annual (b)(3) Instream Water Acquisitions (1994-2007) ........................................... 36 

(b)(11) 

Table 12 Coleman NFH Facility Rehabilitation Phases (1991-2007) ...................................... 48

(b)(13) 

Table 13 Total Gravel Placed (1997-2007) .............................................................................. 54 

(b)(21) 

Table 14 AFSP Projects & cfs Screened, Central Valley (1992-2007) .................................... 64 

(d) Introduction

Table 15 Refuge Water Type and Mandated Target ................................................................ 69 

Table 16 Water Allocations by Refuge from 1989 Reports ..................................................... 70 

(d)(2) 

Table 17 Level 2 and Incremental Level 4 Water Deliveries by Water Year (2002-2007) ....... 73 

(d)(5) –Facility Construction and SJBAP

Table 18 Cumulative Completed Construction Actions by Year (1997-2007) .......................... 75 

(d)(1), (d)(2) & (d)(5) – Refuge Conveyance (Wheeling)

(g) 

Table 19 Ecological and Water System Operations Models (1996-2007) ............................... 79 

(h) 

Table 20 Land Acquired, Retired & Restored by Year at Tranquillity and Atwell

 Island Sites (1992-2007) ........................................................................................... 82 
iv CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2007 ANNUAL REPORT

ACID Anderson-Cottonwood Irrigation District

AEAM Adaptive Environmental Assessment and Management Program

AF acre-feet

AFRP Anadromous Fish Restoration Program

AFSP Anadromous Fish Screen Program 

AWP Annual Work Plan

BA Biological Assessment

BLM Bureau of Land Management

BO Biological Opinion

BWGWD Biggs West Gridley Water District

C2VSIM California Central Valley Simulation Model

CAMP Comprehensive Assessment and Monitoring Program

CALFED ISI CALFED Integrated Storage Investigations

CBDA California Bay-Delta Authority

CCWD Contra Costa Water District

CDWR California Department of Water Resources

CFDG California Department of Fish and Game

CFM Constant Fractional Marking

CFS Cubic Feet per Second

CVHJV Central Valley Habitat Joint Venture

CVJV Central Valley Joint Venture

CVP Central Valley Project

CVPIA Central Valley Project Improvement Act

DCC Delta Cross Channel

DOI (Interior) Department of the Interior

DSM Decision Support Model

DWR California Department of Water Resources

ECOSIM Ecologically Cogent Operations Suite of Integrated Models

EIR Environmental Impact Report

EIS Environmental Impact Statement

ERP Ecosystem Restoration Plan

ES Environmental Statement

ESA Endangered Species Act

FEIS Final Environmental Impact Report

FERC Federal Energy Regulatory Commission

Acronyms
TABLE OF CONTENTS v 

FY Fiscal year

GCID Glenn-Colusa Irrigation District

GLWA Gray Lodge Wildlife Area

GPM Gallons per Minute

GWD Grassland Water District

HGS HydroGeoSphere

HRP Habitat Restoration Plan

IEP Interagency Ecological Program

IFIM Instream Flow Incremental Methodology

ISI Integrated Storage Investigations

IWFM Integrated Water Flow Model

IRWMT Interagency Refuge Water Management Team

LAWS Land Atmosphere Water Simulator

LTRC Long-Term Renewal Contracts

MOU Memorandum of Understanding

NFH National Fish Hatchery

NMFS National Marine Fisheries Service

NOAA National Oceanic Atmosphere Administration

NRDC Natural Resources Defense Council

NWR National Wildlife Refuge

OCAP Operations Criteria and Plan

OMB Offi ce of Management and Budget, (Executive Offi ce 

 of the President, Washington, DC)

PEIS Programmatic Environmental Impact Statement

POD Pelagic Organism Decline

RBDD Red Bluff Diversion Dam

RBRPP Red Bluff Research Pumping Plant

RHEM Riparian Habitat Establishment Model

ROD Record of Decision

SDFF South Delta Fish Facility Forum

SDIP South Delta Improvement Program

SJBAP San Joaquin Basin Action Plan 

SJRA San Joaquin River Agreement 

SJRGA San Joaquin River Group Authority

SMWC Sutter Mutual Water Company

SRSC Sacramento River Settlement Contracts

TAF Thousand acre-feet

TFCF Tracy Fish Collection Facility

TFFIP Tracy Fish Facility Improvement Program

TRRP Trinity River Restoration Plan

USDA U.S. Department of Agriculture

USGS US Geological Survey

USRWQM Upper Sacramento River Water Quality Model

VAMP Vernalis Adaptive Management Plan 

WA Wildlife Area

WAP Water Acquisition Program

WQCP Water Quality Control Plan

WY Water Year
vi CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2007 ANNUAL REPORT
INTRODUCTION 1

For the past 15 years, the Central Valley Project 

Improvement Act (CVPIA or Act) has guided the 

implementation of projects supporting the protection, 

restoration and enhancement of fi sh and wildlife 

associated with the Central Valley Project (CVP). 

The scope of CVPIA also covers a complex system 

of water transfers and contract renewals to ensure 

that adequate supplies remain available to support the 

restoration goals of CVPIA while also meeting demands 

of agriculture, municipal and industrial users, and power 

contractors. To date, more than $957.4 million of federal, 

state and private funds have been obligated to implement 

CVPIA mandates.

The CVP and other water projects have helped make 

the Central Valley the richest agricultural region in the 

I. Introduction

nation and have also allowed California’s population 

to grow beyond that of any other state. California 

leads the nation in water use—both surface water 

and groundwater; the ability to develop and use this 

precious resource has been a boon to the economy of 

the state. The CVPIA has afforded the Department 

of the Interior (Interior) a prime opportunity to help 

restore conditions favorable for fi sh and wildlife in the 

Central Valley, while providing for the continuation of 

its rich agricultural heritage and service to municipal 

and industrial users throughout the state.

This annual report summarizes the actions taken by 

Bureau of Reclamation (Reclamation) and Fish and 

Wildlife Service (Service) personnel, working with 

other federal agencies, the State of California and 

numerous partners and stakeholders during fi scal 

year (FY) 2007 (October 1-September 30). Wherever 

possible, this report includes quantifi ed goals and 

targets to more effi ciently measure progress within 

each individual provision of the Act.

For greater detail on the programs and projects 

described in this report or on the progress towards 

achieving the Act’s goals and objectives, please contact 

either Reclamation or the Service, or the individual 

CVPIA project and program managers.

BACKGROUND

The Central Valley Project’s Role in 

California’s Water Resources

For 72 years, California has depended on the CVP 

for a large part of its water needs, particularly for 

agriculture. With a climate typifi ed by extremely 

variable precipitation, both temporally and regionally, 

the state relies heavily on dams and reservoirs to 

Sunset at Kern National Wildlife Refuge
2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

balance and manage its water resources, and on an 

extensive distribution system to convey water supplies 

for regional needs. Much of the state’s water originates 

in the north and is conveyed southward, primarily 

through the Sacramento River system. Some water is 

diverted along the way, with the remainder fl owing into 

the Sacramento-San Joaquin River Delta, where CVP 

water co-mingles with other supplies such as those 

of the State Water Project (SWP). A portion of the 

water entering the delta is pumped south; the majority 

discharges to the San Francisco Bay and Pacifi c Ocean. 

The CVP today comprises 18 dams and reservoirs 

(able to store 9 million acre-feet of water), 11 power 

plants, 500 miles of canals and aqueducts, three fi sh 

hatcheries, and associated facilities including pumping 

plants and power lines. 

The ecosystems of the Central Valley, Delta Estuary, 

San Francisco Bay and Trinity River are affected by 

water diversions–particularly in drought years–so 

Sacramento

San Francisco

Los Angeles

Figure 1. Central Valley Project System
INTRODUCTION 3

much so that the courts have intervened to ensure 

that adequate fresh water enters these ecosystems. 

Compliance with the Endangered Species Act (ESA) 

and water quality mandates requires water releases from 

CVP dams to regulate water temperatures, salinity and 

instream fl ows, and limits water diversions to protect 

ESA-listed fi sh from the effects of pumping water at the 

Tracy Pumping Plant in the delta. These factors have 

greatly increased the competition for existing water 

supplies and have focused scrutiny on the ways that 

water resources are being used. 

Environmental conditions have greatly changed since 

the CVP was authorized in 1935. Population growth and 

development have increased farm, urban and industrial 

water demands. Concurrently, populations of fi sh 

and wildlife have declined, resulting in some species 

being listed as endangered or threatened due to severe 

habitat loss. In response, a new imperative for resource 

management and ecological stewardship has evolved.

Central Valley Project Improvement Act 

of 1992

In one of its last actions of the session, the 102nd 

Congress in 1992 passed, and the President signed, the 

multi-purpose water legislation known as the Central 

Valley Project Improvement Act. Offi cially designated 

Title 34 of Public Law 102-575, this landmark piece 

of legislation mandates changes in the purposes and 

management of Reclamation’s Central Valley Project. 

It specifi cally focuses Interior on the protection, 

restoration and enhancement of fi sh and wildlife and 

associated habitats and contributes to the state’s interim 

and long-term efforts to protect the San Francisco Bay/

Sacramento-San Joaquin River Delta Estuary. The 

Secretary of the Interior assigned primary responsibility 

for implementing CVPIA’s many provisions to 

Reclamation and the Service, both agencies of Interior.

The purpose of the CVPIA is expressed in six broad 

statements found in Section 3402 of the Act: 

(a) To protect, restore and enhance fi sh, wildlife and 

associated habitats in the Central Valley and Trinity 

River basins of California

(b) To address impacts of the CVP on fi sh, wildlife and 

associated habitats

(c) To improve the operational fl exibility of the CVP

(d) To increase water-related benefi ts provided by the 

CVP to the state through expanded use of voluntary 

water transfers and improved water conservation

(e) To contribute to the state’s interim and long-term 

efforts to protect the San Francisco Bay/Sacramento-San 

Joaquin Delta Estuary

(f) To achieve a reasonable balance among competing 

demands for use of CVP water, including the 

requirements of fi sh and wildlife, agricultural, municipal 

and industrial, and power contractors

The CVPIA Mandate

To achieve the CVPIA fi sh and wildlife restoration 

purposes and the identifi ed goals and objectives, Congress 

incorporated specifi c programs, measures and operational 

and management directives into the Act (Sections 3406 and 

3408) that affect a wide variety of activities, including:

• Restoration of anadromous fi sh populations 

• Water supplies for state and federal refuges and 

wildlife habitat areas

• Retirement of drainage-impaired agricultural lands

• Mitigation for other CVP-impacted fi sh and wildlife

• Revisions to water contracts

• Modifi cation of water management and operations

• System-wide modeling to support decision-making

• Program monitoring to determine effectiveness

• Investigations and studies

Reclamation and the Service were joint lead federal 

agencies for the CVPIA Final Programmatic 

Environmental Impact Statement and its Record of 

Decision (PEIS and ROD). The PEIS and the ROD 

broadly identifi ed the overall program and actions to 

achieve the purposes of CVPIA, including the fi sh and 

wildlife restoration provisions. Although some provisions 

of the CVPIA were implemented beginning in 1993, most 

were not initiated until after the signing of the ROD in 

January 2000.

Reclamation and the Service cooperate and partner 

with other federal and state agencies, tribes and local 

organizations to implement CVPIA actions. Reclamation 

and the Service use interagency agreements, memoranda 

of understanding, grants and cooperative agreements 

to partner with entities that have the authority, interest, 

ability, expertise and/or resources to implement CVPIA 

restoration actions. 
4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Implementation of the CVPIA program is federally 

funded primarily through two types of Congressional 

appropriations: Reclamation’s Water and Related 

Resources Account and the Restoration Fund established 

by CVPIA (Section 3407(c)(2)). (The Trinity River 

Restoration Program (TRRP) also has received Service 

appropriations of about $1.5 million per year for related 

monitoring activities.) The Restoration Fund is an 

account in the United States Treasury that receives 

funds generated through fees collected from CVP 

water and power contractor users, matching payments 

and contributions from the State of California, and 

donated funds. Reclamation is authorized to accumulate 

up to $30 million annually (adjusted for infl ation) in 

Restoration and Mitigation Payments from the CVP 

water and power users. A maximum of $50 million in 

annual appropriations from the Restoration Fund is 

allowed in any year under the CVPIA.

While there were no cost estimates associated with 

CVPIA in 1992, Congress has provided substantial 

annual appropriations of Restoration Funds and Water 

and Related Resources funds. As of 2007, a total of 

$957.4 million has been obligated to CVPIA since its 

implementation in 1993. For FY 2007, $63 million was 

obligated from the Restoration Fund and Water and 

Related Resources Account for the purposes of CVPIA.

IMPLEMENTING THE CVPIA 

Reclamation and the Service work cooperatively under 

Interior to implement the CVPIA. Reclamation’s 

primary responsibilities involve engineering, water 

operations, water acquisitions, construction-related 

activities, and the submission of budgets and project 

funding. The Service has the responsibility for many 

biological issues including fi sh and wildlife restoration 

and related activities, such as managing the Anadromous 

Fish Restoration Program (AFRP), Dedicated Yield 

and the Comprehensive Assessment and Monitoring 

Program (CAMP). Program managers from each agency 

are assigned to develop and manage specifi c program 

activities in accordance with the applicable provisions of 

CVPIA. Although one agency generally is designated as 

the lead, both agencies contribute to annual work plans, 

budget and implementation responsibilities. 

In implementing the restoration portion of CVPIA, 

Reclamation and the Service focus on three main fi sh 

and wildlife restoration initiatives:

• Achieving the anadromous fi sh doubling goal 

• Providing adequate water to wildlife refuges 

• Mitigating terrestrial and other CVP-related impacts

In addition to these fi sh and wildlife initiatives, the 

program focuses on improving operational fl exibility and 

modeling.

The CVPIA also includes specifi c provisions to guide 

restoration in the Trinity River basin. The Trinity River 

is the largest tributary of the Klamath River, and is 

geographically separate from the Central Valley and the 

Sacramento River. However, substantial water from the 

Trinity River has historically been exported through 

a trans-basin diversion, to support water needs in the 

Central Valley. When the CVPIA was enacted, section 

(b)(23) of the law was specifi cally included to direct 

future Trinity River fl ows and restoration actions.

Anadromous Fish Doubling Goal 

The Act directs Interior to 

“... implement a program which makes all reasonable 

efforts to ensure that, by the year 2002, natural 

production of anadromous fi sh 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...” 

The anadromous fi sh doubling goal pertains to Chinook 

salmon, steelhead, striped bass, American shad and 

sturgeon, which are believed to have been affected by 

CVP construction and operation. 

Many of the CVPIA provisions support this goal directly 

or indirectly. Section (b)(1), which authorizes the AFRP, 

is wholly devoted to this purpose, and its process to 

identify reasonable restoration actions is in the 2001 

Final Restoration Plan for the Anadromous Fish 

Restoration Program (AFRP Restoration Plan). Actions 

contained within the AFRP Restoration Plan were 

determined to be reasonable given numerous technical, 

legal and implementation considerations; all AFRP 

actions are covered in the CVPIA PEIS/ROD.

Other CVPIA provisions that support the fi sh doubling 

goal include the fi sh screening activities conducted 

under (b)(4) Tracy (Jones) Pumping Plant Program, 

(b)(5) Contra Costa Canal Pumping Plant, (b)(17) 

Anderson Cottonwood Irrigation District, (b)(20) 

Glenn-Colusa Irrigation District Program, and (b)(21) 
INTRODUCTION 5

Anadromous Fish Screen Program; restoration activities 

such as (b)(12) Clear Creek Restoration Program and (b)

(13) Spawning Gravel Program; and the many modeling 

and monitoring programs that provide data to support 

reoperation and restoration activities, namely, (b)(16) 

CAMP, (b)(1)(B) Modifi ed CVP Operations, and 3406 

(g) Ecological/Water Systems Operations Model. 

Wildlife Refuges

The CVPIA includes several provisions that are 

designed to contribute to the restoration of wetlands and 

wildlife habitat. The Act directs Interior to 

“...provide, either directly or through contractual 

agreements with other appropriate parties, fi rm water 

supplies of suitable quality to maintain and improve 

wetland habitat areas on units of the National Wildlife 

Refuge System in the Central Valley of California; on 

Figure 2. Central Valley Refuges Receiving CVPIA Water Supplies
6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

the Gray Lodge, Los Banos, Volta, North Grasslands 

and Mendota state wildlife management areas; and on 

the Grasslands Resources Conservation District...”

The quantity and delivery schedules of refuge water 

are governed by the concepts of Level 2 and Level 

4 which are outlined in more detail (page 69 of this 

report). CVPIA quantifi es the specifi c amount of water 

that is to be supplied and authorizes Interior to acquire 

water conveyance capacity from non-federal entities 

and construct conveyance facilities as necessary for the 

delivery of water supplies to the refuges (Figure 2.)

Other Resources 

The third focus of the CVPIA is directed at terrestrial 

species and habitats and other resource impacts of the 

CVP. Provisions supporting this initiative include the 

(b)(1)“other” Habitat Restoration Program (HRP), which 

focuses on protecting native habitats that have been 

directly and indirectly affected by construction and 

operation of the CVP, and the 3408(h) Land Retirement 

Program (LRP), which purchases and retires land from 

agricultural production to improve water quality and 

provide for terrestrial habitat restoration.

FUNDING FOR ACTIVE 

PROVISIONS 

Several of the CVPIA provisions are now complete and/

or otherwise not funded in the FY 2007 cycle. As such, 

the following provisions are not discussed in this report:

• 3406 (b)(6) Shasta Temperature Control Device 

(Complete)

• 3406 (b)(7) Meet Flow Standards and Objectives 

(Ongoing through operations)

• 3406 (b)(8) Short Pulse Flows (Ongoing through 

operations)

• 3406 (b)(14) Delta Cross and Georgiana Slough 

(Inactive)

• 3406 (b)(17) ACID Diversion Dam (Complete)

• 3406 (b)(18) Restore Striped Bass Fishery (Inactive)

• 3406 (b)(22) Waterfowl Incentive Program 

(Complete)

• 3406 (c)(2) Stanislaus River Basin Water Needs 

(Complete)

• 3406 (d)(6) Central Valley Wetlands Supply 

(Complete)

• 3406 (e) Supporting Investigations (Complete)

• 3406 (f) Project Fisheries Impact Report (Complete)

• 3408 (i) Water Conservation (Complete)

• 3408 (j) Water Augmentation (Yield Study) 

(Complete)

The remaining provisions have all received 

appropriations to support FY 2007 program activities. 

Table 1 lists each active provision and the amount of 

funding provided.

CONTRACTS AND WATER 

TRANSFERS 

In addition to the work funded through the Restoration 

Fund and the Water and Related Resources Account 

as outlined in the previous section, Reclamation also 

provides funding to administer contract renewals and 

water transfers to support the ongoing operations of 

the CVP.

Contract Renewals

Since passage of CVPIA, Reclamation completed the 

renewals for the Sacramento River Settlement Contracts 

(SRSC) on March 31, 2006. Of the 141 contracts to 

be renewed, 12 contractors elected not to renew and 

one contractor will renew upon resolution of an estate 

proceeding. There are 128 SRSC renewal contracts 

signed to date. 

Eighty-three out of 109 Long-Term Renewal Contracts 

(LTRC) have been signed, representing 60.3 percent 

of the water (3,177,450 of 5,264,031 acre-feet). Sixteen 

additional contracts have been negotiated and are 

awaiting environmental documentation before signing 

and two contracts remain to be negotiated. The eight 

Cross Valley Canal contracts will now be renegotiated 

as two-party agreements and conveyance agreements for 

wheeling this CVP water through state facilities will be 

negotiated.

No renewal contracts were executed in FY 2007 due 

to litigation concerning the Operations Criteria and 

Plan (OCAP) and a resulting decision to reinitiate 

Endangered Species Act (ESA) consultations for the 

individual contracts with the Service and National 

Oceanic and Atmospheric Administration (NOAA) 

Fisheries. Negotiations for a new contract with the El 

Dorado County Water Agency pursuant to Pub. Law 

101-514 (Fazio contract) were completed in 2007. This 
INTRODUCTION 7

3406(b)(1) Anadromous Fish Restoration Program 0 $5,511,100

3406(b)(1) “other” – Habitat Restoration Program 0 $1,516,000 

3406(b)(1) “other” – Trinity River Restoration 

 Program

$6,595,000 $1,001,000

3406(b)(1)(B) Modifi ed CVP Operations 0 0

3406(b)(2) Dedicated 800,000 acre-feet Project 

Yield

0 $904,500

3406(b)(3) Water Acquisition Program - Instream 

Water (includes 3406+(g) [VAMP])

0 $6,468,000

$1,640,900 

$1,332,000 

$8,580,900 

3406(b)(4) Tracy (Jones) Pumping Plant Program $1,821,400 ($10,200)

3406(b)(5) Contra Costa Canal Pumping Plant $76,100 0

3406(b)(9) Flow Fluctuations $80 $52,000

3406(b)(10) Red Bluff Diversion Dam $880,300 0

3406(b)(11) Coleman National Fish Hatchery $(6,050) $44,700

3406(b)(12): Clear Creek Restoration Program $135,200 $813,900

3406(b)(13): Spawning Gravel Program 0 $918,200

$1,900 

3406(b)(15) Head of Old River Barrier $94,200 $80,000

3406(b)(16) Comprehensive Assessment 

and Monitoring Program

0 $398,800

3406 (b)(19) Reservoir Storage 0 0

3406(b)(20) Glenn-Colusa Irrigation District Program $19,900 0

3406(b)(21) Anadromous Fish Screen Program 0 $7,451,400

3406(b)(23) Trinity River Restoration Program $947,900 $0

3406(c)(1) San Joaquin River Comprehensive Plan 0 $3,001,900

3406(d)(1) Refuge Water Supply Level 2 conveyance 

included in (d)(5)

Level 2 

conveyance 

included in 

(d)(5)

3406(d)(2) Refuge Water Supply Level 4 acquisition 

included in (b)(3)

Level 4 

acquisition 

included in 

(b)(3)

3406(d)(5) Refuge Facilities Construction Program $210 $182,300)

$10,544,000 

3406 (d)(5) San Joaquin Basin Action Plan Lands $153,900 $1,123,200

3406(g) Ecological/Water Systems 

Operations Models

$209,200 $428,100 

3408 (h) Land Retirement Program 0 $1,485,900

TOTAL FUNDING OBLIGATED $10,927,340 $53,470,500

Table 1. FY 2007 Funding Obligations by Provision

*Rounded for presentation purposes.

(VAMP)

(state)

Level 4

(state)

(state)

(construction)

(wheeling)

Provision

Water & Related 

Funds* Restoration Funds*
8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

contract is a specifi c exception to the CVPIA prohibition 

against new contracts pending completion of the actions 

required by CVPIA Sections 3406 (b)-(d).

Water Transfers

Water transfers are a means by which existing water 

supplies can be reallocated from one user to another to 

assist in meeting existing and future water needs within 

the state.

In order to assist California urban areas, agricultural 

water users and others in meeting their future water 

needs, CVPIA specifi cally authorizes all individuals or 

districts – who received CVP water under contract – to 

transfer, subject to certain terms and conditions, all or 

a portion of the water they receive under such contracts 

to other water users within the state for any purpose 

recognized as benefi cial under state law.

During the 2007 water year, Reclamation approved the 

transfer of CVP water in the following categories:

• 216,300 acre-feet of CVP of agricultural water was 

transferred for agricultural purposes

• 1,100 acre-feet of CVP of agricultural water was 

transferred for municipal and Industrial purposes

• 4,200 acre-feet of CVP municipal and industrial 

water was transferred for agricultural purposes

• 46,000 acre-feet of agricultural water transferred to 

Reclamation’s Refuge Water Acquisition Program

Figure 3. Total CVPIA Obligations by Action Category and Fund Source (1993-2007)

26%

3%

1%

$56,962

0.01%

26%

8%

36%

Other Fish & Wildlife $104,886,664

Administrative $56,962

Anadromous Fish - Habitat Modification $243,224,585

Anadromous Fish - Structures $335,789,134

Refuges & Waterfowl $234,031,452

Studies/Investigations/Modeling $27,274,538

Monitoring $12,198,176

Action Category

Total obligations: $957,461,511

29%

0.27%

8%

63%

Fund Source

Total obligations: $957,461,511

Water & Related Resources Fund $284,506,647

CVPIA Restoration Fund $594,867,509

State Cost Share $73,294,200

Bay-Delta Fund $4,793,155
INTRODUCTION 9

RECENT DEVELOPMENTS 

Several developments occurred in FY 2007 or are 

planned for FY 2008 that will have a direct effect 

on the implementation of CVPIA actions, including 

the Pelagic Organism Decline (POD), litigation of 

biological opinions (BO), the Operations Criteria and 

Plan (OCAP) BO, and the Offi ce of Management and 

Budget (OMB) Performance Assessment Rating Tool 

(PART) process. 

Pelagic Organism Decline

Abundance indices calculated by the Interagency 

Ecological Program (IEP) through 2007 suggest recent 

marked declines in four pelagic fi shes in the upper San 

Francisco Estuary (the delta and Suisun Bay). These 

fi shes include delta smelt, which are listed under state 

and federal Endangered Species acts and the longfi n 

smelt, which has been proposed for protection under 

those acts. Although several species show evidence 

of long-term declines, the recent low levels were 

unexpected given the relatively moderate winter-spring 

fl ows of the past several years.

In response to this situation, in May 2007, the director 

of the California Department of Fish and Game (DFG) 

asked the director of the Department of Water resources 

(DWR) to “cease pumping water at the Harvey O. Banks 

facility, to the maximum feasible extent consistent with 

health and safety and maintain agricultural barriers 

in the South Delta in an open position.” DWR was 

asked to work with Reclamation to accomplish the 

same goals for the CVP. DFG also notifi ed other delta 

diverters, including agricultural users, Contra Costa 

intake facilities, and energy diverters to “voluntarily 

cease or substantially reduce your diversions from the 

South Delta channels, as your operations allow.” IEP 

also directed that all “non-essential” projects must cease 

fi sh sampling upstream of the Carquinez Bridge and 

downstream of Sacramento on the Sacramento River 

and downstream of Vernalis on the San Joaquin River.” 

Several CVPIA provisions including (b)(15) Head of 

Old River Barrier and (b)(5) Contra Costa Canal Intake 

Fish Screening Project have been affected as diverters 

reduced pumping in response to the POD; this direct 

effect on CVP operations will continue until such time 

as the POD is adequately addressed. 

Litigation of Biological Opinions

On December 14, 2007, a federal judge (U.S. District 

Court Judge Oliver Wanger) ordered state and federal 

water project managers to reduce the amount of water 

pumped from the Sacramento-San Joaquin River Delta 

to protect the threatened delta smelt from extinction in 

the Service BO. 

Judge Wanger ruled in an Interim Remedial Order that 

caused the projects to restrict water deliveries from the 

California delta’s export pumps to the Bay Area, Central 

Valley and Southern California to protect the fi sh. The 

ruling ordered a reduction in pumping from the end of 

December (when the fi sh are ready to spawn) until June 

(when the fi sh can move into Suisun Bay beyond the 

reach of the pumps).

On April 16, 2008, Judge Wanger determined that 

the National Marine Fisheries Service (NMFS) 2004 

BO (see following section) was incomplete and did 

not analyze the recovery of winter-run and spring-run 

Chinook salmon and steelhead species, or the effect 

global climate change may have over the next 25 years. 

Reclamation has not been ordered to follow interim 

restrictions.

Several CVPIA provisions including (b)(4) Tracy 

(Jones) Pumping Plant Program, (b)(15) Head of Old 

River Barrier, and (b)(5) Contra Costa Canal Pumping 

Plant are affected by the decision and pumping will 

be reduced as ordered. This direct effect on CVP 

operations will continue until such time as the POD is 

adequately addressed. 

Operations Criteria and Plan Biological 

Opinions 

The Operations Criteria and Plan (OCAP) Biological 

Assessment (BA) provides a detailed project description 

of the CVP system as a whole, including operations, 

modeling and forecasting. The OCAP BA also 

contains an analysis of the effect of CVP operations 

on federally-listed threatened and endangered species, 
10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

providing a basis for consultation with NMFS and the 

Service regarding mitigation to reduce those effects. 

The Service and NMFS must issue a BO stating its 

conclusions about the potential effects of the OCAP and 

presenting mitigation requirements that will be applied 

to specifi c CVPIA programs. 

The current NMFS BO was issued in October 2004 

and the Service BO was issued in February 2005. A 

revised OCAP Service BO is currently being prepared 

and is expected to be issued in December 2008. The 

court has directed NMFS to issue its BO March 2009. 

The ESA consultation for the operation of the proposed 

new pumping plant at Red Bluff (b)(10) and the planned 

Barrier at Old River (b)(15) will follow the issuance of 

the revised OCAP BO to ensure that future program 

activities comply with OCAP mitigation requirements. 

Performance Assessment Rating Tool 

The OMB Program Assessment Rating Tool (PART) 

was developed to assess and improve the performance 

of federal programs. A PART review helps identify 

a program’s strengths and weaknesses to inform 

funding and management decisions aimed at making 

the program more effective. The PART therefore 

looks at all factors that affect and refl ect program 

performance including program purpose and design; 

performance measurement, evaluations and strategic 

planning; program management; and program results. 

Because the PART includes a consistent series of 

analytical questions, it allows programs to show 

improvements over time and allows comparisons 

between similar programs.

A PART was performed for CVPIA in 2006, and 

the program was given a rating of “adequate.” OMB 

required several improvements actions, some of which 

were implemented in 2007 and some which will extend 

into FY 2008. The major actions include the completion 

of an independent review of the program by a panel of 

experts and completion of a long-term plan to guide 

CVPIA actions over the next 10 years (2009 through 

2019) – these reports are due in FY 2008 and FY 2009. 

The independent review panelists were chosen in 2007 

and the panel will meet throughout 2008 to evaluate 

the fi sh doubling activities with the program and 

prepare specifi c recommendations for improvement. 

Final panel reports will be completed in FY 2008. 

CVPIA also drafted an effi ciency measure and 

continued to refi ne this measure in consultation with 

the OMB. CVPIA also completed a programmatic cost 

estimate in compliance with the recommendations of 

the PART. 

LOOKING AHEAD

Quantifi cation of goals and results will be increasingly 

important as Reclamation and the Service seek to 

focus program dollars on areas that can provide the 

greatest return on investment (ROI). In the case of 

this portion of CVPIA, currently funded through the 

Restoration Fund and focused on Restoration efforts, 

ROI is measured generally by increases in the natural 

production of anadromous fi sh, the delivery of water to 

wildlife refuges that is of suitable quality and quantity, 

the protection and restoration of sensitive species and 

habitats, the retirement and restoration of agricultural 

lands, the completion of structural improvements, 

and the implementation of operational changes to 

affect fl ows. The program also measures completion 

of restoration activities pursuant to the Trinity River 

Restoration Plan, and additional specifi c goals exist 

for individual CVPIA program activities, as discussed 

throughout this annual report.

The data generated from CVPIA modeling and 

monitoring activities support the identifi cation of 

these performance targets and also provide results 

and feedback on the effectiveness of actions. Planning 

and coordination between the various provisions will 

increase the effectiveness of resource allocation and 

decision-making. Closer coordination between the 

programs is seen as critical to the success of the 

long-term goals of the CVPIA. 
EXECUTIVE SUMMARY 11

Since 1992, Reclamation and the Service have worked 

cooperatively to implement the CVPIA, making 

substantial progress towards sustainable doubling of 

natural populations of anadromous fi sh, recovery of 

listed species, habitat restoration, and provision of 

water for refuges. The successes to date would not be 

possible without the participation of the many partnering 

agencies and stakeholders who provide funding, collect 

data, and perform monitoring of ongoing activities. 

The program continues to build upon the knowledge 

gained from ongoing studies and modeling, and adapts 

future actions to refl ect current data. 

II. Executive Summary

The enormity and complexity of the central valley 

ecosystem requires a comprehensive approach with 

participation at all levels. Continued progress towards 

the restoration goals of the program will be based on the 

ongoing partnerships with stakeholders and more closely 

coordinated implementation of activities. The CVPIA 

program managers convened a series of meetings in FY 

2007 to discuss the effectiveness of past actions and 

to identify priority watersheds and opportunities for 

coordinated action that will maximize the effectiveness 

of program dollars. The outcome of these discussions 

will form the basis of an implementation plan that will 

guide the program over the next 10 years.

PROGRESS TOWARDS GOALS

The following paragraphs summarize progress toward 

the broad goals of the CVPIA program. 

Doubling Goal 

As of 2006, the average natural production for all 

races of Chinook salmon is 498,863, or approximately 

50 percent of the doubling target. Progress towards 

the doubling goal is a result of coordinated action 

between programs supporting improvements in 

passage, habitat and fl ow. By focusing on these three 

critical components, CVPIA creates conditions in 

which fi sh populations can begin to recover in a 

sustainable fashion. Indeed, the greatest success in 

watersheds has occurred where these three components 

can be closely controlled, e.g., in Clear, Butte, and 

Battle creeks and the Mokelumne River. In all four of 

these areas, the doubling target has been exceeded. 

Spring-run Chinook salmon in Butte Creek
12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Overall production trends are mixed: 

• Winter-run production numbers have been 

trending upward since 1996, but showed a sharp 

decline in 2007

• Spring-run numbers have generally improved 

since 1991, but are still well below the target 

• Fall-run production was increasing but declined 

precipitously in 2007

• Late fall-run production has increased from 

extremely low levels in the early 1990s, but is still 

well below the target

The Anadromous Fish Restoration Program continues 

to review anadromous fi sh production, life history 

requirements, restoration efforts and the most current 

fl ow regimes in each watershed to better understand 

the requirements of sustainable doubling for these 

species in Central Valley rivers and streams.

Habitat restoration 

The Habitat Restoration Program has acquired and 

protected nearly 100,000 acres since program inception 

(1,603 acres in 2007), while the Land Retirement 

Program has retired more than half of the 15,000 acres 

targeted as part of the pilot project. Of the 8,596 acres 

retired, the Land Retirement Program has restored more 

than 4,000 acres towards sustainable uplands habitat. 

Refuge water 

CVPIA has created Full Level 4 capacity at 14 of the 

19 identifi ed refuges, paving the way for all 19 refuges 

to receive their Full Level 4 water supply. Capacity at 

the remaining fi ve refuges will be addressed through 

construction projects planned and prioritized for the 

next 10 years. The high cost of water continues to limit 

acquisition of Full Level 4 water. Purchase of permanent 

or long-term water, rather than spot market purchases, 

provides the most reliable source for refuge water, but 

these supplies are not readily available on the market and 

are very expensive when they can be found.

2007 ACCOMPLISHMENTS

The following section summarizes the specifi c FY 

2007 accomplishments within the following categories: 

Anadromous Fish – Habitat Restoration, Anadromous 

Fish – Structural Actions, Refuges and Waterfowl, 

Other Fish and Wildlife, and Studies, Investigations, 

and Modeling. 

Anadromous Fish – Habitat Restoration

• The Anadromous Fish Restoration Program 

(AFRP) has completed 17 percent of all 289 

Restoration Plan actions and evaluations identifi ed 

in support of fi sh doubling goals and 41 percent 

are in progress towards completion [(b)(1)]

• Allocated the full 800,000 acre-feet per year of 

Dedicated Yield water, plus 195,000 acre-feet of 

banked water from 2006 [(b)(2)]

• Purchased 92,145 acre-feet of water (46 percent of 

the 200,000 acre-feet target) to improve instream 

fl ows and habitat restoration [(b)(3)]

• The (b)(9) Flow Fluctuation Program used 

(b)(2) water and re-operations pursuant to (b)(1)

(B) to augment fl ows on CVP streams to prevent 

fl uctuations during critical periods

• The Clear Creek Restoration Program 

successfully met fl ow objectives related to 

controlling water temperature during critical 

seasons: 60°F from June 1 through September 15, 

and 56°F from September 15 through October 31 

and completed Phase 3B of the channel restoration 

project [(b)(12)]

• The Spawning Gravel Replenishment Program 

completed environmental permitting for the 

addition of gravel at eight sites in the Stanislaus 

River (at Knights Ferry) and completed studies in 

the American River to prioritize gravel placement 

for FY 2008 [(b)(13)]
EXECUTIVE SUMMARY 13

Anadromous Fish – Structural Actions

• The Tracy (Jones) Pumping Plant program 

continued progress on the 23 total identifi ed 

actions that make up the program target (10 

actions have been completed as of 2006) [(b)(4)]

• The Contra Costa Canal Pumping Plant program 

provided $50,000 in mitigation payments to the 

Service for the Pelagic Organism Decline effort to 

address the recent decline in delta smelt [(b)(5)]

• The Red Bluff Diversion Dam program 

implemented operational changes to avoid further 

impacts to green sturgeon holding below the dam; 

a Final EIR/EIS on the proposed new pumping 

plant is expected in FY 2008; the plant will 

increase pumping capacity fourfold, providing a 

more reliable water supply [(b)(10)]

• The Head of Old River Barrier program continued 

design of the barrier; the Final EIR/EIS was 

issued in FY 2006 and the design phase is 

expected to continue through FY 2008 [(b)(15)]

• The Glenn-Colusa Irrigation District Program 

completed the biological and hydraulic testing and 

monitoring that was begun in 2001; the results 

indicate that fi sh survival in the vicinity of the 

screens is not impaired [(b)(20)]

• The Anadromous Fish Screen Program completed 

the Tisdale Positive Fish Barrier in Sutter County, 

screening the largest (960 cfs) unscreened diversion 

remaining on the Sacramento River; the program 

also initiated a three-year monitoring program of 

screens on the Sacramento River watershed system 

and delta; the program will collect fi sh loss data to 

assess the biological benefi ts of screening and help 

prioritize future actions [(b)(21)]

• The Trinity River Restoration Program 

demonstrated that steelhead numbers have 

increased substantially, with 2007 recording the 

largest numbers in recent years (more than 50,000 

fi sh); the program completed construction of 

three mechanical channel rehabilitation projects 

and 21 infrastructure improvements, supporting 

the increase in peak fl ow releases of up to 11,000 

cfs in compliance with the ROD; the program 

has achieved full ROD fl ows since 2005 and has 

identifi ed nine priority watershed projects for 

future implementation [(b)(23)]

Refuges and Waterfowl

• In 2007, the refuge water supply program acquired 

and conveyed 92 percent of Level 2 and 35 percent 

of Incremental Level 4 water. The program also 

negotiated a third amendment to the groundwater 

pumping reimbursement agreement with the 

California Department of Fish and Game (DFG) to 

supplement Level 2 water at Gray Lodge Wildlife 

Area up to the full Level 2 allocation. [(d) (1), (2), 

and (5)]

• To date, the refuge facilities construction program 

has completed 31 of the 46 actions or projects 

identifi ed in the environmental documents and 

related design and specifi cation documents 

(the 31st completed in 2007). The remaining 15 

construction actions will be implemented over the 

next 10 years. [(d) (1), (2) and (5)]

Pintails fl ying over Sacramento National Wildlife Refuge
14 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Other Fish and Wildlife

• The Habitat Restoration Program protected an 

additional 1,603 acres of new habitat and restored 

117 acres of habitat [(b)(1)Other] 

• The San Joaquin River Comprehensive Plan 

Program initiated organization and management 

actions to prepare for the long-term structure of the 

San Joaquin River Restoration Program (SJRRP); 

a Stipulation of Settlement reached in 2006 led to 

the San Joaquin River Restoration Act that is now 

being considered by the House and Senate and will 

set terms and conditions for the implementation of 

the SJRRP Plan [(c)(1)]

• The Land Retirement Program acquired 213 acres 

in the Atwell Island site, and restored 475 acres of 

former agricultural lands [3408(h)]

Studies, Investigations, and Modeling

• The Comprehensive Assessment and Monitoring 

Program completed an annual report that 

synthesizes and analyzes data from 1992 through 

2006 on 13 watersheds and acquired 82 reports 

providing rotary screw trap data; data will be 

assessed in FY 2008 to provide information 

on relative effectiveness; obligated $96,000 to 

monitor production of juvenile Chinook salmon 

on the Stanislaus River to assess the success of 

restoration activities such as gravel placement and 

modifi cation of river fl ow regimes [(b)(16)]

• The Modifi ed CVP Operations program 

reoperated the system several times to provide 

benefi ts to anadromous fi sh on Clear Creek without 

impacting other CVP obligations or authorized 

purposes; the program completed a number of 

essential macroinvertebrate fl ow-habitat studies on 

CVP streams, and also completed monitoring for 

spring- and fall-run Chinook salmon and steelhead 

fry and juvenile rearing, as well as for redd 

dewatering and juvenile Chinook and steelhead 

stranding [(b)(1)(B)]

• The Ecological/ Water Systems Operations 

Models program currently operates the integrated 

CVP/SWP model and six other models – two 

more are currently under development; developed 

new datasets in 2007 for CalSim III and 

completed initial program activities to support the 

Riparian Habitat Establishment Model (RHEM) 

parameter study [3406(g)]
3406 (b)(1) 15

CVPIA Section 3406(b)(1)

“The Secretary . . .is authorized and directed 

to . . . develop within three years of enactment 

and implementation a program which makes all 

reasonable efforts to ensure that , by the year 2002, 

natural production of anadromous fi sh 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.” The section also states, “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 identifi ed adverse 

environmental impacts of the Central Valley Project 

not specifi cally enumerated in this section.”

Based on the language in the Act, Interior developed 

the Anadromous Fish Restoration Program (AFRP) as 

the overarching program to address anadromous fi sh 

doubling in the Central Valley. The CVPIA goal is to at 

least double the natural production of anadromous fi sh on 

a long-term, sustainable basis. The specifi c system-wide 

doubling targets for natural production of anadromous 

fi sh are categorized by fi sh run/species, per year: 

• Chinook salmon

- Winter-run 110,000

- Spring-run 68,000

- Fall-run 750,000

- Late Fall-run 68,000

• Steelhead 13,000

• Green sturgeon 2,000

• White sturgeon 11,000

• Striped bass 2,500,000

• American shad 4,300

Subsequent to the passage of the Act, the AFRP 

developed a series of planning reports that culminated 

in the Final AFRP Restoration Plan (Plan) in 2001. 

As acknowledged in the CVPIA Record of Decision 

(ROD), the Plan guides the implementation of the 

actions and evaluations which were developed to address 

the doubling goal. The 289 actions and evaluations in 

the Plan are categorized by six programmatic-level 

objectives: 

III. 2007 Programmed Activities 

and Accomplishments

Anadromous Fish 

Restoration Program Sacramento

San Francisco

Los Angeles
16 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

1) Improve habitat for all life stages of anadromous 

fi sh through provision of fl ows of suitable quality, quantity, and timing, and improved physical 

habitat

2) Improve survival rates by reducing or eliminating 

entrainment of juveniles at diversions

3) Improve the opportunity for adult fi sh to reach 

their spawning habitats in a timely manner

4) Collect fi sh population, health, and habitat data to 

facilitate evaluation of restoration actions

5) Integrate habitat restoration efforts with harvest 

and hatchery management

6) Involve partners in the implementation and evaluation of restoration actions

AFRP projects implemented from actions and 

evaluations in the Restoration Plan since 1995 have 

addressed environmental limiting factor categories that 

were derived from Central Valley watershed limiting 

factors listed in the AFRP Working Paper. The Working 

Paper was developed under the direction of a scientifi c 

core group composed of experts from state and federal 

agencies, private industry, and academia with specifi c 

knowledge of anadromous fi sh species in Central Valley 

rivers and streams. It lists potential factors or stressors 

that may limit natural production of anadromous fi sh 

and the ideal type and number of restoration actions 

that, if implemented in their entirety, would address 

these factors and likely result in at least doubling natural 

production of anadromous fi sh.

Measuring Success

Actions and Evaluations

The Restoration Plan determined the process by 

which Working Paper actions could be evaluated for 

reasonableness and includes lists of these actions 

specifi c to each watershed in the Central Valley. 

Watersheds, or parts of watersheds, are prioritized 

based on a combination of biological and nonbiological 

factors. Watersheds that support, or have the potential to 

support species or races of special status are assigned 

priority over those watersheds that do not. To date, 

17 percent of all 289 Restoration Plan actions and 

evaluations have been completed and 41 percent 

are in progress towards completion. Table 2 shows 

progress made towards addressing implementation/

completion of the restoration actions and evaluations 

in each watershed.

Table 2. Summary of Final Restoration Plan Actions and Evaluations Addressed (1995-2007)

Watershed

Number of 

actions & 

evaluations 

addressed 

in FY07

Number of 

actions & 

evaluations 

addressed to 

date

Total number 

of actions & 

evaluations 

listed in Plan

Percentage 

actions & 

evaluations 

addressed

American River 2 13 15%

Antelope Creek 0 2 0%

Battle Creek 1 11 12 92%

Bear Creek 0 2 0%

Bear River 0 8 0%

Big Chico Creek 2 6 10 60%

Butte Creek 1 35 39 90%

Calaveras River 1 2 6 33%

Central-Valley Wide 11 15 73%

Clear Creek 7 7 100%

Colusa Basin Drain 1 2 50%

Final Restoration Plan
3406 (b)(1) 17

Key actions and evaluations undertaken or completed 

in 2007, as indicated in Table 2, include the following 

(grouped by program objectives):

Objective 1: Improve habitat for all life stages 

of anadromous fi sh through provision of fl ows of 

suitable quality, quantity, and timing, and improved 

physical habitat

Mokelumne River–In partnership with East Bay 

Municipal Utility District, AFRP provided spawning 

gravel materials for an ongoing project to increase 

spawning gravel quantity and improve gravel quality 

at known spawning sites for fall-run Chinook salmon 

and steelhead downstream of Camanche Dam. 

1

 Service, 1995. Working paper on restoration needs, habitat restoration actions to double natural production of anadromous fi sh in the 

Central Valley of California, Volume 3, AFRP. [http://www.delta.dfg.ca.gov/afrp/workingpaper.asp].

Table 2, Continued

Watershed

Number of 

actions & 

evaluations 

addressed 

in FY07

Number of 

actions & 

evaluations 

addressed to 

date

Total number 

of actions & 

evaluations listed 

in Plan

Percentage 

actions & 

evaluations 

addressed

Cosumnes River 3 5 9 56%

Cottonwood Creek 4 5 80%

Cow Creek 2 4 50%

Deer Creek 4 5 80%

Elder Creek 0 2 0%

Feather River 0 12 0%

Merced River 3 8 38%

Mill Creek 4 5 80%

Miscellaneous 

Stream Tributaries

1 1 100%

Mokelumne River 2 5 13 38%

Ocean 0 3 0%

Paynes Creek 0 2 0%

Upper Mainstem 

Sacramento River

17 22 77%

Sacramento-San 

Joaquin Delta

3 29 10%

Mainstem San 

Joaquin River

2 13 15%

Stanislaus River 1 3 9 33%

Stoney Creek 0 1 0%

Thomes Creek 0 6 0%

Tuolumne River 4 10 40%

Yuba River 3 1 14 7%

All Watersheds 14 133 289 46%

Final Restoration Plan
18 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Cosumnes River–Permitting and fi nal phases of 

project planning were completed for the Cosumnes 

River Gravel Augmentation Project. This project will 

enhance fall-run Chinook salmon spawning habitat 

at two contiguous sites by: 1) placing appropriately 

sized gravel in a riffl e that has historically supported 

one of the highest density of spawners in the lower 

Cosumnes River, and 2) providing additional gravel in 

a pool located immediately upstream of this riffl e to 

be redistributed downstream. Project construction is 

scheduled for the summer of 2008.

Stanislaus River–Instream spawning habitat was 

created using 25,000 tons of material to enhance 

habitat. This is the largest instream project ever 

conducted on the Stanislaus River and will provide 

additional spawning habitat, improved rearing 

habitat and reduced predator habitat. 

Objective 2: Improve survival rates by reducing or 

eliminating entrainment of juveniles at diversions

Battle Creek–The fi sh bypass pipe was replaced 

at the Orwick Diversion site, increasing survival of 

outmigrating juvenile salmonids.

Objective 3: Improve the opportunity for adult fi sh to 

reach their spawning habitats in a timely manner

Big Chico Creek–Funds were provided to complete 

the permitting and environmental documentation 

required to begin construction of the Iron Canyon 

Fish Ladder, which will provide more consistent 

access to quality spring-run Chinook salmon habitat. 

The fi nal phases (phases 3 and 4) are expected to be 

completed in 2009. 

Butte Creek–Completed construction of the White 

Mallard Dam and fi sh ladder, facilitating fi sh 

passage and reducing entrainment. Preliminary 

engineering and environmental assessment of the 

Five Points/Behring Ranch Diversion Canal were 

completed.

Objective 4: Collect fi sh population, health and habitat 

data to facilitate evaluation of restoration actions

Yuba River–Fluvial geomorphology, sediment 

transport dynamics, and in-stream hydraulics of 

key spawning reaches were characterized to build 

a predictive model for adult spawning locations. 

Gravel movement was monitored with tracer rocks 

and redd surveys for a future pilot gravel injection 

for spring-run Chinook directly below Engelbright 

Dam. Data was collected from fi sh passage 

events to better understand the timing, abundance, 

population trends, and response to changing fl ow 

and temperature conditions of adult spring–and fallrun Chinook salmon and Central Valley steelhead in 

the Lower Yuba River. 

Calaveras River–Data was collected on 

steelhead and fall-run Chinook salmon passage 

and stranding to provide information to improve 

fl ow management and inform prioritization and 

evaluation of passage impediments. 

Merced River–Administered an agreement to 

operate a rotary screw trap and collect data January 

23 to June 1. A draft report on the natural and 

hatchery juvenile Chinook salmon movement was 

completed. Monitoring of juvenile outmigration 

allows evaluation of the effectiveness of previous 

restoration actions. 

Restoration at MJ Ruddy, Tuolumne River, Summer 2006
3406 (b)(1) 19

Stanislaus River–Initiated a pilot project to codedwire tag emigrating juvenile salmonids as well as 

an evaluation of environmental variables effecting 

juvenile Chinook salmon outmigration at a rotary 

screw trap monitoring location. Information will 

also be used to evaluate effectiveness of restoration 

actions.

Objective 5: Integrate habitat restoration efforts with 

harvest and hatchery management

Mokelumne River–Conducted analyses of fallrun Chinook salmon otoliths to determine the 

ratio of hatchery to wild fi sh. Data will be used to 

inform calculations of natural production by better 

identifying the hatchery contribution to escapement 

estimates. Pilot study to conclude FY09. 

Objective 6: Involve partners in the implementation 

and evaluation of restoration actions

The AFRP continued to work extensively with 

partners to develop and implement restoration 

projects. AFRP works closely with local 

landowners, watershed groups, agencies, 

professional societies and other interested parties 

to share restoration and anadromous fi sh expertise, 

leverage resources and represent program goals at 

public and technical meetings. For example, AFRP 

worked with the Stanislaus River Fish Work Group 

on development of a draft fi sheries restoration plan, 

and a salmon life history model was completed for 

Big Chico Creek in cooperation with California 

Department of Fish and Game.

Natural Production Doubling

In addition to assessing progress by implementation of 

the Restoration Plan actions and evaluations, progress 

toward achieving the doubling goals can be assessed by 

calculating the production of naturally spawning fi sh. 

Although AFRP has production goals for all anadromous 

fi sh, the program’s restoration actions and evaluations 

have focused on Chinook salmon, as, in general, AFRP 

restoration activities benefi t all anadromous fi sh. Table 

3 summarizes the status of Central Valley-wide natural 

production of Chinook salmon in relation to the doubling 

goals and the baseline period.

The Final Restoration Plan also provides doubling goals 

for specifi c rivers and creeks. Doubling production by 

implementing a reasonable set of actions (i.e., a subset 

of the Working Paper actions) is less certain than if all 

the actions were implemented; however, AFRP has been 

able to make progress towards doubling production of 

some Chinook salmon runs on some streams. As an 

example, substantial gains to date are seen in watersheds 

where suffi cient investment has been made in fl ow and 

passage (Butte and Clear creeks) and habitat restoration 

(Clear Creek). Average Chinook salmon production for 

the period of 1992-2006 has exceeded the doubling goal 

target on Battle, Butte, and Clear creeks, and on the 

Mokelumne River, as seen in Table 4.

In order to more accurately assess natural production 

doubling efforts, AFRP is demonstrating new 

escapement counting technologies, Alaskan weir 

(Stanislaus River), Vaki-infra-red counting systems 

(Stanislaus and Yuba rivers) and hydroacoustics (Mill 

Creek). The AFRP is also supporting a study which 

should better defi ne the percentage of hatchery-origin 

fi sh in escapement by looking at sulfur isotope (S32:S34) 

ratios in otoliths taken from natural spawning Chinook 

salmon from the Mokelumne River and compare these 

to ratios in observed in hatchery produced stocks. 

This information will provide methods to derive more 

accurate estimates of natural production. This two year 

pilot study began in 2007 and should conclude at the end 

of 2008. 
20 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Table 4. Chinook salmon AFRP production, in Battle, Butte and Clear creeks, and Mokelumne River (1992-2006)

Chinook 

Salmon 

Species

and 

Watershed1

AFRP 

annual 

doubling 

goals2

Average 

baselines 

(1967-91)3

Average 

natural 

production 

(1992-06)4

Average % 

natural 

production 

difference from 

baseline5

Battle Creek 

fall-run 10,000 5,012 22,052 340%

Battle Creek 

late-fall-run 550 273 677 148%

Butte Creek 

fall-fun 1,500 763 3,266 328%

Butte Creek 

spring-run 2,000 1,017 11,504 1,031%

Clear Creek 

fall-run 7,100 3,574 12,317 245%

Mokelumne River 

fall-run 9,300 4,679 9,567 104%

Table 3. Chinook salmon AFRP production, Central Valley, (1992-2006)

1Only streams and rivers with complete salmon production data sets (1992-2006) are shown.

2Annual doubling goals were derived from “Mills, T.J. and F. Fisher. 1994. Central Valley Anadromous Sport Fish Annual Run-size, Harvest, and Population 

Estimates, 1967 through 1991, California Department of Fish and Game. 62pp” and published in “USFWS. 2001. Final Restoration Plan for the Anadromous Fish Restoration Program, A Plan to Increase Natural Production of Anadromous Fish in the Central Valley of California. Released as a Revised Draft 

on May 30, 1997 and adopted as fi nal on January 9, 2001. CVPIA, AFRP, Stockton, CA. [http://www.delta.dfg.ca.gov/afrp/restplan_fi nal.asp].” 3Baseline escapement data were derived from Mills and Fisher (1994) and used to generate natural production estimates for the doubling goal baseline 

period, 1967 through 1991.

4Grand Tab, California Department of Fish and Game. Data from this publication was used to generate natural production estimates for the doubling goal, 

1952 through 1966, and the doubling period, 1992 through 2006.

5

The percent of increased natural production over baseline for each watershed was calculated by subtracting baseline natural production (1967-1991) from 

natural production (1992-2006) and dividing the result by baseline natural production (1967-1991).

Chinook 

Salmon Species

and Watershed1

AFRP 

annual 

doubling 

goals2

Average 

baselines 

(1967-91)3

Average 

natural 

production 

(1992-06)4

Average % 

natural 

production 

difference 

from baseline5

All Chinook runs, all 

Central Valley streams

990,000 497,240 498,863 0.3%

Fall-run, all Central 

Valley watersheds

750,000 374,217 453,800 21%

Winter-run, all 

Central Valley streams

110,000 54,417 8,328 -85%

Spring-run, all 

Central Valley streams

68,000 34,425 16,567 -52%

Late fall-run, all 

Central Valley streams

68,000 34,182 20,141 -41%
3406 (b)(1) Other 21

CVPIA Section 3406(b)(1) “other”

“...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 identifi ed adverse 

environmental impacts of the CVP not specifi cally 

enumerated in this section.”

The Habitat Restoration Program (HRP), under section 

(b)(1) “other”, benefi ts federally listed Central Valley 

species and their habitats that were adversely impacted 

by operation and construction of the CVP and are 

not specifi cally addressed in the Fish and Wildlife 

Restoration section of the CVPIA. Habitat loss and 

fragmentation due to urbanization and agriculture 

conversion occurred on an estimated 2.7 million acres as 

a result of CVP construction.

The HRP’s priority actions, considered most effective 

and critical to species’ protection and recovery, include 

purchase of fee title or conservation easements on lands 

where threats are signifi cant, targeted restoration of 

CVP-impacted habitats where actions will markedly 

improve conditions, research to facilitate species 

recovery, and public outreach/education/planning/

management. These actions support the program’s 

output goal of contributing to restoring the 2.7 million 

acres impacted by construction and operation of the 

CVP.

To help direct conservation actions into high-priority 

areas and assist applicants in developing competitive 

proposals, in 2006 the program developed a GISbased “Project Area Map,” that defi nes the program’s 

geographic focus area. The program also developed a 

“High Priority Species List” that defi nes species identifi ed 

in various recovery plans (both resources are available on 

the HRP Web site: http://www.usbr.gov/mp/cvpcp). 

Measuring Success

Species Protection

To date, the HRP has allocated more than $23 million to 

fund 89 projects supporting the recovery of threatened 

and endangered species such as:

• San Joaquin kit fox

• Giant kangaroo rat

• Blunt-nosed leopard lizard

• California red-legged frog

• Giant garter snake

• Bay checkerspot butterfl y

• Valley elderberry longhorn beetle

• Riparian brush rabbit

• Riparian woodrat

• Lange’s metalmark butterfl y

• Vernal pools species (plants and invertebrates)

• Gabbro soil plants

Figure 4 maps the HRP project locations from 1996-

2007.

Habitat Protection

HRP funds have been used to acquire and protect 

approximately 100,000 acres of the 2.7-million-acre goal 

Habitat Restoration Program Sacramento

San Francisco

Los Angeles
22 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Project Site

Major Highway

County

CP/HRP Priority Project Area

2007 Projects

Source: Reclamation, Division of Environmental Affairs, 2008.

Red-Legged

Frog Surveys,

Cottonwood Creek

Vernal Pool

Wetland Restoration

Tracts G & H

Restoration

Giant Garter Snake 

Study at CNWR

Southern Water Snake Surveys

Yolo Co. Vernal Pool Restoration

Stone Lakes NWR Acquisition

Valensin Ranch Acquisition

Livermore Hydrology Study

Palmate-Bracted Birds Beak Study

Livermore Large

Flowered Fiddleneck Monitoring

Serpentine

Vegetation Study

Simon Newman Ranch

Conservation Easement

Romero Ranch

Conservation Easement

Grasslands Giant

Garter Snake Study

Alkali SinkFencing Project

San Joaquin

Kangaroo Rat Study

Doyen’s

Dune Weevil Survey

Nickell Ranch Acquisition

Buena Vista Lake Shrew Survey

Tulare Basin Riparian

Conservation and

Outreach Plans

Springtown Alkali

Sink Unit Livermore Study

Captive Breeding and Rearing

of Langes Metalmark Butterfly

Restoration

Hagemann Unit SJNWR Research

Fenwood Property Acquisition

Ohm Riparian Restoration

Stone Ridge Ranch Acquisition

Llano Seco Riparian Restoration

Boeger and Ward Acquisition

Prioritizing Gabbro Soils Study

Deer Creek Hills Acquisition

Ben Brown Ranch Acquisition

Schneider Ranch Acquisition

Howard Ranch Acquisition

Least Bell’s Vireo Surveys

Dos Rios Working Landscape Project

Dos Rios Ranch Acquisition

Snobird Ranch Restoration

Giant Garter Snake Surveys –

Priority 1-3 Recovery Tasks

Fine Gold Creek Acquisition

Jensen Ranch Acquisition & Restoration

Stone Corral Ecological 

Reserve Acquisition

Kaweah Oaks Preserve 

Management Plan

Herbert Ranch Preserve 

Acquisition

Allensworth Ecological Reserve

Acquisition

Southern San Joaquin Valley CAPP

Tipton Kangaroo Rat Relocation

Study at Allensworth

GGS Genetics Study

Riparian Brush Rabbit and Riparian 

Woodrat Study

Spivey Pond 

Red-Legged Frog Restoration

Vernal Pool Restoration–

Soil Biota Study

Drumheller Slough

Riparian Restoration

Figure 4. Habitat Restoration Program Project Locations (1996-2007)
3406 (b)(1) Other 23

In addition, the HRP has funded eight riparian restoration 

projects, contributing more than 1,000 restored acres. 

Riparian vegetation at several locations (e.g., Llano Seco) 

has experienced an approximately 80 percent survival 

rate. Table 5 lists the number of acres acquired and 

restored by year since 1996. (Acquisition only covers the 

purchase of the land; further effort is required to restore 

the desired habitat.) As shown, the bulk of the acreage 

was acquired in 1998 as part of the Wells Fargo (Simon 

Newman and Romero Ranches) project.

Recipients of 2007 HRP funds ($1,147,636) were projects 

that focused on high-priority species and habitats 

impacted by the CVP (Table 6). Progress reports are 

available for all projects and may be requested from the 

HRP program managers. Table 6 summarizes the FY 

2007 projects.

Habitat Protection

(acres protected via 

fee title acquisition 

and conservation 

easements)

Habitat Restoration 

(acres restored)

1996 4,356 0

1997 284 708

1998 74,360 0

1999 1,340 0

2000 1,426 206

2001 2,831 100

2002 2,211 0

2003 2,866 0

2004 719 432

2005 2,520 1,480

2006 192 731

2007 1,603 117

TOTAL 94,708 3,774

Table 5. Acres of Habitat Protected & Restored per Year (1996-2007)

(nearly 4 percent) of related habitat for these species, 

including vernal pool, riparian, alkali scrub, foothill 

chaparral, valley-foothill hardwood and grassland.
24 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Table 6. Recipients of FY 2007 HRP Funds

Project Status Significance

Antioch Dunes National 

Wildlife Refuge - Captive 

propagation of the Lange’s 

metalmark butterfl y and 

restoration of dune habitat 

for the Lange’s metalmark 

butterfl y, Contra Costa 

wallfl ower and Antioch Dunes 

evening primrose in Contra 

Costa County

Ongoing

Captive propagation 

is taking place at two 

locations and dunes 

restoration has begun; 

providing funding in FY 

2008 to continue the study

Supports habitat and species protection: 

The Lange’s metalmark butterfl y is on 

the verge of extinction and found only 

at Antioch Dunes NWR; restoration 

of dunes habitat will enhance; native 

buckwheat host plant survivability and 

enhance recovery of the wallfl ower 

and evening primrose, two federally 

endangered plants

Tulare Basin Wildlife 

Partners - Preparation of 

conservation and outreach 

plans for a riparian wildlife 

corridor for several counties

Ongoing

Completed three 

Conservation Plan 

Summaries and a listing 

of Priority Conservation 

Projects for distribution 

and review; project will 

continue until July 2009

Supports habitat protection: Helps 

provide essential public support, gauge 

issues critical to implementation of four 

Conservation Plans, and lay the basis 

for obtaining funds needed for future 

project implementation 

UC Davis – Research on 

importance of soil biota in 

vernal pool restoration and 

success of vernal pool plant 

species in several counties

Ongoing

Seed has been collected, 

germination protocols have 

been refi ned and the large 

pot experiment has been 

set up in a greenhouse; 

project will continue until 

July 2009

Supports habitat and species protection: 

examines role of soil biota in plant 

growth and establishment, compares 

effects from natural and artifi cial or 

restored pools, etc.; benefi ts numerous 

federally listed vernal pool plant species 

River Partners – Restoration 

of riparian habitat on the 

San Joaquin River at the 

Hagemann Unit of the San 

Joaquin River NWR in 

Stanislaus County

Ongoing

Soil testing, seed collection, 

mapping, hydrology 

and planning have been 

completed; planting will 

begin in fall 2008

Supports habitat protection to benefi t 

endangered species: riparian bush 

rabbit, riparian woodrat, least Bell’s 

vireo (bird), valley elderberry longhorn 

beetle

Tuolumne River Trust – 

Acquisition of 1,603-acre 

Dos Rios Ranch in 

Stanislaus County 

Ongoing

Appraisal, land and 

environmental surveys 

complete; efforts to secure 

needed additional funding 

is underway

Supports habitat protection: Acquisition 

of property will benefi t the least Bell’s 

vireo, valley elderberry longhorn beetle, 

and riparian brush rabbit

Endangered Species 

Recovery Program – 

Assessment of the success 

of a relocation effort in 

Tulare County for the 

Tipton kangaroo rat 

Ongoing

Preliminary study design 

complete; ready for fi eld 

work phase 

Supports species protection: Longterm monitoring to evaluate success of 

relocation effort
3406 (b)(1) Other 25

Project Status Significance

Eric Hansen, Private 

Consultant – Continuation 

of assessment of the current 

status and distribution of the 

giant garter snake (GGS) in 

Merced and northern Fresno 

counties

Ongoing

For the second year, 

potential presence of 

GGSs north and east of 

the San Joaquin River 

and the current status 

of declining historical 

populations south and 

east of the San Joaquin 

River in the Grassland 

Ecological Area, Merced 

County, California, were 

investigated; historical 

populations at Mendota 

Wildlife Area, Fresno 

County, were also 

sampled; trapping done 

May-September 8, 2007; 

64 traplines established 

with 48,762 trap days 

accrued; fi nal report due 

April 15, 2008

Supports species protection: Assesses 

current status and distribution of the 

GGS, a species that is disappearing in 

the San Joaquin Valley

CSU Chico - Continuation of a 

genetic analysis of giant garter 

snake (GGS) populations 

in the San Joaquin and 

Sacramento Valleys.

Ongoing

Study continues to 

analyze genetics of 

Central Valley GGS 

populations; project 

will continue until 

December 2008

Supports species protection: Continues 

work on the range-wide population 

genetic structure of the GGS, to help 

determine if the nearly extirpated San 

Joaquin Valley populations represent 

distinct population segments worthy of 

special protection

Table 6, Continued
26 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(b)(1) “other” and 

3406(b)(23)

“...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 identifi ed adverse 

environmental impacts of the CVP not specifi cally 

enumerated in this section;” and

“In order to meet Federal trust responsibilities to 

protect the fi shery resources of the Hoopa Valley 

Tribe, and to meet the fi shery restoration goals 

of the Act of October 24, 1984, Pub. L. 98-541, 

provide through the Trinity River Division, for 

water years 1992 through 1996, an instream release 

of water to the Trinity River of not less than 340,000 

acre-feet per year for the purposes of fi shery 

restoration, propagation, and maintenance...”

The completion of the Trinity and Lewiston Dams in 

1964 allowed water from the Trinity River to be diverted 

to the Sacramento River and California’s Central 

Valley for power generation and irrigation purposes. 

The dams barred salmonids from more than 100 miles 

of upstream habitat, and deteriorated downstream 

spawning and rearing habitat by reducing the magnitude 

and variability of water fl ows. By the 1990s, salmonid 

production in the Trinity River had dropped by more 

than 80 percent. 

The Trinity River Restoration Program (TRRP) is 

dedicated to the improvement of anadromous fi sheries 

habitat in the Trinity River Basin. The Trinity River 

Mainstem Fishery Restoration EIR/EIS and its 

accompanying Record of Decision (ROD) was completed 

and signed by the Secretary of the Interior, with 

concurrence of the Hoopa Valley Tribe, in December 

2000. The ROD identifi ed a series of restoration actions, 

including a monitoring and assessment program, to 

make program adjustments as required. Since 2001, the 

TRRP has been implementing these restoration activities, 

focusing on the upper 40 miles of the Trinity River 

between Lewiston Dam and the confl uence with the 

North Fork of the Trinity River. 

Reclamation plans and implements restoration activities 

and adaptively manages the program based on 

Lewiston Dam

Trinity Dam

Lewiston Reservoir

Trinity River Grass Valley Creek

Trinity River Restoration Area

Figure 5. Trinity River Restoration Program Map

Trinity River Restoration 

Program Sacramento

San Francisco

Los Angeles

Weaverville

Redding
3406(b)(1) Other and 3406(b)(23) 27

information generated by monitoring and evaluation. 

Enabling legislation (PL 98-541, as amended) established 

a series of goals to achieve and maintain healthy, stable 

fi sheries populations. A combination of outcome-based 

goals and output-based goals were developed to measure 

the progress of the program. 

The outcome-based goal is indicated by natural and 

hatchery-produced adult spawner escapement to the 

Trinity River, as indicated in Table 14.

The output-based goals are indicated by four criteria:

1) Increasing minimum fl ow releases – Measured by 

annual acre-feet of instream fl ow releases to meet tribal 

trust responsibilities and fi shery restoration goals 

a. Target: Between 369,000 and 815,000 acre-feet 

per year (varies by water year type), with peak fl ows 

to 11,000 cfs by 2008 and annually thereafter

 2) Implementing construction projects–Measured by 

progress toward completion of 47 mechanical channel 

rehabilitation projects and all necessary infrastructure 

improvements 

a. Channel rehabilitation target: Complete 24 

channel rehabilitation projects by the end of 2008, 

with the remainder by 2012 

b. Infrastructure improvements target: Completion 

of infrastructure improvements to allow fi shery fl ow 

releases of up to 11,000 cfs by 2008

3) Sediment management–Measured by progress 

in placing cubic yards of coarse sediment (gravel) in, 

and removing cubic yards of fi ne sediment from, the 

mainstem Trinity River to provide adequate spawning 

habitat and other geomorphic benefi ts

a. Target: Placement of up to 10,000 cubic yards of 

gravel per year, as determined by monitoring data

b. Target: Removal of up to 20,000 cubic yards 

of fi ne sediment per year, depending on existing 

conditions 

4) Watershed restoration–Measured by the cubic 

yards of sediment reduced annually from the tributaries 

compared to baselines

a. Target : 240,000 to 480,000 cubic yards annually 

based on water year conditions and monitoring data

Measuring Results

Outcome-based Target – Escapement 

Increases 

Monitoring suggests there has generally been an 

improvement in health and vigor of outmigrating 

juveniles as well as returning adult spawners of all 

species since 2000. Preliminary data suggest an upward 

trend in coho salmon run size, along with decreased 

prevalence of disease and improved egg/sperm viability 

of spawners of all species. 

Based on weir counts (adult runs), steelhead numbers 

have increased signifi cantly, with 2006 and 2007 

recording the largest runs in recent years. In 2006, 

total run size of adult steelhead was 41,488 fi sh, and 

a preliminary estimate for 2007 is more than 50,000 

fi sh. The DFG responded to this increase in steelhead 

numbers by proposing a larger take limit for hatchery 

steelhead for recreational anglers in the Trinity River 

during the 2008 fi shing season. While much of the 

increased population consists of hatchery-produced fi sh, 

this suggests a response to system-wide improvements 

in temperatures and reduced fi ne sediment that likely is 

benefi cial to all species.

Target Trinity River Natural Escapement

Target Trinity River Hatchery-produced Adult 

Spawner Escapement

62,000 fall-run Chinook salmon 9,000 fall-run Chinook salmon

6,000 spring-run Chinook salmon 3,000 spring-run Chinook salmon

40,000 steelhead 10,000 steelhead

1,400 coho 2,100 coho

Table 7. Target Natural Escapement, Trinity River
28 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Output-based Targets 

1) Increasing minimum fl ow releases 

Reclamation has achieved full ROD fl ows since 

2005, following successful resolution of litigation 

that initially constrained ROD fl ows in 2001-2004. 

Water year types since 2005 have included Normal, 

Extremely Wet, and Dry, with volumes ranging 

from 453,000 acre-feet to 815,000 acre-feet. Water 

Year 2007 was classifi ed as a dry year, with 452,600 

acre-feet–meeting the minimum fl ow release–and a 

peak fl ow of 4,500 cfs as required by the ROD. Full 

implementation of ROD releases are now possible 

based on water year type. Approximately 1.5 million 

acre-feet more water has been released to the river 

over the past seven years than would have occurred 

without the ROD. 

2) Implementing construction projects

Since 2001, the CVPIA Restoration Fund has 

allocated $7.1 million to the TRRP. The program 

has implemented eight of the 47 target mechanical 

channel rehabilitation projects and all of the 

infrastructure improvements necessary to allow the 

program to regularly achieve annual fl ow release 

goals, including dam releases, of up to 11,000 cfs in 

an extremely wet year, such as:

• Construction of eight channel rehabilitation projects 

(Hocker Flat, four sites near Canyon Creek and three 

sites near Indian Creek)

• Construction of three replacement bridges and 

upgrade of an approach road/culvert 

• Completion of a comprehensive inventory of 

fl oodplain structures for more than 500 privately 

owned parcels

• Improvement of 1.5 miles of road accessing private 

homes

• Relocation of one house and modifi cation of more 

than 25 other smaller structures

• Renovation of 37 domestic water or sewer systems 

In FY 2007, three mechanical channel rehabilitation 

projects and 21 infrastructure improvements were 

completed. Environmental documentation and 

designs were prepared to allow a construction 

contract award for eight additional channel 

rehabilitation projects in the summer of 2008.

3) Sediment Management 

In 2007, the program placed 4,500 cubic yards of 

gravel adjacent to the Trinity River Fish Hatchery 

in the mainstem of the Trinity River to improve 

spawning and rearing habitat, as well as facilitate 

the creation of needed geomorphic features further 

downstream. A total of 2,500 cubic yards also was 

stockpiled at two locations along the river in the 

Lewiston area for injection during peak fi shery 

restoration fl ows in May 2008. To date, the program 

has added 8,000 cubic yards of coarse sediment 

(spawning/rearing gravel) to the river.

As part of the program’s routine maintenance of 

settling ponds at the mouth of Grass Valley Creek, 

TRRP partners implemented a contract in 2007 

to excavate 16,000 cubic yards of material from 

the lower pond, thus restoring it to its full holding 

capacity. This action helps ensure that fi ne sediment 

(decomposed granite) from the Grass Valley Creek 

drainage will not enter the mainstem Trinity River 

and degrade spawning and rearing habitat.

4) Watershed Restoration

In 2007, TRRP partners collaborated with the TRRP 

to identify nine priority watershed projects for 

implementation, and worked to obtain over $300,000 

in matching funds. Analyses are currently underway 

to better refi ne the calculation of sediment entering 

the mainstem Trinity River from the tributaries and 

construction is expected to begin in 2008.

While some short-term habitat benefi ts will probably 

be achieved, most of the program’s projects focus 

on longer-term objectives; therefore, is diffi cult to 

draw defi nitive cause and effect relationships at this 

point in the program. The fi rst of the eight channel 

rehabilitation projects completed to date was just 

fi nished in 2005; it will likely take several more 

years before preliminary results can be inferred 

about benefi cial effects of the increased rearing 

habitat for Chinook salmon within their life cycle. 

One positive short-term indicator was data recently 

provided by the DFG indicating that more than 

39,000 natural Chinook spawners returned to the 

Trinity River in 2007 despite concern over low 

2005-2006 Chinook fall-run numbers. Program 

biologists from several agencies continue to evaluate 

these data.
3406 (b)(1)(B) 29

CVPIA Section 3406(b)(1)(B)

“As needed to achieve the goals of this program, 

the Secretary is authorized and directed to modify 

CVP operations to provide fl ows of suitable quality, 

quantity, and timing to protect all life stages of 

anadromous fi sh, except that such fl ows shall be 

provided from the quantity of water dedicated to 

fi sh, 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 confl ict with the fulfi llment of the Secretary’s 

remaining contractual obligations to provide CVP 

water for other authorized purposes. Instream fl ow 

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.”

The fl ow of water in rivers and streams is essential 

for all fi sh life stages: spawning, fry emergence, 

juvenile development, outmigration, and passage back 

to spawning grounds. Flows help maintain a healthy 

environment for fi sheries by maintaining suffi cient 

stream depth and optimal temperatures for spawning 

and rearing. Periods of high fl ow also move sediments 

downstream that establish and maintain the river 

bottom. Reclamation and the Service are dedicated to 

creating optimal fl ows to increase anadromous fi sh 

populations consistent with the doubling goal. 

Interior modifi es base condition CVP operations using 

(b)(2) water, (b)(3) water, and by “reoperating” the 

system to provide instream benefi ts to anadromous 

fi sh. Reoperating the system is done by changing and 

coordinating planned releases between CVP dams when 

doing so improves instream conditions without impacting 

other CVP obligations or authorized purposes. 

Determining the instream fl ow needs in CVP streams is 

an ongoing process that is being addressed in part by the 

Instream Flow Requirements Program, which provides 

scientifi c information to the CVPIA program to assist 

in developing recommendations for instream fl ow needs 

for anadromous fi sh in Central Valley streams. The 

Instream Flow Incremental Methodology (IFIM) is a 

habitat-based model developed by the Service to assess 

instream fl ow needs for aquatic resources, including 

anadromous fi sh. The program goal is to provide up to 

nine specifi ed instream fl ow studies, although no time 

period is specifi ed for this goal. Studies funded under 

section (b)(1)(B) focus on CVP streams (Sacramento, 

American, Stanislaus, and Clear Creek). Studies funded 

under section (b)(1) focus on all other Central Valley 

streams. Generally there is an IFIM modeling project 

for each life stage of anadromous fi sh within each 

segment of the Sacramento, American, Merced and 

Yuba rivers and Clear and Butte creeks. 

The Service uses the IFIM program to demonstrate 

the effect of varying fl ows of water within specifi c 

watersheds. The information developed by IFIM 

are used by (b)(2) program managers in developing 

recommendations for instream fl ow in CVP streams 

Modifi ed CVP Operations Sacramento

San Francisco

Los Angeles
30 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

and by other Service program managers for other 

Central Valley streams.

The IFIM process follows four basic steps:

1) Monitoring, consisting of data collection 

2 Modeling, consisting of analysis 

3) Peer Review by U.S. Geological Survey (USGS), 

CALFED, consultants or academics

4) Production of a fi nal report

Since 1995, IFIM studies have been completed for 

Sacramento, American, Merced rivers and Butte Creek, 

and the data generated by these studies have been used 

by the Service to negotiate fl ow changes that have a 

dramatic effect on fi sh production. For instance, the 

Butte Creek IFIM study showed that increasing water 

fl ows from 40 to 120 cubic feet per second (cfs) during 

the fall season would increase the amount of spawning 

habitat for spring-run Chinook salmon by a signifi cant 

72 percent. Based on these data, the Service’s Energy 

and Instream Flow branch negotiated changes to annual 

operating plans that resulted in an increase in fall fl ows 

to 60 cfs in 2004 and 2007 and 75 cfs in 2005 and 2006. 

These fl ows were agreed to between resource agencies 

and Pacifi c Gas & Electric (PG&E) during development 

of the annual operating plan. Establishment of these 

fl ow-habitat relationships was critical to the development 

of the annual operating plan for Butte Creek.

Based on these data, in FY 2008 the Service will 

recommend that the Federal Energy Regulatory 

Commission (FERC) consider new terms for Butte 

Creek between the Centerville Dam and Powerhouse 

that would allow the full 120 cfs fl ow in Butte Creek 

from September 1 to March 15—a critical period 

covering the spawning and emergence of fry.

Another example of the use of IFIM data is the 

Sacramento River IFIM study (2006) which 

demonstrated that substantial juvenile stranding and 

redd dewatering could be avoided by keeping fl ows 

above 3,750 cfs. “Stranding” is a term used to describe 

fi sh that are trapped in pools of water that have no 

connectivity to the larger stream because of insuffi cient 

fl ow. Similarly, redd dewatering occurs when redds (fi sh 

egg “nests”) are left exposed by receding water levels. In 

2007, the data from this IFIM study were used to justify 

operational changes in the allocation of (b)(2) water in 

the Sacramento River and fl ows were maintained above 

the 3,750 cfs level to minimize juvenile stranding and 

redd dewatering.

As noted above, the Service has completed modeling 

for the Sacramento (2003, 2005), Merced (1997) 

and American (2003) rivers and Butte Creek (2003), 

generating valuable data to determine optimum fl ows. 

The Service has continued to prioritize additional rivers 

for IFIM modeling. Prioritization is based on a number 

of factors: 

• Feasibility - Is there an upcoming FERC relicensing 

that provides a platform for change?

• T&E species - Are there threatened and endangered 

species that would benefi t from operational changes? 

• Species - How many salmonid races/species are 

present?

• Complications - Are other actions needed to improve 

passage and access to spawning grounds before 

operational fl ow changes would have an effect? 

Based on these factors, in 2001 to 2007 the Service 

added the Yuba and Tuolumne rivers and Clear Creek 

to the priority list of rivers to be modeled over the next 

fi ve years.

Collecting IFIM fi eld data in Clear Creek
3406 (b)(1)(B) 31

Measuring Success

In 2007, the CVP reoperated the system several times 

to provide benefi ts to anadromous fi sh on Clear Creek 

without impacting other CVP obligations or authorized 

purposes. As an example, in November 2007, base 

condition releases from Keswick Dam on the Sacramento 

River were decreased by 100 cfs while base condition 

releases from Whiskeytown Dam into Clear Creek were 

increased by 100 cfs for approximately three weeks. This 

reoperation improved conditions on Clear Creek without 

changing the total amount of CVP water being released. 

Similar reoperations took place for short periods in April 

and June between releases from Nimbus Dam on the 

American River and Whiskeytown Dam into Clear Creek.

Since 1995, the program has completed 11 IFIM studies. 

Table 7 illustrates progress on the studies that were active 

in 2007. (Dates indicate completion of an activity.)

As shown in Table 7, the major accomplishments for 

2007 include the following:

Sacramento River - Completion of fi nal reports for 

macroinvertebrate fl ow-habitat and redd dewatering 

and juvenile Chinook and steelhead stranding.

Yuba River – Completion of monitoring for springand fall-run Chinook salmon and steelhead fry and 

juvenile rearing; and completion of monitoring 

for redd dewatering and juvenile Chinook and 

steelhead stranding.

Clear Creek – Completion of fi nal report for springrun Chinook salmon and steelhead upper reach 

spawning.

Tuolumne River – Completion of modeling for 

fl oodplain inundation as a function of fl ow. 

Table 8. IFIM Studies Completed and Planned as of 2007

River IFIM Modeling Project

Peer 

Review

Final 

Report

Sacramento Macroinvertebrate fl ow-habitat 

complete

FY 2001 FY 2005 FY 2006 FY 2007

Redd dewatering and juvenile 

Chinook and steelhead stranding

FY 2004 FY 2005 FY 2006 FY 2007

Yuba Spring- and fall-run Chinook 

salmon and steelhead fry and 

juvenile rearing

FY 2007 FY 2008 Expected 

FY 2008

Expected 

FY 2008

Redd dewatering and juvenile 

Chinook and steelhead stranding 

FY 2007 FY 2008 Expected 

FY 2008

Expected 

FY 2008

Spring- and fall-run Chinook 

salmon and steelhead spawning

FY 2004 FY 2006 FY 2006 Expected 

FY 2008

Clear Creek Spring-run Chinook salmon and 

steelhead upper reach spawning

FY 2005 FY 2006 FY 2007 FY 2007

Fall-run Chinook salmon and 

steelhead lower reach spawning

Started in 

FY 2007

Expected 

FY 2008

Expected 

FY 

2009-10

Expected 

FY 

2009-10

Juvenile spring-run Chinook 

salmon and steelhead upper 

reach rearing 

Started in 

FY 2007 

FY 2008 Expected 

FY 

2009-10

Expected 

FY 

2009-10

Juvenile spring-run and fall-run 

Chinook salmon and steelhead 

lower reach rearing 

Started in 

FY 2007

Expected 

FY 2009

Expected 

FY 

2009-10

Expected 

FY 

2009-10

Tuolumne Floodplain inundation as a 

function of fl ow (La Grange Dam 

and river mile 22)

N/A FY 2007 FY 2008 Expected 

FY 2008

Monitoring Modeling
32 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406 (b)(2)

“...dedicate and manage annually 800,000 

acre-feet of Central Valley Project yield for the 

primary purpose of implementing the fi sh, wildlife, 

and habitat restoration purposes and measures 

authorized by this title; to assist the State of 

California in its efforts to protect the waters of 

the San Francisco Bay/Sacramento-San Joaquin 

Delta Estuary; and to help meet such obligations 

as may be legally imposed upon the Central Valley 

Project under state or federal law following the 

date of enactment of this title, including but not 

limited to additional obligations under the federal 

Endangered Species Act...”

Interior has the responsibility to annually dedicate and 

manage 800,000 acre-feet of CVP (b)(2) water for fi sh, 

wildlife and habitat restoration purposes. This water 

is provided per increased CVP releases and decreased 

CVP export pumping, relative to a hypothetical preCVPIA baseline operation. The accounting of the 

water is obtained from changes in operations on the 

American River (Nimbus Dam), Sacramento River 

(Keswick Dam), Stanislaus River (Goodwin Dam), 

Clear Creek (Whiskeytown Dam) and the delta pumps 

(see Figure 1 for location map). 

Water Management

The 2000 CALFED Programmatic Record of Decision 

established an Environmental Water Account (EWA) 

program with the purpose of providing protection 

(supplemental to a hypothetical pre-EWA baseline 

level of protection) to the fi sh of the Bay-Delta Estuary. 

Although accounted differently, the management of 

(b)(2) water is closely coordinated with the management 

of CALFED’s EWA, since both (b)(2) and the EWA 

contribute to the CVPIA’s goal of doubling natural 

production of anadromous fi sh and provide concurrent 

Dedicated 800,000 acre-feet 

Project Yield Sacramento

San Francisco

Los Angeles

Figure 6. Average Annual (b)(2) Water Use

in thousand acre-feet (TAF) (2002-2005)
3406 (b)(2) 33

benefi ts to other fi sh and wildlife, including endangered 

fi sh species. The program includes monitoring and 

evaluation to assess the effectiveness of the use of the (b)

(2) water.

In 2003 and 2004, the U.S. Court of Appeals for the 

Ninth Circuit stated that the “primary purpose” to 

which the 800,000 acre-feet should be dedicated is the 

implementation of “fi sh, wildlife and habitat restoration 

purposes authorized by (CPVIA)...” The statute gives 

Interior discretion to allocate the 800,000 acre-feet 

among fi sh and wildlife, state water quality control plan 

fi shery requirements and endangered species obligations, 

as long as Interior’s allocation accounts for the hierarchy 

of purposes established in Section 3406 (b)(2).

Due to legal decisions by the Federal District 

Court, Interior released a revised Final Decision on 

implementation of Section 3406 (b)(2) on May 9, 2003 

which set out a calculation of CVP water use (the method 

for accounting for use of the dedicated 800,000 acre-feet 

of water and procedures for management of the water).

In general, (b)(2) fi sh actions include CVP pumping 

reductions and additional fl ow releases relative to 

pumping and releases the CVP would make given 

current demands and hydrologic conditions, but under 

pre-CVPIA regulatory requirements. Generally, the 

objective for these actions are as described below: 

(1) Instream fl ow augmentations on CVP-controlled 

streams to protect salmon and steelhead and 

contribute toward meeting AFRP fl ow objectives 

(2) Increased releases from New Melones Reservoir 

to help meet the 1995 Water Quality Control Plan 

(WQCP) requirements for San Joaquin River 

fl ows at Vernalis

(3) Increased releases from Shasta and/or Folsom 

reservoirs to help meet the WQCP delta outfl ow 

requirements

(4) Export reductions at the CVP Tracy pumps to 

protect at-risk fi sh species (notably salmon, steelhead and delta smelt) 

Monitoring and Evaluation

Real-time fi sh monitoring helps inform (b)(2) decisions 

on when and where actions should be taken. On a 

weekly basis, fi shery biologists and CVP and SWP 

operators update the CALFED Data Assessment 

Team on fi sh movements and project operations in the 

Sacramento River, San Joaquin River and the delta. 

The sites sampled include the mainstem Sacramento 

and San Joaquin rivers, their major tributaries and 

various locations in the delta, including the export 

facilities. Reclamation and the Service provide 

preliminary daily (b)(2) accounting periodically though 

the year and a fi nal detailed accounting of (b)(2) fi sh 

actions on an annual basis, usually in December following 

the close of the water year. This information is posted 

on the U.S. Bureau of Reclamation, Mid-Pacifi c Region, 

Central Valley Operations Offi ce home page at www.usbr.

gov/mp/cvo.

2001 800,000 798,000

2002 800,000 793,000

2003 800,000 796,000

2004 800,000 800,000

2005 800,000 672,000 128,000

2006 800,000 422,000 183,000 198,000

2007 800,000 798,000

 (b)(2) Allocated Fisheries Other CVP Project Banked

Year (acre-feet) (acre-feet) Purposes* (acre-feet) (acre-feet)

Use of Dedicated Water (approximate)

Table 9. Allocation vs. Use of (b)(2) Water (2001-2007)

* Section 3406 (b)(2)(D): If the quantity of water dedicated under this paragraph, or any portion thereof, is not needed for the purpose of this section, based 

on a fi nding by the Secretary, the Secretary is authorized to make such water available for other project purposes.
34 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Measuring Success

The 800,000 acre-feet annual allocation has been 

fully utilized each water year since 2000 when the (b)

(2) accounting began, except for water year 2006. As 

shown in the Table 8, in wetter precipitation years 

(2005 and 2006) a portion of the dedicated water was 

banked pursuant to Section 3408(d) for use in the 

subsequent year.

In addition to other restoration activities, the increased 

instream fl ows, made possible by CVPIA’s (b)(2) 

Table 10. FY 2007 Use of (b)(2) Water

River Action Date Results

American Augmented low base fl ows to 

maintain 1,500-2,000 cfs 

Late October 2006–

mid-April 2007 

Improved instream conditions 

for fall-run Chinook and 

steelhead during spawning, 

incubation and rearing periods

Sacramento Augmented low base fl ows 

with Water Year (WY) 2007 

and 2006 (b)(2) water and 

banked WY 2006 water in 

Shasta Reservoir to maintain 

4,500-5,500 cfs; unused WY 

2006 banked water made 

available to other 

CVP purposes

November 

2006-March 2007

Improved instream conditions 

for fall-run and late-fall-run 

Chinook and steelhead during 

spawning, incubation and 

rearing periods

Clear Creek Augmented low base fl ows 

throughout 2007

FY 2007 Improved habitat conditions 

for anadromous fi sh, including 

Chinook salmon and steelhead 

and their upstream migration, 

spawning, egg incubation, 

rearing and downstream 

migration

Stanislaus Augmented low base spring 

pulse fl ow for outmigrating 

fall-run Chinook smolts

April 20-May 20; 

coordinated with 

2007 Vernalis 

Adaptive 

Management 

Program (VAMP)

Assisted outmigrating fall-run 

Chinook smolts; needed due to 

low base fl ows

CVP Jones 

Pumping Plant

Reduced higher base CVP 

exports prior to VAMP

Reduced higher base CVP 

exports to approximately

 850 cfs during VAMP period

March 22-April 21

April 22-May 22*

Assisted in meeting WQCP 

requirements

Protected outmigrating salmon 

smolts as well as larval and 

juvenile delta smelt

provision, have helped maintain or improve salmon and 

steelhead habitat and populations in CVP-controlled 

streams, and export reductions at critical times have 

helped protect delta smelt as well as salmon and 

steelhead in the delta.

In 2007, Reclamation dedicated 800,000 acre-feet of 

2007 water and used approximately 195,000 acre-feet of 

banked 2006 water through the (b)(2) program. Uses of 

(b)(2) water in 2007 are listed in Table 9.

* In the post-VAMP period, higher base CVP exports were reduced using EWA wate to approximately 850 cfs and then ramped up gradually (May 22-June 18).
3406(b)(3) and (g) 35

CVPIA Sections 3406(b)(3) and 3406(g)

“The Secretary . . . is authorized and directed to 

develop and implement a program in coordination 

and in conformance with the plan required under 

paragraph (1) of this subsection for the acquisition 

of a water supply to supplement the quantity of 

water dedicated to fi sh and wildlife purposes under 

paragraph (2) of this subsection.... The program 

should identify how the Secretary intends to utilize, 

in particular the following options: improvements 

in or modifi cations of the operations of the project; 

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.”

The Water Acquisition Program (WAP) acquires 

water to supplement the 800,000 acre-feet of dedicated 

CVP yield for fi sheries. The target for acquisitions is 

approximately 200,000 acre-feet per year, for use on the 

San Joaquin and Sacramento rivers and their tributaries, 

as described in the CVPIA PEIS/ROD. The WAP also 

acquires water for CVPIA-designated refuges and 

wildlife management areas. WAP activities for refuge 

water acquisitions are discussed in Section (d)(2) Water 

Acquisition Program-Refuge Water.

The WAP is designed to meet two primary objectives in 

support of the Anadromous Fish Restoration Plan:

• Improve spawning and rearing habitat 

• Increase migration fl ows for fall-, winter- and springrun Chinook salmon and steelhead

In support of the second goal, WAP acquires instream 

fl ows in support of the Vernalis Adaptive Management 

Plan (VAMP) which is a component of the San Joaquin 

River Agreement (SJRA). This acquired water provides 

additional spring and fall fi shery fl ows on the Stanislaus, 

Tuolumne, Merced, and lower San Joaquin rivers.

Managing fl ows pursuant to SJRA and VAMP

VAMP is a scientifi cally based fi shery management plan 

that determines the relationships between fl ows, exports, 

and other factors on fi sh survival in the SacramentoSan Joaquin Delta. The SJRA includes VAMP and 

governs the operation of water on the San Joaquin River 

to ensure that pulse fl ows and other fl ows are provided 

to support restoration of anadromous fi sh in the river. 

Specifi cally, the spring fl ows assist in the outmigration 

of juvenile salmonids and can help meet water quality 

requirements. Fall fl ows assist adult salmon migrating 

into the tributaries prior to spawning.

WAP acquires, and with the Central Valley Operations 

Offi ce (CVO), in cooperation with the member agencies 

of the San Joaquin River Group Authority (SJRGA) 

manages water to provide additional spring and fall 

fi shery fl ows on the Stanislaus, Tuolumne, Merced and 

Lower San Joaquin rivers. The increased fl ows primarily 

benefi t Chinook salmon, which can account for more 

than 70 percent of the statewide commercial harvest, as 

well as numerous resident and anadromous fi sh species. 

Water Acquisition Program – 

Instream Water Sacramento

San Francisco

Los Angeles
36 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Measuring Success

Since 2001, the program has acquired an average of 

approximately one half of the 200,000 acre-feet annual 

target. The actual volume of water acquired each year 

fl uctuates based on the basin hydrology, reservoir 

storage and the water supplies available to WAP 

pursuant to the SJRA. The costs for the water acquired 

pursuant to the VAMP agreement are fi xed by the SJRA.

Reclamation has yet to acquire the full 200,000 acrefeet of target fl ows, due to a lack of willing sellers 

as well as the high cost of water on the open market. 

In addition to the water identifi ed in the SJRA, on 

occasion WAP has been able to acquire instream fl ows 

by entering into one-year transfers with local water 

agencies that have transferable water to sell. Table 10 

shows the volume of water purchased for the years 

1994 through 2007. The 2007 water includes 35,000 

acre-feet purchased for fl ows to protect the federally 

listed delta smelt.

Year

Annual Water 

Acquisitions in acre feet 

(percentage of 200,000 

area feet target)

1994 76,441 (38%)

1995 0

1996 16,161 (8%)

1997 155,983 (78%)

1998 80,000 (40%)

1999 174,498 (87%)

2000 108,880 (54%)

2001 109,785 (55%)

2002 68,105 (34%)

2003 91,526 (46%)

2004 98,211 (49%)

2005 148,500 (74%)

2006 148,500 (74%)

2007 92,145 (46%)

Table 11. Annual (b)(3) Instream Water 

Acquisitions (1994-2007)
3406 (b)(4) 37

CVPIA Section 3406(b)(4)

“Develop and implement a program to mitigate for 

fi shery impacts associated with operations of the 

Tracy Pumping Plan. Such program shall include, 

but is not limited to improvement or replacement 

of the fi sh screens and fi sh recovery facilities and 

practices associated with the Tracy Pumping Plant.”

The original Tracy Fish Collection Facility (TFCF) 

was built in the 1950s to protect fi sh entering the Delta 

Mendota Canal (DMC) by way of the Jones Pumping 

Plant (JPP). The facility provides multi-use water 

from the Sacramento-San Joaquin Delta (Delta) to the 

Central Valley of California. The primary purpose of the 

program is to mitigate for south Delta fi shery impacts 

at the federal JPP. The current primary objective of the 

program is to develop and implement new, modern day 

cost-effective fi sh collection, holding, transport and 

release technology and operational procedures that will 

signifi cantly improve fi sh protection in the South Delta 

at the entrance to the JPP. The data and information 

generated will help evaluate present-day operations 

and effi ciencies for TFCF, as well as assisting the DWR 

with improvements to their fi sh screens located at the JF 

Skinner Fish Protection Facility (Skinner). 

Tracy Fish Facility Improvement Program (TFFIP) 

research is performed in cooperation between 

Reclamation’s Mid-Pacifi c Region and research and 

engineering groups at the Denver Technical Service 

Center. Research planning and execution is enhanced 

through coordination, review and assistance from 

other agencies including the DFG, DWR, the Service, 

and the National Marine Fisheries Service (NMFS). 

Universities, private consultants and the San Luis Delta 

Mendota Water Authority also provide assistance.

Due primarily to budgetary constraints, Reclamation 

and DWR decided in 2005 not to proceed with 

construction of new full-scale testing/fi sh screen 

facilities in the south Delta, instead opting to develop 

and implement actions at the existing TFCF and Skinner 

(including improved technology and operational 

Tracy (Jones) Pumping Plant 

Program 

Clifton Court

Forebay

Tracy Fish Collection Facility

Suisun

Bay

San

Francisco

Bay

Tracy (Jones)

Pumping Plant

Delta-Mendota Canal

Figure 7. Tracy (Jones) Pumping Plant
38 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

procedures) to reduce fi sh losses and improve fi sh 

salvage success while meeting the goal of the CVPIA. 

This was the outcome of the CALFED South Delta 

Fish Facility Forum (SDFF) discussions in 2005 which 

included representatives from the state and federal 

water agencies, regulatory agencies, and stakeholders 

interested in South Delta exports and fi shery impacts. 

Many of the regulatory requirements were also 

contained in the 2004 NOAA Fisheries and Service CVP 

Operating Criteria and Plan (OCAP) biological opinions.

To date, Reclamation has identifi ed 23 “actions” related 

to improving fi sh protection at the existing TFCF. 

Implementation of these actions has been ongoing since 

1992 at TFCF and full implementation is not expected 

until 2013 at the earliest. Additional actions could be 

added to the program as needed, in response to any 

unforeseen issues or concerns that may require further 

analysis, assessment and improvements. The program 

has not defi ned fi sh loss reduction targets; rather, the 

program’s present goal is to implement and complete the 

23 identifi ed actions. 

Although the refocused 2005 TFCF improvement 

program has not been in place long enough for complete 

assessment, preliminary results have revealed that 

several factors have made the Tracy facility less 

effective towards screening and salvaging fi sh than it 

was in the 1950s: 

1) Changes in South Delta hydrology - Implementation 

of the SWP, in addition to increased pumping at 

Jones and other delta actions, lowered the water 

elevation at Tracy by a few feet and increased 

primary channel velocities 

2) Invasive species - Introduction of new vegetative 

species such as water hyacinth and egeria densa

(pond weed) have caused clogging of screens and 

other equipment, resulting in a higher level of 

fi sh stress and mortality and causing the louvered 

bypass system to operate less effi ciently, thus 

resulting in fewer fi sh making it to the holding 

tanks for transport back out to the delta

3) Predators - An increase in predators, such as 

striped bass, within the TFCF has caused a significant increase in fi sh mortality during the salvage 

process, prior to and including fi sh holding and 

hauling

Measuring Success

Program Actions

To date, the program has completed 10 of 23 actions, 

or 43 percent of the program’s present goal. Actions in 

2007 included continued study efforts to determine the 

TFCF’s present-day fi sh salvage effi ciency, assessment 

of above-ground holding tanks in the Denver lab, 

reassessment of the outdated Bates Table used for 

establishing fi sh hauling densities during transport, 

improvement to debris and predator management as well 

as hydraulic control of the facility, collection of water 

quality data at the entrance to the DMC, distribution of 

various Tracy Research Volume Series and publications, 

and updating of the Tracy Research Web site. Also, 

Reclamation proceeded with replacement of fi sh transfer 

buckets and new fi sh haul trucks and tanks, and began 

construction of a new onsite research building.

Since the program was implemented, physical and 

operational changes have already signifi cantly shown 

improvement in Reclamation’s ability to successfully 

salvage all species of delta fi sh, including anadromous 

fi sh, and release them safely back into the delta estuary. 

However, since the decision to focus on improving 

existing South Delta fi sh screens instead of moving 

forward on construction of new fi sh screens in the 

South Delta was made in 2005, Reclamation estimates 

that it will take approximately another seven to 10 

years to fully assess the existing TFCF and implement 

and evaluate all remaining physical and operational 

improvements presently identifi ed at TFCF. 

Program Research

The program has produced 23 volumes of researchrelated activities to date. The information from the 

Tracy Research Volume Series is used by Reclamation 

in implementing improvements at the TFCF as well 

as by DWR for implementing improvements at the 

Skinner facility. In addition, information generated 

from the research and assessment efforts at the TFCF 

is used by other scientists when assessing fi shery 

impacts at the export pumps on a delta-wide scale. In 

2007, the program completed distribution of Tracy 

Research Volume Series Nos. 31-33, 35, 36, 38 and 40 

and distribution of Tracy Technical Bulletin 2006-1, and 

facilitated ongoing development of the Tracy Research 

technical Web site and enhanced data accessibility. 
3406 (b)(4) 39

The information contained on the Web site is used by 

many scientists and engineers studying the SacramentoSan Joaquin Delta region for fi shery and water quality 

affects and concerns. 

In 2008, the program will continue to address the three 

primary areas of concern, namely improved debris 

management, improved predation management, and 

improved hydraulic control of the facility.

Tracy Fish Collection Facility
40 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(b)(5)

“...”Develop and implement a program to mitigate 

for fi shery impacts resulting from operations of the 

Contra Costa Canal Pumping Plant No. 1. Such 

a program shall provide for construction and 

operation of fi sh screening and recovery facilities, 

and for modifi ed practices and operations.”

Part of the Contra Costa Canal is the backbone of the 

Contra Costa Water District (CCWD), delivering water 

from the delta to the district’s treatment facilities and 

raw-water customers. The canal is a 48–mile–long 

facility that starts at Rock Slough in East Contra Costa 

County and ends at the Terminal Reservoir in Martinez. 

Four pumping stations currently lift water 124 feet above 

sea level from Rock Slough, after which gravity propels 

the water to its terminus in Martinez. 

Operation of the pumps without adequate screening 

or alternative mitigation results in fi sh mortality. 

In addition to the CVPIA mandate, the 2004 Los 

Vaqueros biological opinion (BO) extension, requires 

that a fi sh screen be built at Rock Slough. This program 

is focused on improving the operation of the Rock 

Slough Intake to minimize the loss of fi sh through 

three main activities: 

• Designing and constructing a fi sh screen for 

CCWD’s Pump #1 and one or more new intake 

structures 

• Working with CCWD to modify operations 

(change the pumping schedule)

• Making interim annual mitigation payments to 

compensate for presumed losses of delta smelt 

during continued operation of the Contra Costa 

Pumping Plant in the absence of a fi sh screen

Contra Costa Canal 

Pumping Plant Contra Costa

Canal Pump

Suisun

Bay

San

Francisco

Bay

Contra Costa

Canal Pump

Contra Costa Canal

Rock Slough

Figure 8. Contra Costa Canal Pumping Plant 
3406(b)(5) 41

Because fi sh losses at pumping stations, dams and 

diversions are of concern throughout the CVP 

system, currently several CALFED Stage 1 studies 

are underway, including the Los Vaqueros Reservoir 

Expansion Study, Rock Slough Water Quality 

Improvement Study, and various ecosystem restoration 

projects and studies. These studies may benefi t other 

agencies, including the Tracy Fish Collection Facility 

(b)(4), the Anadromous Fish Screen Program (b)(21), and 

other Central Valley actions for endangered species. 

These studies have the potential to signifi cantly alter 

the currently designed fi sh screen facility at Rock 

Slough or to eliminate the need for a screened diversion 

altogether. As a result of these developments, alternative 

short-term, lower-cost fi sheries mitigation measures 

are being investigated and developed, including shortterm operational fl exibility, alternative exclusionary 

measures, and/or monitoring and salvage procedures. 

Measuring Success

Fish Screen

In 1996, the Contra Costa Fish Screen Management 

Team and the Contra Costa Technical Advisory 

Committee (Team),1

 were formed to provide technical 

assistance to the (b)(5) program, reviewing preliminary 

designs and recommending cost-saving alternatives 

and improvements. By 2002, the group had completed 

90 percent of the fi sh screen designs and related 

environmental documents. However, because of 

concerns regarding the cost and effectiveness of the 

proposed screen design, Reclamation reassessed all 

available design alternatives, completing this review in 

2007. Also in 2007, Reclamation contracted an interim 

Cumulative Impacts Assessment for the Contra Costa 

Canal Mitigation Program, which will serve as the 

basis for future NEPA documentation. This document 

presents the potential effects of the currently identifi ed 

potential fi sh screen alternatives. 

Modifying Operations

In 1997, water supply through Rock Slough was reduced 

to approximately 17 percent of the CCWD total. This 

reduction was made possible by the Los Vaqueros 

Project, which constructed a new screened intake at Old 

River, allowing a greater amount of water to be pumped 

from that location.

With the 1997 reduction in water intake at Rock Slough, 

the Service agreed to extend the deadline date for 

construction of a fi sh screen until 2008. The program is 

currently consulting with the Service on the Los Vaqueros 

biological opinion as it relates to the environmental 

commitment of the Rock Slough Fish Screen.

Mitigation Payments 

In 2007, the program provided $50,000 to the Service 

for the Sacramento-San Joaquin Delta Pelagic Organism 

Decline effort to address the dramatic recent decline of 

species such as the delta smelt.

1

The Team is made up of representatives from California Department of Fish and Game (CDFG), Department of Water Resources (DWR), U.S. Fish and 

Wildlife Service (Service), U.S. Bureau of Reclamation (Reclamation), NOAA Fisheries, and the Contra Costa Water District (CCWD)
42 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Sections 3406(b)(9) and 

3406(b)(19)

“(9) Develop and implement a program to 

eliminate, to the extent possible, losses of 

anadromous fi sh due to fl ow fl uctuations caused by 

the operation of any Central Valley Project storage 

or re-regulating facility...”

“(19) Reevaluate existing operational criteria in 

order to maintain minimum carryover storage at 

Sacramento and Trinity River reservoirs to protect 

and restore the anadromous fi sh of the Sacramento 

and Trinity Rivers in accordance with the mandates 

and requirements of this subsection and subject to 

the Secretary’s responsibility to fulfi ll all project 

purposes, including agricultural water delivery.”

The timing and volume of water fl ows are critically 

important to the successful spawning, rearing and outmigration of anadromous fi sh. River and stream fl ow 

fl uctuations caused by operation of any CVP storage or 

reregulating facility can therefore result in fi sh losses 

through redd dewatering and isolation or stranding of 

juveniles. The CVPIA (b)(9) Flow Fluctuation Program’s 

goal is to minimize these losses by moderating changes 

in CVP releases on Clear Creek and the Sacramento, 

American, and Stanislaus rivers to the extent possible 

to protect and restore anadromous fi sh to the Central 

Valley (see Figure 1 for location map).

The tools available to minimize losses include (b)(1)B 

reoperation (changing dam operations based on (b)(1)B 

data) and the use of the dedicated yield in Section 3406 

(b)(2). To date, a specifi c performance goal has not been 

established for this program. 

Supporting the (b)(9) Flow Fluctuation Program is the 

(b)(19) Reservoir Storage Program, which evaluates 

water storage across the Sacramento, American and 

Trinity rivers to meet anticipated demands for water by 

fi sheries as well as agricultural, municipal and industrial 

users. The Reservoir Storage Program seeks to maintain 

carryover water storage and to deliver appropriately 

timed fl ows and fl ows of adequate quality to support 

fi sheries restoration as well as meet other project 

purposes. To date, a specifi c performance goal has not 

been established for this program.

Measuring Success

Clear Creek: Outside of fl ood control periods or large 

precipitation events, there typically are no extreme fl ow 

fl uctuations on Clear Creek. In 2007, Clear Creek fl ows 

were maintained using a combination of (b)(2) water and 

(b)(1)B reoperation. Large fl ow fl uctuations originating 

from Whiskeytown Dam did not occur. 

Flow Fluctuations and 

Reservoir Storage Sacramento

San Francisco

Los Angeles
3406 (b)(9) and (b)(19) 43

Sacramento River: On December 1, 2006, a fl ow 

fl uctuation study was published by the Service (pursuant 

to Section 3406 (b)(1)(B) that identifi ed the relationships 

between fl ow fl uctuations and redd dewatering and 

juvenile stranding for Chinook salmon and Steelhead 

in the Sacramento River between Keswick Dam and 

Battle Creek. Using this information, Reclamation 

and the Service convened weekly interagency (b)(2) 

team meetings in 2007 to determine how to minimize 

damaging fl ow fl uctuations on the Sacramento River 

to the extent possible. In 2007, Sacramento River fl ows 

were augmented using a combination of (b)(2) water and 

(b)(1)(B) reoperation. Severe fl ow fl uctuations during 

critical fi sh periods did not occur. 

American River: On December 11, 2001, a 1997-2000 

fl ow fl uctuation study was published by the DFG that 

documented the optimal fl ow rates and fl ow timing to 

support fi sheries restoration for salmon and Steelhead 

in the lower American River. In 2007, the data and 

conclusions from this study were used as guidance in 

discussions about the operation of Folsom Reservoir 

(the major contributor to fl ows in the lower American) 

at monthly American River Group meetings with 

stakeholders as well as for weekly (b)(2) interagency 

team meetings. American River 2007 fl ows were 

augmented using a combination of (b)(2) water and 

(b)(1)(B) reoperation. Large fl ow fl uctuations during 

critical fi sh periods did not occur.

Stanislaus River: In July 2004, the DFG completed 

an early draft report on the Stanislaus River fl ow 

fl uctuation study, which will be completed in 2008. 

Data and conclusions from this study will be used in 

future years to facilitate discussion and decision-making 

regarding the operation of fl ows on the Stanislaus River, 

including the operation of Goodwin, Tulloch and New 

Melones dams, which are the primary generators of 

fl ows. In the winter and spring of 2007, fl ows were 

higher than normal (due to high carryover storage) and 

damaging fl ow fl uctuations during critical fi sh periods 

did not occur. 

The American River from Guy West Bridge
44 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(b)(10)

“Develop and implement measures to minimize 

fi sh passage problems for adult and juvenile 

anadromous fi sh at Red Bluff Diversion Dam...”

The Red Bluff Diversion Dam (RBDD) is located on the 

Sacramento River about four kilometers southeast of the 

city of Red Bluff. The dam diverts water to the TehamaColusa and Corning canals to provide water for farmers, 

the Sacramento National Wildlife Refuges (SNWR), 

and minor municipal and industrial uses. In the summer, 

the dam creates a seasonal lake in a wide portion of the 

Sacramento River, which attracts wildlife as well as 

recreational users. 

As recently as 1987, the RBDD gates remained closed 

year round, impeding migration of salmonids above the 

dam and preventing passage of sturgeon. In 1987, the 

gates were opened between December 15 and April 1, 

and the program saw a resultant change in spawning 

distribution with less spawning below the RBDD and 

more spawning in colder water above the dam. However, 

the improved passage still delayed or blocked many 

adult winter- and spring-run Chinook and continued 

to cause spawning in downstream waters too warm for 

successful egg incubation. Adult green (ESA-listed) 

sturgeon and white sturgeon also were blocked and 

losses of out-migrating juvenile salmon also were 

measured at up to 50 percent. Increased feeding and 

ambush settings created a dysfunctional predator-prey 

relationship between the out-migrating salmonids and 

the native Sacramento pikeminnow. 

The purpose of the Red Bluff Fish Passage Improvement 

Project is to minimize anadromous fi sh passage 

problems to allow access to and safe egress from 

upstream habitat while maintaining water deliveries to 

the SNWR and other water contractors. The program 

focuses on one outcome target and two output targets, as 

follows. 

Figure 9. Red Bluff Diversion Dam

Red Bluff Diversion Dam 

Red Bluff

Diversion Dam

Sacram

e nto Ri ver

Trinity Shasta Lake

Lake

Redding

Black

Butte

Reservoir

Te hama- C o

ul sa Canal

Corning

Canal

Stony

Creek

Red Bluff

Diversion Dam

Corning Canal

Lake Red Bluff

Sacramento River

Tehama-Colusa Cana
3406 (b)(10) 45

• Outcome target: achieve annual passage of 80 to 

100 percent of adult spring-run salmon, and 

100 percent of adult green sturgeon

• Output target: complete RBDD infrastructure 

improvements as necessary to achieve annual 

fi sh passage targets 

• Output target: Supply Full Level 4 water to the 

SNWR 

Reclamation’s stated preference to help achieve fi sh 

passage targets is for a two-month gate closure and 

construction of a new pumping plant, which will provide 

a more reliable supply of water while also protecting 

fi sh through the use of screens. However, operations of 

a new pumping plant would be determined as part of the 

Operations Criteria and Plan (OCAP) ESA consultation 

and the biological opinion (BO) which is expected 

to be issued in 2008. Operational performance goals 

related to passage of migrating salmonids and green 

sturgeon would be developed following issuance of the 

BO. Also, funding has not yet been secured. Therefore, 

a specifi c timeframe for achieving the infrastructure 

improvements and the fi sh passage targets has not been 

determined.

Measuring Success

Fish Passage

Achievements 1993 to Date

A 1993 BO required that the gates remain out of 

the river or “open” for eight months of the year 

(from September 15 through May 15); as a result the 

population index dramatically increased and juvenile 

predation dropped.

Based on the current operation of the facility (fourmonth closure of the gates), approximately 20 percent 

of the adult spring-run Chinook and approximately 50 

percent of the green sturgeon achieve passage. However, 

winter-run Chinook spawning returns showed a 

signifi cant population increase from nearly 700 to 17,000 

after 1998 through 2006, and both the fall- and winterrun spawning distributions changed signifi cantly before 

and after the raised gates period–after gates were raised, 

fi sh spawned further upriver (see fi gure 9).

2007 Operational Changes Address Loss of 

Green Sturgeon

In 2007, Reclamation implemented operational changes 

at RBDD in response to the loss of at least 10 adult green 

sturgeon at or below the dam. The loss is attributed to 

the observation that an unusually large number of green 

sturgeon were “holding” in the vicinity of the dam, and 

the inference that the fatalities occurred when the gates 

were lowered for a brief, emergency closure and/or when 

the gates were closed for the season. To protect the fi sh 

from further losses, when possible, gates are kept “open” 

or raised a minimum of one foot from the river fl oor. 

No further fatalities were observed in 2007 following 

implementation of this operational change.

Refuge Water Conveyance Capacity

The mandated goal to supply Full Level 4 water to 

the Sacramento National Wildlife Refuges mandated 

in 3406(b)(10) has been met. The goal was met after 

evaluation of eight options by installation of a siphon on 

the Glenn-Colusa Irrigation District (GCID) Canal at 

Stony Creek to allow year-round deliveries. Use of the 

RBDD for this purpose was therefore abandoned.

Infrastructure Improvements

Reclamation and the Service issued a draft EIS/EIR in 

2002 to evaluate six combinations of a new pumping 

plant, gravity diversions, fi sh ladders and gates’ open/

close timing. Delays resulted from the listing of the 

green sturgeon as a threatened and endangered species; 

it was decided to recirculate the EIS/EIR in 2006 to 

include discussion of OCAP and its requirements as well 

as potential impacts to the green sturgeon. Alternative 

2b was identifi ed as the preferred alternative, and 

includes keeping gates out or “open” for 10 months of 

the year (closing them only in July and August), adding 

a fourth pump to the Red Bluff Research Pumping Plant 

(RBRPP) and building a 1,680-cubic-feet-per-second 

(cfs) pumping plant that would increase the existing 

pumping capacity fourfold, providing a more reliable 

water supply. (Subsequent ESA consultations have 

assumed construction of a 2,500 cfs facility, forgoing 

any reliance on the existing pumping plant.) 

A fi nal EIS/EIR and Record of Decision is anticipated in 

summer 2008 following completion of ESA consultation 
46 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

on the planned construction. Decisions concerning 

operation will be deferred until completion of the 

OCAP consultation, which involves ESA consultation 

for the CVP as a whole and will likely include specifi c 

requirements for the pumping plant related to the listing 

of green sturgeon as a threatened species.

200 fish

Endangered

ESA

listing 1994

118,000 fish

1969

RBDD Gates

Raised 8 month

17,000 fish

2006

1967 1971 1975 1979 1983 1987 1991 1995

YEAR

1999 2003

140

120

100

80

60

40

20

0

Number of Fish in Thousands

Figure 10. Spawning Returns, Winter-Run Chinook, Sacramento River (1967-2006) 

Open gates at Red Bluff Diversion Dam
3406 (b)(11) 47

CVPIA Section 3406(b)(11)

“Rehabilitate and expand the Coleman National 

Fish Hatchery by implementing the U.S. Fish and 

Wildlife Service’s Coleman National Fish Hatchery 

Development Plan, and modify the Keswick Dam 

Fish Trap to provide for its effi cient operation at 

all project fl ow release levels and modify the basin 

below the Keswick Dam spillway to prevent the 

trapping of fi sh...”

The Coleman National Fish Hatchery (NFH) Complex 

is one of the largest production facilities of salmon and 

steelhead in the United States. The hatchery, located 

on Battle Creek near the town of Anderson, was 

constructed in 1942 to partially offset impacts to salmon 

and steelhead populations caused by the construction 

of the Shasta and Keswick dams–which had eliminated 

almost 200 miles of salmon and steelhead habitat.

In order to continue to mitigate the effects of these 

dams, the goals of Section 3406(b)(11) of the CVPIA are 

as follows:

• Rehabilitate and expand the Coleman NFH by 

implementing the Station Development Plan for 

Coleman NFH on Battle Creek

• Modify the fi sh trap at Keswick Dam to ensure 

effi cient operation at all project fl ow release levels

• Modify the basin below the Keswick Dam spillway 

to prevent the trapping of fi sh 

The program has an output-based performance goal to 

complete the infrastructure improvements to enhance 

conditions for anadromous fi sh and maintain hatchery 

production targets as identifi ed in the 1987 Coleman 

National Fish Hatchery Station Development Plan (SDP) 

and subsequently modifi ed over the last 20 years by 

management requirements.

Coleman National Fish 

Hatchery

Coleman

Fish Hatchery

Shasta Dam

Keswick Dam

Trinity

Lake Shasta

Lake

Sacra me nto R vi er

Anderson

Ba t tle Cr

Coleman Fish

Battle Creek

Hatchery

Figure 11. Coleman Fish Hatchery 
48 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Specifi c modifi cations to the SDP include non-completion 

of Phases 6, 7 and 8, which called for expansion of 

a water treatment facility up to 65,000 gallons per 

minute (gpm) and the construction of 20 additional 

15-foot by 150-foot raceways for juvenile rearing. 

Further, while the SDP called for provisions to 

produce winter Chinook salmon at Colman NFH, 

a multi-agency decision resulted in the use of $1 

million of CVPIA funds for the construction of the 

Livingston Stone National Fish Hatchery in 1997 

below Shasta Dam for the production of that species. 

Subsequently, the production targets, as identifi ed in 

the Coleman NFH’s 2001 biological assessment, are 

as follows: 

• Livingstone Stone NFH: Approximately 200,000 

winter-run Chinook salmon pre-smolts 

• Coleman NFH: 12 million fall-run Chinook salmon 

smolts, 1 million late-fall-run Chinook salmon 

smolts and 600,000 steelhead smolts

Measuring Success

The 1987 SDP outlined a nine-phase strategy to 

rehabilitate the hatchery and implementation was 

authorized through the 1992 passage of CVPIA 

legislation. As shown in Table 11, four of these phases 

were largely implemented prior to 1994/CVPIA 

funding with approximately $11.2 million from the 

Service. Since CVPIA funding of (b)(11) began in 

1994, CVPIA has invested an additional $22 million 

to further the goals of the SDP. Due to fi sh production 

modifi cations and resource management decisions by 

program management, to date three phases have been 

cancelled or suspended. The two phases that remain to 

be implemented are expected to be completed by 2010.

Table 12. Coleman NFH Facility Rehabilitation Phases (1991-2007)

Phase Status Funding

1. Water treatment facility to 

 20,000 gpm

Completed pre-1999 Service, Reclamation

2. Facility Rehabilitation In process Service, Reclamation

3. Feed storage building Completed 1991 Service

4. Barrier weir and fi sh ladder Completed 1992 Service

5. Pollution abatement system Completed 1992 Service

6. Increase treatment plant size to 

 ozone generation from 20,000 

 gpm to 45,000 gpm 

Ozone water treatment and water 

fi ltration facilities reached 30,000 

gpm and 45,000 gpm capacities, 

respectively; No plans to further build 

out ozone facility to full capacity as 

prescribed by Phase 6 of the SDP

Reclamation for completed portion

7. Construction of 20 additional 

 15-foot by 150-foot raceways for 

 juvenile rearing

No longer applicable No longer applicable

8. Increase plant size from 

 45,000 gpm to 65,000 gpm

No longer applicable No longer applicable

9. Improve visitor facility In process Reclamation
3406 (b)(11) 49

Fish Production Targets

Fish production targets have essentially been met since 

the 1998 construction of Livingston Stone NFH. Actual 

annual production may vary around the target depending 

on factors such as numbers of available brood stock and 

egg survival rates. 

Ozone Water Treatment Facility

Since the ozone water treatment facility reached full 

ozone production capacity of 30,000 gallons per minute 

(gpm) in 2000 (full water fi ltration capacity of 45,000 

gpm reached in 2002), juvenile fall-run Chinook from 

brood years 1999-2006 were reared and released with no 

incidence of viral disease. This was a fi rst in the history 

of the hatchery. Also important is that the construction 

of the water treatment facility supports the CALFEDfunded Salmon and Steelhead Restoration Project’s 

efforts to restore 42 miles of habitat in upper Battle 

Creek by promoting/allowing opportunity for passage 

of adult anadromous salmonids above the hatchery’s 

water source. Although the anadromous salmonids that 

ascend Battle Creek above the hatchery’s water source 

carry a variety of pathogens, the ozone water treatment 

plant disinfects the water and reduces the likelihood of 

on-station disease outbreaks. 

Domestic Water System and Visitor Facility 

Improvements

In 2005 and 2006, CVPIA implemented a program to 

rehabilitate the domestic water system to ensure highquality treated drinking water for station staff and the 

tens of thousands of visiting public. The program did 

not receive any funding in FY 2007 and therefore no 

specifi c objectives for the year were identifi ed. However, 

in 2006, the program began design of a visitor kiosk 

and informational panels at the Coleman NFH and 

construction is expected to be complete in 2008.

Modifi cations to Keswick fi sh trap
50 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

The original construction of McCormick-Saeltzer 

Dam in 1903 with modifi cations in 1912 and its 

continued operation, in addition to the construction 

of Whiskeytown Dam in the 1960s and aggregate and 

gold mining in the Clear Creek, caused widespread 

degradation of the creek habitat and led to precipitous 

drops in Chinook and Steelhead salmon spawning and 

juvenile development. In order to reverse the trend, 

CVPIA developed and implemented a restoration 

program that improved instream habitat allowing greater 

spawning and rearing success.

The program focuses on fi ve distinct problem areas and 

uses the following goals to track progress:

1) Instream fl ow: Approximately 80,000 acre-feet of 

(b)(2) water dedicated annually; variable target 

dependant on hydrology and biological conditions, allowing provision of at least 90 percent of 

the maximum possible habitat; temperature targets met at least 98 percent of days with no more 

than two consecutive temperature exceedence 

days

2) Fish passage: Unimpeded fi sh passage provided 

past McCormick-Saeltzer Dam site through its 

removal

3) Gravel placement: 347,288 square feet of usable 

spawning habitat that existed before construction 

of Whiskeytown Dam recreated by 2020 by adding 17,000 tons of gravel annually

4) Channel restoration: Two stream miles restored 

by 2010

5) Erosion control: Highest priority and cost effective 

erosion control projects implemented by 2003

CVPIA Section 3406(b)(12)

“Develop and implement a comprehensive program to 

provide fl ows to allow suffi cient spawning, incubation, 

rearing, and outmigration for salmon and steelhead 

from Whiskeytown Dam as determined by instream 

fl ow studies conducted by the California Department 

of Fish and Game after Clear Creek has been restored 

and a new fi sh ladder has been constructed at the 

McCormick-Saeltzer Dam...”

Figure 12. Gravel Injection and Channel 

Restoration Sites

Whiskeytown

Lake

Channel Restoration

Project Site

C el ar Creek

Sacramento River

Gravel Injection Sites

Channel Restoration Project Site

Peltier Valley

Whiskeytown Dam

Saeltzer Dam Phase 3A

Clear Creek Road Bridge

Placer Road Bridge

NEED Camp

Clear Creek Restoration 

Program Sacramento

San Francisco

Los Angeles
3406 (b)(12) 51

Measuring Success

Progress against the fi ve program goals is 

summarized in the following section.

Instream Flow

An average of approximately 70,000 acre-feet of (b)

(2) water is used annually to meet fl ow requirements, 

and the temperature objectives are being met. PreCVPIA baseline fl ows were 50 cfs between January 

and October, and 100 cfs in November and December. 

Flows have increased to 200 cfs from mid-September 

through mid-June and to approximately 70 to 90 cfs 

during the summer. 

Flows to achieve temperature control of 60°F 

from June 1 through September 15 and 56°F from 

September 15 through October 31 were met 100 

percent of the time in 2006 and 99 percent of the time 

in 2007. Lastly, the program has met the instream 

habitat goal of 90 percent weighted useable area for 

the last fi ve years. 

Passage

Passage at McCormick-Saeltzer Dam was achieved 

in 2000 through the dam’s complete removal and the 

opening of 12 additional miles of habitat. 

Gravel Placement

Since 1995, an estimated 103,371 tons of gravel 

have been injected at specifi c locations on the creek, 

resulting in a steady increase in spawning habitat. This 

added gravel has recharged spawning gravel within 

approximately three miles of creek.

Channel Restoration

The two-mile stream channel is 80 percent restored 

(Figure 15). Phases 1, 2A, 2B, and 3A are complete. 

Phase 3B channel relocation and fl oodplain 

reconstruction was completed November 2007. Phase 

3B fl oodplain revegetation began in September 2007 

and will continue through March 2008. Phase 3C is not 

complete.

1998 1999 2000 2001 2002 2003 2004 2005

3500

3000

2500

2000

1500

1000

500

JUVENILE CHINOOK PER ADULT FEMALE

0

2001 2002 2003 2004 2005 2006 2007

200

180

160

140

120

100

80

60

40

20

AUGUST SNORKEL COUNT

0

1967-1991 2007

5000

4000

3000

2000

1000

0

Figure 13. Fall–Run Chinook Salmon Escapement, 

Clear Creek (2007)

Figure 14. Adult Spring-Run Chinook Salmon 

Population, Clear Creek (2001-2007)

Figure 15. Juvenile Fall-Run Chinook Salmon 

Produced/Adult Female, Clear Creek (1998-2005) 
52 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Erosion Control

The highest priority erosion areas were completed 

prior to 2003 (specifi cally, work on approximately 13 

miles of dirt roads). An Erosion Inventory Report was 

completed in 1996. Between 1997 and 2001, the highest 

priority erosion control projects were implemented by 

cooperators from the National Park Service (NPS), the 

Service, and the Bureau of Land Management (BLM). 

All feasible and cost-effective projects were fi nished by 

2001 and no further work is expected.

Through addressing these fi ve problem areas, the 

Clear Creek Restoration Program has increased fallrun Chinook escapement, and steelhead and springrun Chinook populations. In 2007, fall-run Chinook 

escapement was 4,129 compared to the average baseline 

escapement of 1,689 between 1967 and 1991, as shown 

in Figure 12. Similarly, adult steelhead populations 

Figure 16. Clear Creek Channel Restoration Project Phases

also continued to increase, as indicated by redd counts, 

increasing from approximately 38 in 2001 to 162 in 

2007. Figure 13 depicts the increase of adult spring-run 

Chinook from a low of zero in 2001 to 194 in 2007.

Despite the increases in adult populations, juvenile 

production has decreased since 1996 from 7.4 to 

3.4 million fi sh, and the number of juvenile fall-run 

Chinook produced per adult female has decreased from 

about 2,900 in 1998 to 375 in 2005, as shown in Figure 

14. These decreases are due in part to excessive amounts 

of fi ne sediment in the stream channel that could be 

removed by intermediate fl ows that would fl ush the 

sediment downstream. The Clear Creek Restoration 

Program is pursuing the use of fl ushing fl ows from the 

(b)(3) Environmental Water Program to remove fi ne 

sediment from the stream channel.
3406 (b)(13) 53

CVPIA Section 3406(b)(13) 

“Develop and implement a continuing program...

to restore and replenish spawning gravel... on the 

American, Stanislaus and Sacramento Rivers...shall 

include preventive measures...”

The construction and operation of CVP dams on the 

Sacramento, American and Stanislaus rivers and 

associated bank protection projects have signifi cantly 

reduced the availability of spawning gravel and rearing 

habitat in downstream reaches. The gravel replacement 

program is an ongoing effort to restore and replenish 

spawning gravel, as needed, in the Upper Sacramento 

River from Keswick Dam to Red Bluff Diversion Dam, 

and in the American and Stanislaus Rivers downstream 

from the Nimbus and Goodwin dams, respectively. 

The average annual gravel defi cits on CVP streams are 

as follows: 

• Sacramento River–50,000 cubic yards

(current fl ow regime) 

• Stanislaus River–20,000 cubic yards 

(pre-Goodwin Dam fl ow regime) 

• American River–57,200 cubic yards 

(current fl ow regime)

With gravel defi cits of this magnitude and considering 

the high cost of acquiring gravel, the program focuses 

on targeting high-priority sites to make the best use of 

available funds. Two criteria guide the identifi cation of 

gravel placement sites: the need for spawning habitat and 

accessibility to the river by truck, helicopter or sluice 

Spawning Gravel Program Sacramento

San Francisco

Los Angeles

Sacramento

San Francisco

Eureka

South Lake Tahoe

San Jose

Monterey

Fresno

Coalinga

Solvang

1

Sacramento R iver Stanislaus River

A merican River

Clear

Creek

New Melones

Reservoir

Folsom

Lake

Shasta

Lake

Whiskeytown

Lake

Pacific Ocean

Keswick Dam

Red Bluff Diversion Dam

Nimbus Dam

Goodwin Dam

Shasta 

Lake

Sacramento

River

Keswick 

Dam 

Gravel Sites

Gravel Sites

Gravel Sites

San

Joaquin

River Stanislaus

River

Suisun

Bay Goodwin Dam

Gravel Sites

80

80

5

280

5

Figure 17. Gravel Placement Sites

to deliver the gravel. All gravel is placed according to 

criteria developed by the DFG and the NOAA’s National 

Marine Fisheries Service (NMFS), which stipulates the 

size and relative proportion of the various gravel sizes, 

and also stipulates the timing for gravel placement. 

Once the gravel is placed, Reclamation and the Service 

continue to monitor and document the spawning 

densities of the downstream reaches by salmonids to 

determine the effi cacy of the program. The program 

uses two criteria to determine success: 
54 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

• Percent of spawning salmonids within a specifi c 

area using placed gravel for building redds as 

opposed to non-placed gravel (this percentage 

indicates the suitability of placed gravel)

• Redds per square meter in areas of gravel 

placement 

The goal for the Sacramento River gravel placement 

areas is 25 percent of spawning salmonids; the goal for 

the Stanislaus River gravel placement areas is 10 percent 

of spawning salmonids. The goal for the American 

River is 0.05 redds per square meter on emplaced gravel 

(Sailor Bar, Lower Sunrise, and Sacramento Bar sites) 

and less than 10 percent egg retention.1

Measuring Success

Gravel Placement

Since 1997, the program has placed more than 151,500 

cubic yards of gravel, primarily on the Sacramento River 

(Table 12).

Permeability of Gravel

The permeability of the gravel—its ability to be used by 

spawning salmon—is an important indicator of success 

and is used to determine future gravel placement 

actions. Ongoing gravel permeability studies examine 

areas where gravel was placed in the past to determine 

the ongoing suitability of the placed gravel for egg 

survival.

All gravel placements now utilize the data collected 

on the Stanislaus River in 2005 that determined the 

optimum size of gravel to create adequate permeability. 

The 2005 studies compared man made riffl es created 

with varying sizes of gravel and determined that 

survival (egg to fry) was best in the smaller sized gravel 

placement areas.

2007 studies in the American River identifi ed existing 

areas of high-density spawning by salmonids. 

Reclamation has not yet replenished the gravel in these 

areas, and the observed low natural permeability of the 

gravel suggests that survival would not be high. The 

program used this data in FY 2007 to prioritize future 

gravel placement to improve these conditions.

Spawning Densities

Since the implementation of the program, monitoring has 

shown improvement in spawning distribution relative 

to total escapement (Sacramento and Stanislaus rivers) 

and redd density per square meter (American River). 

Salmonids have been observed spawning on the gravel 

at each of the placement sites on the three rivers. Aerial 

photography and onsite ground surveys have documented 

the location of salmon redds and juvenile salmonids have 

been observed rearing in the vicinity of the gravel.

River

Total gravel placed

 (cubic yards)

Gravel placed in 2007

(cubic yards)

Percent of 

target for 2007

Sacramento 123,077 4,615 9%

Stanislaus 10,769 3,077 15%

American 4,615 0* N/A

* In 2007, the program purchased 5,385 cubic yards to be placed in FY 2008.

Table 13. Total Gravel Placed (1997-2007)

1 Egg retention refers to female salmon that die before before spawning. It is determined by cutting dead salmon open and examining the proportion of 

total eggs remaining (retained).
3406 (b)(13) 55

Sacramento River 

The average percentage located upstream of Highway 

44 from 1981 to 1992 (pre-CVPIA) was 6.9 percent. 

From 1993 through 2005 (period since CVPIA was 

enacted), the average percentage was 15.6 percent. River 

conditions were unsuitable for collecting spawning 

surveys in 2006 and 2007; therefore, redd survey data 

is not available. The average percentage of the total 

potential redds located upstream of Highway 44 on 

the Sacramento River from 1981 to 2005 (the entire 

period for which records of escapement and winter-run 

Chinook spawning are available) was 12.1 percent, 

versus the program target of 25 percent. 

Stanislaus River 

In 2007, environmental permitting was acquired for 

gravel addition at eight new sites in the Stanislaus River 

at Knights Ferry and 3,077 cubic yards of spawning 

gravel and boulders were added to create three riffl es in 

Knights Ferry. (Riffl es are faster, shallower sections of 

a river that provide spawning habitat and also provide 

habitat for invertebrate production which is the major 

food source for juvenile fi sh.) Surveys (compared to 

control sites) showed that spawning in the areas where 

gravel was placed has increased from eight percent in 

2006 to nearly 14 percent of the total potential redds in 

the entire river. Chinook redds also were mapped on 

gravel addition areas and the mapping confi rmed that 

more than 50 percent of the fi sh in the river spawned 

on the gravel addition sites. On average, since gravel 

placement began, approximately 150 female Chinook 

salmon have spawned in Goodwin Canyon each year 

on the new gravel. This number of Chinook spawners 

should produce about 745,000 eggs, which should 

produce about 400 adult Chinook annually in the 

Stanislaus River.

American River

On the American River, aerial photos were reviewed 

in 2007 to determine spawning densities back to 2002, 

showing that there are more anadromous fi sh than 

available spawning habitat. Gravel placements in 2008 

will be based on the data from this survey.

Salmon and trout on a gravel placement project in the Stanislaus River
56 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(b)(15)

“Construct, in cooperation with the State of 

California and in consultation with local interests, a 

barrier at the head of Old River in the SacramentoSan Joaquin Delta to be operated on a seasonal 

basis to increase the survival of young outmigrating 

salmon that are diverted from the San Joaquin River 

to Central Valley Project and State Water Project 

pumping plants and in a manner that does not 

signifi cantly impair the ability of local entities to 

divert water...”

The South Delta Improvement Program (SDIP) is a 

joint federal and state program that covers a series of 

proposed actions to improve water levels and water 

quality in the southern part of the Sacramento-San 

Joaquin Delta, improving water supply reliability for 

south-of-delta contractors and environmental uses, while 

protecting salmon in the San Joaquin River. 

In support of SDIP, to reduce the number of fall-/late 

fall-run Chinook salmon that enter the Old River and to 

reduce entrainment at the CVP and State Water Project 

(SWP) pumping facilities, CVPIA has authorized the 

construction of a permanent operable fi sh gate at the 

head of the Old River to keep young salmon in the San 

Joaquin River as they migrate to the ocean in the spring. 

In addition, a planned fi sh ladder at the head of Old 

River will give passage to those adult salmon entrained 

into delta channels to the spawning grounds in the San 

Joaquin River.

The gates and limited dredging will protect water levels 

and water quality in the South Delta channels. Water 

levels are protected by keeping the gates open when the 

tide is coming in (fl ood) and closing the gates to trap 

some of the tide at a specifi c elevation. Water quality 

is improved during periods of poor San Joaquin River 

water quality by the circulation of water caused by 

the gates’ operation. After structural improvements 

(new operable gates, dredging and agricultural intake 

modifi cations) are complete, a supplemental EIS/EIR 

would allow for an increased permitted limit in the 

diversion rate at Clifton Court Forebay. This would 

Head of Old River Barrier North Canal

Clifton Court

Forebay Grant Line Canal

Victoria Canal

Old River

Middle River

San Joaquin River

Flow

Control

Gates

Flow

Control

Gate

Head of

Old River

Barrier

Stockton

Temporary Head of Old River Barrier
3406 (b)(15) 57

barrier was not installed in four years (1995, 1998, 1999, 

2005) due to high fl ows. Until the permanent gates are 

constructed, temporary barriers will continue to be 

placed to reduce salmonid fi sh losses, unless there is a 

confl ict with the in-delta habitat fl ow requirements for 

the delta smelt.

Program Stages

Success is measured based on completion of three 

key stages, namely (1) planning and environmental 

documentation, (2) design, and (3) construction. The 

project completed the fi rst stage in 2006 with the 

issuance of the Final EIS/EIR; design is expected to 

continue through 2008. 

However, fi nal design and construction is tied to the 

issuance of BOs by the Service and the NMFS. The 

BOs will identify mitigation requirements related to the 

effects of the proposed construction, operation of gates 

and implementation of dredging operations. The SDIP 

BOs are on hold pending the resolution of the Section 

7 consultation on OCAP. This broader consultation 

addresses the CVP as a whole and will include specifi c 

requirements for the SDIP gate operations. 

Conceptual Model 

In order to illustrate the benefi ts of the project’s 

implementation, in 2007 Reclamation and the 

DWR developed a conceptual model that shows 

the relationships between Chinook salmon and 

environmental factors occurring in the delta. The 

conceptual model describes the hypotheses regarding 

Chinook salmon migration periods and pathways and 

how key habitat factors (e.g., fl ow, temperature) and 

operations (e.g., Head of Old River Barrier, CVP and 

SWP pumping rates, salvage facilities) infl uence the 

survival of Chinook salmon juveniles in the lower San 

Joaquin River and delta. 

increase the water deliveries to state and federal water 

contractors and for environmental uses south of the delta 

by improving the operational fl exibility of the SWP 

Banks pumping plant. 

The (b)(15) target was to have a permanent operable gate 

designed, constructed and operational by 2009. Unlike 

temporary gates, the permanent gate is expected to be 

100 percent effective and can be in place and operable 

when San Joaquin River fl ows are high. Although the 

Final EIS/EIR to study the potential impacts and benefi ts 

of the proposed SDIP was completed in December 2006 

and the agencies have continued to move the project 

toward the construction and implementation phase, the 

issuance of OCAP biological opinions (BOs) by the 

Service and the NMFS must occur prior to construction. 

As these BOs are delayed, the construction target is now 

yet to be determined. 

In the absence of a permanent operable gate, the Head 

of Old River Barrier is closed with a temporary rock 

barrier from April 15 to May 15 to allow salmon smolts 

to stay in the San Joaquin River as they migrate out to 

the ocean. In October and November, the rock barrier is 

closed again to protect fl ows in the San Joaquin River, 

which helps to increase dissolved oxygen in the river and 

keep more of the returning adult salmon in the river. 

Measuring Success

Fish Diversion

A seasonal, temporary rock barrier at the head of Old 

River has been installed for 11 of the 14 CVPIA years 

(1992-2007), helping to keep fi sh in the San Joaquin 

River. As the temporary barrier is not 100 percent 

effective, from 2001 to 2004, the most fi sh diverted into 

the Old River annually was 8,467, and the least was 

1,805, with an annual average of 4,508. The temporary 
58 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(b)(16)

“...Establish, in cooperation with independent 

entities and the State of California, a comprehensive 

assessment program to monitor fi sh and wildlife 

resources in the Central Valley to assess the 

biological results and effectiveness of actions 

implemented pursuant to this subsection....”

The Comprehensive Assessment and Monitoring 

Program (CAMP) generates or facilitates access to data 

regarding the biological results and effectiveness of fi sh 

restoration actions implemented pursuant to CVPIA. 

CAMP activities focus on nine anadromous fi sh taxa: 

Chinook salmon (fall-, late-fall-, winter-, and springrun), steelhead, striped bass, American shad, white 

sturgeon and green sturgeon. 

CAMP also assesses progress toward Anadromous Fish 

Restoration Program (AFRP) fi sh doubling goals by 

monitoring natural production of adult anadromous fi sh 

in the Central Valley and comparing these data to AFRP 

production targets. 

CAMP primarily relies on other entities (e.g., the AFRP 

or DFG) to collect the information it analyzes and 

synthesizes. To the extent that funding is available, the 

program works with partners to provide partial funding 

to complete high-priority monitoring projects. 

The CAMP Implementation Plan describes how the 

program will monitor anadromous fi sh species in 

California’s Central Valley and assess the biological 

results and effectiveness of different categories of 

restoration activities. The CAMP Implementation Plan 

also contains programmatic objectives and descriptions 

of how adult fi sh production should be calculated, a 

recommended juvenile salmonid monitoring program, 

data analysis methods, data management protocols, and 

a fi ve-year budget and funding-needs estimate.

Benchmarks for assessing the success of the CAMP are 

refl ected in three categories that include the production 

of annual reports, the collection of new monitoring data, 

and implementation of program planning and evaluation 

activities.

Comprehensive Assessment 

and Monitoring Program Sacramento

San Francisco

Los Angeles

Weir installation for fi sh monitoring on the Stanislaus River
3406 (b)(16) 59

Measuring Success

Annual Reports

CAMP has produced fi ve annual reports since program 

inception. These documents were fi nalized in 1998, 

1999, 2001, 2002 and 2007. Each report monitors the 

production of anadromous fi sh and assesses progress 

toward the AFRP fi sh production targets during 

different periods.

The 2007 annual report synthesizes and analyzes 

anadromous fi sh monitoring data collected between 

1992 and 2006 on 13 watersheds (Figure 17). Overall 

it concludes that the majority of the AFRP production 

targets have not been met on a regular basis, suggesting 

that a substantial increase in restoration efforts will be 

required to promote measurable increases in production 

of the above-mentioned nine anadromous fi sh taxa in 

order to achieve the AFRP production targets.

Collecting Monitoring Data

In 2007, CAMP acquired 82 reports that provide rotary 

screw trap data that were collected between 1994 and 

2006. Analysis of these data may allow CAMP to assess 

the relative effectiveness of past restoration activities.

In addition, in an effort to collect data, CAMP 

obligated $96,000 in 2007 to monitor production of 

juvenile Chinook salmon on the Stanislaus River to 

assess the success of restoration activities such as 

gravel augmentation projects and modifi cation of river 

fl ow regimes.

A new Web site (www.fws.gov/sacramento/CAMP/

index.htm), implemented in 2007, functions as a 

resource for all reports and documents pertaining to 

CAMP, including the CAMP Implementation Plan, 

annual reports and data collected with CAMP funding. 

Figure 18. Estimated Total Natural Chinook Production, Central Valley (1992-2007)

0

50

100

150

200

250

300

350

400

450

500

550

600

Number of Fish in Thousands

Chinook Run Season:

650

700

750

800

850

Fall Late Fall Winter Spring

1992 1993 1994 1995 1996 1997 1998 1999

YEAR

2000 2001 2002 2003 2004 2005 2007 2006
60 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Program Planning & Evaluation

With guidance from the CAMP Implementation Plan, 

the program developed the Final Hatchery Marking 

Program Report in 2000, which was an investigation 

of the feasibility, effectiveness and cost of a constant 

fractional marking (CFM) program at Central Valley 

fi sh hatcheries. (A CFM program includes marking a 

fi xed percentage of hatchery juveniles before they are 

released in order to later more accurately count hatchery 

versus wild spawning adult salmon.) It concluded that 

a CFM program should be implemented to improve the 

accuracy of natural production estimates and assist in 

meeting CAMP monitoring and reporting goals. With 

implementation of the CFM program in 2007, many of 

the recommendations from the Final Hatchery Marking 

Program Report have been incorporated into the 

procedures that are part of the ongoing CFM program. 

The 2004 Statistical Procedures for Defi ning and 

Detecting the CVPIA Natural Chinook Salmon 

Production Doubling Goal Report was an investigation 

of statistical procedures for assessing progress toward 

the fi sh doubling goal and determining sustainability of 

production increases. Recommendations in the document 

cite a need for better data, including watershed-specifi c 

escapement estimates for naturally spawned and 

hatchery fi sh; watershed-specifi c juvenile production; 

and ocean, mainstem and tributary catches. As 

appropriate, these recommendations are refl ected in 

CAMP funding requests to obtain the funds needed to 

develop more accurate and precise population estimates 

and better determine if the AFRP fi sh production targets 

are being met.

In addition, CAMP currently is conducting an internal 

evaluation to determine the program’s future scope, 

direction and costs. The assessment will include the 

following information: 

• Review of past and ongoing monitoring projects to 

identify data gaps

• Quantifi cation of the cost for completing critical 

monitoring activities between 2008 and 2012

• Identifi cation of partnerships CAMP should pursue 

to cooperatively fund projects where a partner may 

share a common interest

• Identifi cation of mechanisms for providing 

monitoring information to interested parties

The results from the assessment will be included in a 

programmatic document that updates the 1997 CAMP 

Implementation Plan. A completion deadline for the 

updated document has not yet been established. 

In 2008, the program will launch a pilot program to 

develop watershed-specifi c documents that describe the 

potential relationship between restoration activities and 

the production of adult and juvenile Chinook salmon.
3406 (b)(20) 61

CVPIA Section 3406(b)(20)

“Participate with the State of California and 

other federal agencies in the implementation of 

the on-going program to mitigate fully for the 

fi shery impacts associated with operations of the 

Glenn-Colusa Irrigation District’s Hamilton City 

Pumping Plant. Such participation shall include 

replacement of the defective fi sh screens and fi sh 

recovery facilities associated with the Hamilton City 

Pumping Plant...”

In the 1980s it was determined that the operation of 

the Glenn-Colusa Irrigation District (GCID) Pumping 

Plant was inadvertently trapping small fi sh in the intake 

channel due to the high pumping velocity and that 

modifi cations to the existing fi sh screens were required. 

The program installed additional screening mechanisms 

and modifi ed the intake and discharge channels to 

improve hydraulic conditions for returning fi sh to the 

river. These interim measures allowed GCID to continue 

to pump part of its water allocation while screening and 

bypassing back to the Sacramento River up to 20 million 

juvenile salmon and other species per year.

Following a lengthy design, environmental analysis and 

permitting process that spanned more than 10 years, 

construction began spring 1998 on the retrofi t and 

extension of the existing fi sh screen and modifi cations to 

the open channel. A replacement water control structure 

and access bridge was completed just downstream from 

the fi sh screen structure. Construction of all features 

was completed in the spring of 2001; to determine if the 

facility is operating per the design criteria, biological 

and hydraulic testing has been ongoing. 

Glenn-Colusa Irrigation 

District Program 

Lake

Oroville

Black

Butte

Lake

GCID-Hamilton 

City Pump Plant

Sacra m ento

Rive r

Glenn C- olusa Canal

GCID Hamilton City

Pumping Plant

Glenn-Colusa Canal

Oxbow Outlet Channel

Sacramento River

Figure 19. Glenn-Colusa Irrigation District 

Pumping Plant
62 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Measuring Success

Mitigating Project Impacts

The biological and hydraulic testing and monitoring 

program of the screen system started in the summer of 

2001. To date, the testing program has not found any 

damage to fi sh attributed to the operation of the fi sh 

screen system. 

The primary impact on terrestrial species involved 

the federally–listed valley elderberry longhorn beetle, 

which existed adjacent to the pumping plant and would 

likely be affected by the construction. Mitigation was 

accomplished by transplanting 211 elderberry shrubs 

from the fi sh screen construction area to 29 acres of land 

purchased in fee for the Service along the river. The 

program also planted 6,718 elderberry bush associate 

plants to mimic natural riparian habitat conditions, and 

is providing 10 years of maintenance and monitoring 

on the adjacent site to ensure survival of all species. 

The Service has accepted the mitigation areas and will 

incorporate them into an existing refuge. 

2007 Accomplishments

The principal effort in 2007 was the completion of 

the biological and hydraulic testing and monitoring 

program that began in 2001. Challenges to completing 

the program included problems with designing, 

building and operating a facility to capture a suffi cient 

amount of test fi sh; obtaining suitable small Chinook 

fry during the important summer test times; tagging 

salmon fry from Coleman Fish Hatchery; and 

measuring the approach velocity at the screen face. 

FY 2007 was the fourth year that salmon fry were able 

to be used for the biological testing, constituting an 

acceptable data set. Biological testing was completed 

in 2007; fi sh survival tests at the fi sh screens showed 

that survival of fi sh in the vicinity of the screens is not 

impaired due to the design of the screens.

As of FY 2007, the funding for the project is 99 percent 

complete, and the project and related testing and 

monitoring is 99 percent complete for the total project. 

Hydraulic testing is expected to be completed in 2008. 

The completed facility screens up to 105,000 acre-feet of 

fi rm annual water supply to 20,000 acres of Sacramento 

National Wildlife Refuge lands.

Glenn-Colusa Irrigation District Fish Screen
3406 (b)(21) 63

CVPIA Section 3406 (b)(21)

“Assist the State of California in efforts to develop 

and implement measures to avoid losses of 

juvenile anadromous fi sh...shall not be limited to 

construction of screens on unscreened diversions, 

rehabilitation of existing screens, replacement of 

existing non-functioning screens, and relocation of 

diversions to less fi shery-sensitive areas.”

The Anadromous Fish Screen Program (AFSP) 

assists the State of California in efforts to develop 

and implement measures, including construction, 

replacement and rehabilitation of fi sh screens and 

relocation of diversions, to protect juvenile Chinook 

salmon, steelhead trout and green and white sturgeon 

from entrainment at priority diversions throughout the 

Central Valley and delta.

The NOAA Fisheries has estimated that up to 10 million 

anadromous salmonid fi sh fry are lost annually to 

diversions from the Sacramento River alone. Currently, 

there are many unscreened diversions in the Central 

Valley, including:

• 750 in the Sacramento River system 

• 950 in the San Joaquin River system

• 2,500 in the Sacramento-San Joaquin Delta 

• 360 in the Suisun Marsh basin

A process is underway with the State of California to 

identify high-priority diversions; therefore the exact 

number of screens to be constructed in the future has 

not yet been defi ned. As such, a deadline has not been 

identifi ed for program actions. 

The AFSP also provides assistance to irrigation districts 

and water companies with fi sh screening in two main 

areas:

Design: The AFSP, comprised of experts from federal 

and state agencies, provides fi sh screen design review 

and technical guidance to the diverter and their 

consultants throughout a project.

Construction: The AFSP has provided signifi cant 

funding and technical resources that are essential in 

implementing fi sh screen projects. The AFSP can 

provide up to 50 percent of the cost of a fi sh screen 

project. Thus far, the CALFED Ecosystem Restoration 

Program (ERP) has provided the majority of the 

required non-federal cost-share funds.

Measuring Success

Since 1994, the AFSP has assisted irrigation districts 

and water companies with fi sh screening at 23 diversions 

ranging from 17 cfs to 960 cfs. Cumulatively, the AFSP 

has supported/funded the screening of more than 4,200 

cfs (Table 13). 

In 2007, Sutter Mutual Water Company (SMWC) 

completed construction of their Tisdale Positive Barrier 

Fish Screen Project in Sutter County, which is designed 

Anadromous Fish Screen 

Program Sacramento

San Francisco

Los Angeles
64 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

to screen the largest unscreened diversion (960 cfs) on 

the Sacramento River. Signifi cant funding assistance 

($10 million) was received from the AFSP over the 

life of the project. This fi sh screen project protects 

out-migrating spring-, fall- and winter-run Chinook 

salmon and Central Valley steelhead as well as resident 

game and non-game fi sh from entrainment. In addition, 

AFSP continued to fund construction of the RD 108 

Fish Screen project to screen three diversions at a new, 

consolidated 300-cfs diversion on the Sacramento River 

in Sutter County.

The AFSP is currently providing technical assistance 

(design, environmental and permitting) for several 

large fi sh screen projects which have not yet secured 

needed construction funding from other federal and 

non-federal funding sources as necessary per cost share 

requirements in the Act, including:

• Natomas Mutual: Project to consolidate fi ve 

diversions totaling 630 cfs into two screened 

diversions on the Sacramento River

• Meridian Farms: Project to consolidate three 

existing diversions totaling 165 cfs on the 

Sacramento River in Sutter County; partial 

construction funding provided

• Pleasant Grove-Verona: Project to screen existing 

diversions totaling 175 cfs on the Natomas Cross 

Channel, which is a tributary to the Sacramento River 

• Patterson Irrigation: Project to screen a 190 cfs 

diversion on the San Joaquin River

• RD 2035: Project to screen a 400 cfs diversion on the 

Sacramento River

• City of Yuba City Fish Screen: Project to screen a 61 

cfs municipal diversion on the Feather River; funding 

was provided to Yuba County Water Agency to 

complete a fi sh screen feasibility study for a south 

diversion at Daguerre Point Dam on the Yuba River

The AFSP also funds research to assess the biological 

benefi ts of fi sh screening and to help prioritize future 

fi sh screening efforts. In 2007, the program completed 

a federal funding agreement to initiate a three-year 

screening and monitoring program in partnership with 

the Family Water Alliance in the Sacramento River 

watershed system and delta. This program includes 

collection of fi sh loss data prior to installation of fi sh 

screens, in order to assess the biological benefi ts of fi sh 

screening and to help prioritize future fi sh screening 

efforts. Also, the AFSP continues support of a literature 

search and data analysis of fi sheries losses at unscreened 

diversions within California and the Pacifi c Northwest. 

This effort will be completed in 2008.

Number of Projects CFS Screened

1992-1996 0 0

1996 2 80

1997 9 420

1998 10 420

1999 15 1,637

2000 17 2,489

2001 17 2,489

2002 17 2,489

2003 19 2,489

2004 20 2,959

2005 21 3,204

2006 22 3,304

2007 23 4,264

Table 14. AFSP Projects and cfs Screened, Central Valley (1992-2007)

Cumulative Results

Year
3406 (b)(21) 65

Figure 20. CVPIA Fish Screens Constructed (1992-2007)

Wilson

Ranch

Parrot-Phelan

(M&T Ranch)

Adams Ranch

Gorrill

Land Co.

Western Canal Princeton-CorderaRD1004

Maxwell ID

Lower Butte Creek

Sutter Mutual WC

Browns Valley ID

RD 999

Dayly Lee

Banta Carbona ID

Suisun Resource

Conservation District

Stanislaus River

San Joaquin River

Mokelumne R iver

Americ an River

Fea ht er R vi er

Yuba River

Bu tte Creek

Mill Creek

Sacramento

R iver

Joint AFSP- / CALFED-Funded Fish Screen Projects

AFSP- Funded Fish Screen Projects

 RD 108 (Wilkins Slough)

RD 108 Combined PP

Pelger Mutual WC

City of Sacramento Fairburn

2007 Projects 

Glen & Provident ID
66 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(c)(1)

“The Secretary shall . . . develop a comprehensive 

plan which is reasonable, prudent, and feasible to 

address fi sh, wildlife, and habitat concerns on the 

San Joaquin River, including but not limited to the 

streamfl ow, channel, riparian habitat, and water 

quality improvements that would be needed to 

reestablish where necessary and to sustain naturally 

reproducing anadromous fi sheries from Friant 

Dam to its confl uence with the San Francisco Bay/

Sacramento-San Joaquin Delta Estuary.”

The San Joaquin River is a major tributary to the 

Sacramento-San Joaquin Delta, historically providing 

fl ows from the southern Central Valley. Section 3406(c)

(1) mandates the preparation of a reasonable, prudent 

and feasible comprehensive plan to reestablish and 

sustain naturally reproducing salmon in the San Joaquin 

River below Friant Dam to the confl uence with the 

Sacramento-San Joaquin Delta Estuary. 

Legal Challenges

The fl ow of water in the San Joaquin River has been the 

subject of an 18-year legal challenge, known as NRDC, 

et al., v. Kirk Rodgers, et al. whereby the Natural 

Resources Defense Council (NRDC)-led coalition of 

13 conservation and fi shing groups sued Reclamation, 

Interior, U.S. Department of Commerce, NMFS and 

the Service over its operation of Friant Dam and the 

renewal of water supply contracts for the Friant Water 

Users Authority. This lawsuit has effectively delayed 

development of a comprehensive plan. A Stipulation of 

Settlement (Settlement) was reached on September 13, 

2006. The settling parties (Natural Resources Defense 

Council, Friant Water Users Authority, and the U.S. 

Departments of the Interior and Commerce) reached 

agreement on the terms and conditions of the Settlement, 

which was subsequently approved by Federal Court on 

October 23, 2006.

San Joaquin River 

Comprehensive Plan 

Friant Dam

Suisan

Bay

San

Francisco

Bay

Monterey

Bay Mendota Pool

S a n Joa quin Riv er

San Joaquin River 
3406 (c)(1) 67

The Settlement’s two primary goals are:

• Restoration–To restore and maintain fi sh 

populations in “good condition” in the main stem 

of the San Joaquin River below Friant Dam to 

the confl uence of the Merced River, including 

naturally reproducing and self-sustaining 

populations of salmon and other fi sh

• Water Management–To reduce or avoid adverse 

water supply impacts to all of the Friant Division 

long-term contractors that may result from the 

interim fl ows and restoration fl ows provided for in 

the Settlement

The San Joaquin River Restoration Program

The Settlement states that the Secretary of the Interior 

will implement the terms and conditions of the 

Settlement. The San Joaquin River Restoration Program 

(SJRRP) is currently authorized under the CVPIA and 

the agencies responsible for the management of the 

program include Reclamation, the Service, NMFS, 

DWR, and DFG.

Additional funding and amended authorization is 

pending passage of federal legislation that would 

approve terms and conditions of the Settlement. The 

San Joaquin River Restoration Act (House Resolution 

4074) passed out of the House Committee on Natural 

Resources in November 2007 and further action by the 

House and the Senate is anticipated in 2008. Once terms 

and conditions are approved, the program will continue 

to move forward with the development of a plan to 

reestablish salmon in the San Joaquin River.

Other Activities 

Although development of the comprehensive plan has 

been delayed by the lawsuit, several key activities have 

been completed since 1992 in support of the future 

plan’s goals. For example, physical improvements 

to 1.5 miles of the San Joaquin River (MilburnHansen Project); efforts to enhance the recovery 

of the federally listed valley elderberry longhorn 

beetle (the Endangered Species Recovery Program 

(ESRP)); data collection and study model development 

and calibration to benefi t the ongoing development 

of temperature, hydraulic, and operational models 

for Millerton Reservoir and the San Joaquin River 

downstream to the confl uence with the Merced River; 

San Joaquin River water quality monitoring; inventory 

and documentation of the current status, distribution 

and condition of the aquatic fauna and fl ora within the 

San Joaquin River between Friant Dam and the mouth 

of the Merced River; bird monitoring and development 

of a long-term monitoring plan to evaluate bird 

communities along the river; and development of an 

SJRRP-focused integrated information management 

system (IIMS) for centralizing the data required to 

support the management of river systems.

Measuring Success

In 2007, the program initiated organizational and 

management actions in order to move towards a longterm structure for the SJRRP, including creation of a 

program management structure for the coordinated 

involvement of all agencies and parties.

Using CVPIA authority and funding, the program 

completed the following actions towards the 

development of the San Joaquin River Comprehensive 

Plan: preparation of a Program Management Plan 

(PMP), establishment of dedicated technical work groups 

comprised of implementing agencies, development of 

a structured process for coordination with the settling 

parties, development of a comprehensive public 

involvement and outreach program, and development of 

a process for preparation and publication of the technical 

documents in support of development of the PEIS/R. 
68 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(d)(1), (2) & 

(5) 

“(d)(1)Upon enactment of this title, the 

quantity and delivery schedules of water 

measured at the boundaries of each 

wetland habitat area described in this 

paragraph shall be in accordance with 

Level 2 of the “Dependable Water Supply 

Needs” table for those habitat areas 

as set forth in the Refuge Water Supply 

Report and two-thirds of the water supply 

needed for full habitat development for 

those habitat areas identifi ed in the “San 

Joaquin Basin Action Plan/Kesterson 

Mitigation Action Plan Report...”

“(d)(2) Not later than ten years after 

enactment of this title, the quantity and 

delivery schedules of water measured at 

the boundaries of each wetland habitat 

area described in this paragraph shall 

be in accordance with Level 4 of the 

“Dependable Water Supply Needs” table 

for those habitat areas as set forth in the 

“Refuge Water Supply Report” and the 

full water supply needed for full habitat 

development for those habitat areas 

identifi ed in the “San Joaquin Basin 

Action Plan/Kesterson Mitigation Action 

Plan Report...”

Introduction to the Refuge 

Water Supply Program Sacramento

San Francisco

Los Angeles

“(d)(5) The Secretary is authorized and directed to 

construct or to acquire from non-Federal entities such 

water conveyance facilities, conveyance capacity, and 

wells as are necessary to implement the requirements 

of this subsection; provided, that such authorization 

shall not extend to conveyance facilities in or around 

the Sacramento-San Joaquin Delta Estuary...”

Figure 21. Central Valley Refuges Receiving CVPIA Water 

Supplies
3406 (d)(1), (d)(2) and (d)(5) 69

The Refuge Water Supply Program (RWSP) 

encompasses several CVPIA provisions: 

Water Acquisition

• (b)(3) Water Acquisition Program (WAP) for 

acquisition of Incremental Level 4 quantities specifi ed 

in (d)(2); and

• (d)(1) Provide Level 2 Water

Conveyance

• (d)(1), (2) & (5) Refuge Conveyance (wheeling)–

delivery of Level 2 water and Incremental Level 4 

water 

Construction

• (d)(5) Refuge Facilities Construction–specifi c 

facilities construction to support delivery of water 

to those lands identifi ed in the Report on Refuge 

Water Supply Investigations March 1989 report; 

Water Type

Volume Required by the Act 

(Acre-Feet Per Year)

Level 2 water 396,244

Incremental Level 4 water 159,271

Full Level 4 water 555,515

Table 15. Refuge Water Type and Mandated Target

and

• (d)(5) San Joaquin Basin Action Plan–specifi c 

facilities construction to support delivery of water 

to the lands specifi ed in the San Joaquin Basin 

Action Plan Lands/Kesterston Mitigation Plan 

December 1989 report 

The goal of the RWSP is to ensure that all wetland 

habitat areas, hereinafter referred to as refuges, annually 

receive water of specifi ed quantity and suitable fl ow 

rate and quality to support their wetland and aquatic 

environments. The program serves 19 refuges as 

shown in Figure 21. The RWSP provisions (acquisition, 

conveyance and construction) work together to 

implement these CVPIA provisions. 

The specifi ed water quantities are defi ned as Level 2 

water, Incremental Level 4 water, and Full Level 4 water 

(Table 15). 

Level 2 is a specifi ed amount of water required for 

minimum wetlands and wildlife habitat management, 

based on historic annual deliveries prior to 1989. 

Reclamation is required to provide full Level 2 water 

annually, either from the yield of the CVP or from 

other sources based on preexisting contracts or similar 

arrangements. Most Level 2 water is provided from the 

yield of CVP water. Some Level 2 water is provided 

from other non-CVP sources. The Level 2 annual water 

delivery target is 396,244 acre-feet. 

Full Level 4 is the total annual amount of water 

identifi ed for each refuge in CVPIA as required for 

optimum wetlands and wildlife habitat development and 

management. The Full Level 4 water delivery target for 

the 19 refuges is 555,515 acre-feet. 

Incremental Level 4 water is the difference between 

Level 2 and Full Level 4 (159,271 acre-feet). Each year, 

Reclamation strives to provide as much Incremental 

Level 4 water as possible. The CVPIA specifi es that 

Reclamation must acquire this Incremental Level 4 

water supply through voluntary measures such as water 

conservation, conjunctive use, purchase, lease, donation, 

or similar activities. This term was not used in the Act.

Level 2 and Full Level 4 allocation numbers were 

derived from two reports titled “Report on Refuge Water 

Supply Investigations March 1989” and “San Joaquin 

Basin Action Plan/Kesterson Mitigation Plan December 

1989” published by Interior and incorporated into 

CVPIA by reference. These studies collated all existing 

information on current and desired water use, power 

needs, surface water delivery systems, groundwater 

availability, recreation and wildlife resources, and 

habitat management objectives for all of the refuges. 

Based on this information, alternative plans were 

formulated for each refuge to provide dependable water 

supplies, utilizing several water delivery “options,” 

including Level 2 and Level 4.

Table 16 shows the Level 2 and Incremental Level 4 

amounts of water allocated to each refuge according to 
70 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Refuge Name - Region

Full Lavel 4 Water 

(Acre-Feet)

Level 2 Water 

(Acre-Feet)

Incremental 

Level 4 

Water 

(Acre-Feet)

Grassland Water District (private) - San Joaquin Valley

Grassland Resource Conservation 

District 180,000 125,000 55,000

CA Department of Fish and Game - Sacramento Valley

Gray Lodge Wildlife Area 44,000 35,400 8,600

CA Department of Fish and Game - San Joaquin Valley

Volta Wildlife Area 16,000 10,000 6,000

Los Banos Wildlife Area 25,000 16,670 8,330

Salt Slough Unit 10,020 6,680 3,340

China Island Unit 10,450 6,967 3,483

Mendota Wildlife Area 29,650 18,500 11,150

U.S. Fish and Wildlife Service – Sacramento Valley

Sacramento National Wildlife Refuge 50,000 46,400 3,600

Delevan National Wildlife Refuge 30,000 20,950 9,050

Colusa National Wildlife Refuge 25,000 25,000 0

Sutter National Wildlife Refuge 30,000 23,500 6,500

U.S. Fish and Wildlife Service – San Joaquin Valley

San Luis Unit 19,000 13,350 5,650

Kesterson Unit 10,000 3,500 6,500

West Bear Creek Unit 10,810 7,207 3,603

Freitas Unit 5,290 3,527 1,763

Merced National Wildife Refuge 16,000 13,500 2,500

East Bear Creek Unit 13,295 8,863 4,432

U.S. Fish and Wildlife Service - Tulare Lake Basin

Kern National Wildlife Refuge 25,000 9,950 15,050

Pixley National Wildlife Refuge 6,000 1,280 4,720

TOTAL 555,515 396,244a 159,271a

Table 16. Water Allocations by Refuge from 1989 Reports

a

 The totals of 396,244 ac-ft of Level 2 water and 159,271 ac-ft of Incremental Level 4 water from the “1989 Reports” differ from the totals 

of Level 2 and Incremental Level 4 water under the Water Supply Contracts by 26,007 ac-ft. Level 2 water under the Water Supply Contracts includes Replacement water of 26,007 ac-ft. Replacement water is water which Reclamation provides from Central Valley Project 

yield to certain CVPIA refuges through contracts with refuge managing agencies executed prior to the passage of CVPIA. Under the 

Water Supply Contract, the Incremental Level 4 amounts have been reduced by this same amount.
3406 (d)(1), (d)(2) and (d)(5) 71

Long-term supply contracts provide stability 

for refuge operators

To ensure reliability for refuge operators, Reclamation 

entered into long-term water supply contracts with the 

three refuge managing agencies: California Department 

of Fish and Game (DFG), U.S. Fish and Wildlife Service 

(Service), and Grassland Water District (GWD). These 

contracts have a performance period of 25 years and 

are renewable, representing Reclamation’s commitment 

under CVPIA to provide suffi cient water for wetlands and 

aquatic habitats. 

Each year in February or March and monthly thereafter, 

Reclamation’s Central Valley Operations Offi ce 

announces the water supply available to the CVP 

contractors for the current year, including the amount of 

Level 2 water available out of the yield of the CVP for 

the refuges. The Interagency Refuge Water Management 

Team then establishes the water delivery schedule for 

both Level 2 water and Incremental Level 4 water for 

each refuge. This team is comprised of representatives 

from Reclamation, the Service, DFG, and GWD. The 

creation of this team was established through a provision 

in the long-term water supply contracts. 

Use of groundwater for refuge water supplies

Availability of surface water supplies on the open market 

from willing sellers is limited in some years, leaving the 

RWSP unable to meet its Incremental Level 4 acquisition 

goals. The RWSP is attempting to expand its current 

diversifi cation of sources of water to meet the needs 

of the refuges in the absence of suffi cient funding for 

water acquisition. For example, the RWSP has pursued 

groundwater projects in partnership with local water 

districts. The primary advantage of groundwater is 

that usually it does not require external conveyance 

if the groundwater sources can be located at or near 

the refuges. The lower cost of groundwater is also 

an advantage, although one downside is that in some 

locations groundwater has poorer quality, particularly 

in the San Joaquin Valley. It is critical to monitor 

groundwater quality so as not to degrade the general 

quality of water on the refuges.

The Pixley and Merced National Wildlife Refuges and 

the Gray Lodge Wildlife Area have utilized groundwater 

in supplementing some of their Level 2 supplies, and will 

continue to use groundwater. Reclamation is carrying 

out and participating in several pilot studies that may 

result in further increases in groundwater usage as part 

of long-term refuge water supplies. For instance, recent 

studies at the East Bear Unit of the San Luis National 

Wildlife Refuge have indicated that salinity levels at 

some locations are not as high as previously thought, 

allowing Reclamation and the Service to consider 

conjunctive groundwater use at this refuge.

Improving quality of water supplies 

In late 2007, Reclamation entered into an agreement 

for GWD to implement a water quality monitoring 

program on lands within the Grassland ecological 

area. GWD will be monitoring water quality on both 

GWD and DFG refuge lands. When implemented, the 

data generated will be used to manage wetlands more 

effi ciently and monitor the quality of water leaving the 

refuges. In 2008, Reclamation expects to enter into a 

similar agreement with the Service for water quality 

monitoring on their refuge lands within the Grassland 

ecological area.

The RWSP has developed a draft Refuge Water Quality 

Best Management Practices (BMP) Plan, with the 

Service as project lead. The BMP Plan is consistent 

with the requirement in the 2005 CALFED legislation 

to reduce water quality impacts of refuge discharges 

that receive federal water and discharge into the San 

Joaquin River. A fi nal report is expected in 2008 and 

the conclusions of this report will be put into practice in 

future years. One of the proposed practices is additional 

water quality monitoring to track fl ows and discharges 

from refuges to the San Joaquin River.

the 1989 reports. Allocations under the refuge water 

supply contracts between Reclamation and refuge 

management agencies vary somewhat between Level 2 

and Incremental Level 4 amounts, and this is footnoted 

in Table 16. However, the total Level 4 allocations for 

each refuge remains the same.
72 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Sections 3406(b)(3) and 3406(d)(2) 

Per the Act, 2002 is the date by which Full Level 4 

was to be delivered to all CVPIA refuges on an annual 

basis. From 2002 to 2006, the Water Acquisition 

Program (WAP) has acquired between 68,000 and 

85,000 acre-feet each year of Incremental Level 4 

water (Table 17). These acquisitions rely primarily 

on transfers from the San Joaquin River Exchange 

Contractors, one-year transfers from other CVP 

contractors such as the Cross Valley Canal Contractors, 

and occasional groundwater purchases. The annual 

average of this volume represents approximately 57 

percent of the mandated quantity (as represented in the 

Water Supply Contracts).

The water made available for the Exchange Contractors 

varies year by year based on infl ow projection to the 

Shasta Reservoir in Northern California. The amount of 

water provided for transfer by the Exchange Contractors 

is allocated to agriculture, municipal and industrial 

Water Acquisition Program – 

Refuge Water Sacramento

San Francisco

Los Angeles

contractors, and the CVPIA refuges, depending on the 

hydrology of the year. In dry years, the agricultural 

users generally are offered a larger portion of the 

available water. In wetter years, the refuges receive a 

larger portion of the available water. 

Due to the dry hydrologic conditions in Water Year 

(WY) 2007, the WAP acquired only 41,111 acre-feet of 

Incremental Level 4 water. Specifi cally, the WAP was 

only able to purchase 30,000 acre-feet of water from 

the Exchange Contractors, and entered into a one-year 

acquisition with the Kern-Tulare/Rag Gulch Water 

Districts for 11,111 acre-feet for the year for a total of 

41,111 acre-feet. The high cost of water acquisition and 

the lack of willing sellers made the WY 2007 market 

very diffi cult. The continuation of these conditions 

is expected into WY 2008 and is one of the primary 

reasons the full target of 133,264 acre-feet (see footnote 

in Table 17) has not been attained and probably will not 

be attained in the near future. 
3406(b)(3) and (d)(2) 73

Table 17. Level 2 and Incremental Level 4 Water Deliveries by Water Year* (2002-2007)

Water Year*

Level 2 - Actual Deliveries and 

Percent of Target 422,251** 

(Acre-Feet)

Incremental Level 4 – Actual 

Deliveries and Percent of 

Target 133,264** (Acre-Feet)

2002 383,842 (91%) 80,970 (61%)

2003 391,635 (93%) 77,053 (58%)

2004 385,731 (91%) 68,262 (51%)

2005 388,803 (92%) 83,211 (62%)

2006 380,072 (90%) 90,545 (68%)

2007 388,521 (92%) 45,049 (34%)

 * Water Year is defi ned as beginning on the fi rst day of March through the last day of February of the following year.

** This table refl ects deliveries starting with Water Year 2002, the beginning year that CVPIA mandated Full Level 4 deliveries for all refuges 

[Section 3406(d)(2)]. The target values used for total Level 2 and Incremental Level 4 water amounts (see column headers) are those identifi ed 

from the Water Supply Contracts.
74 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(d)(5)

As of 2007, Reclamation has the physical ability to 

deliver Full Level 4 supplies to 14 of the 19 CVPIA 

refuges. 

The Refuge Facilities Construction Program and the 

San Joaquin Basin Action Plan Construction Program 

identifi ed 17 construction projects (with a total of 46 

major structures/actions) required to provide Full Level 

4 conveyance capacity to all CVPIA refuges. These 

infrastructure improvements can be divided into two 

categories: 

• Modify existing facilities–Existing conveyance 

facilities can be upgraded to overcome capacity 

constraints 

• Construct new facilities–New facilities are 

constructed where there is no existing system, or 

where modifi cations to an existing system would not 

be suffi cient to meet demand 

To date, these two programs have completed 31 of the 46 

major structures/actions identifi ed in the environmental 

documents and related design and specifi cation 

documents. Table 18 lists all major structures/actions 

completed, with 1997 being the fi rst year for completion.

Measuring Success

Refuge Facilities Construction Program – 2007 

Accomplishments

Reclamation completed important revisions to the 

Conveyance of Refuge Water Supply South San Joaquin 

Valley Study Area Mendota Wildlife Area Pre-Public 

Refuge Facilities Construction 

Program and San Joaquin 

Basin Action Plan Lands 

Program 

Sacramento

San Francisco

Los Angeles

Draft Environmental Assessment/Impact Statement 

(EA/IS) with an emphasis on potential actions to 

provide annual reliable Full Level 4 water supplies to 

the Mendota Wildlife Area (WA) as required by CVPIA. 

The Conveyance of Refuge Water Supply South San 

Joaquin Valley Study Area Mendota Wildlife Area 

Public Draft EA/IS was released for comments in May 

2007 and fi nal comment period was closed in August 

2007. 

The program continued implementation on work to 

support completion of the draft Design Data Report on 

conveyance facilities of the Biggs-West Gridley Water 

District (BWGWD) for conveyance of Refuge water 

supplies to Gray Lodge WA, covering canal water level 

study, fl ow measurement study, seepage study, proposed 

system improvements, and cost estimates.

A fi nal draft Design Data Report is scheduled to be 

complete in Spring 2008, which will allow selection 

of the preferred alternative and cost estimates for 

construction. 

San Joaquin Basin Action Plan - 2007 

Accomplishments

Work in FY 2007 consisted of the continued 

construction of Phase I, Bear Creek Pumping Plant and 

Pipeline. The revised estimated completion for this 

project is March 2008. 

Field data collection for the installation of a temporary 

pumping plant and delivery points on the San 

Joaquin River to supply water from Island C Canal 
3406 (d)(5) 75

Fiscal 

Year

Number of Major Structures/

Actions (Completion Percent 

of 46 Major Structures/Actions 

Target)

1997 3 actions (7%) 

1998 5 actions (11%) 

1999 11 actions (24%) 

2000 21actions (46%) 

2001 22 actions (48%)

2002 23 actions (50%)

2003 24 actions (52%)

2004 28 actions (61%)

2005 30 actions (65%)

2006 30 actions (65%)

2007 31 actions (67%)

Early in 2007, engineers laid pipeline that will distribute 

delivered water onto the East Bear Creek Unit in 

Merced County

Table 18. Cumulative Completed Construction 

Actions by Year (1997-2007)

was completed. A cost estimate for the design and 

construction was given to MP-400 for their action. 

The O’Banion Bypass within the Central California 

Irrigation District was completed. 
76 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Refuge Water Conveyance 

(Wheeling) Sacramento

San Francisco

Los Angeles

CVPIA Sections (d)(1), (d)(2) and (d)(5)

Reclamation delivered approximately 91 percent of the 

mandated Level 2 water on average, between Water 

Year (WY) 2002 and WY 2007. This includes water 

from sources other than Central Valley Project yield. 

In WY 2007, approximately 388,521 acre-feet of water 

was delivered to the refuges. This delivery number 

includes groundwater provided to the Pixley and 

Merced National Wildlife Refuges and the Gray Lodge 

Wildlife Area, and an estimated 8,100 acre-feet of water 

delivered to the Merced National Wildlife Refuge under 

an existing mitigation agreement pursuant to the Federal 

Energy Regulatory Commission license to Merced 

Irrigation District. In addition, approximately 45,049 

acre-feet of Incremental Level 4 water was delivered to 

the refuges. The Incremental Level 4 deliveries include 

38,194 acre-feet (after carriage losses) of water acquired 

by the WAP; 5,355 acre-feet of water from Reclamation’s 

purchase of permanent partial water rights from four 

water districts in the Sacramento Valley; and 1,500 acrefeet of water provided through an existing mitigation 

agreement under a Federal Energy Regulatory 

Commission license with Merced Irrigation Distrct.

In order to deliver the water, Reclamation has entered 

into several conveyance agreements with water 

delivering entities throughout the Central Valley 

to utilize their existing conveyance systems. This 

approach was deemed more effi cient and cost-effective 

than construction of a separate independent federal 

delivery system for exclusive delivery to refuges. 

These agreements stipulate that the conveying entity 

will deliver up to a specifi ed quantity of water through 

facilities that it owns or controls to a certain refuge or 

group of refuges. 

In FY 2007, Reclamation negotiated a third amendment 

to the groundwater pumping reimbursement agreement 

with CDFG for the purpose of supplementing Level 2 

surface water supplies at Gray Lodge Wildlife Area up 

to full Level 2 allocation. Reclamation also negotiated 

a reimbursement agreement between Reclamation and 

CDFG for reimbursement of Level 2 water conveyance 

costs to CDFG for Level 2 water deliveries to Mendota 

Wildlife Area.

Reclamation continued the cost share development 

process to determine current cost share apportionment 

for the State of California related to Incremental Level 

4 water supplies, including water acquisition, certain 

conveyance facilities construction, and water delivery 

costs. This process is covering the last six federal 

fi scal years, and efforts are coordinated with the 

Service, DFG, and the California Department of Water 

Resources. A fi nal task order resulting from this process 

is anticipated to be completed by December 2007.

Reclamation continued its funding support for the 

Grassland Wetlands Modifi ed Hydrology Study. 

This project involves water quality monitoring and 

wildlife studies of modifi ed water management in the 

Grassland ecological wetlands to determine if water 

management changes could minimize water quality 

impacts to the San Joaquin River and still meet wildlife 
3406 (d)(1), (d)(2) and (d)(5) 77

habitat management goals. These efforts have potential 

application for development of water quality BMPs for 

various wildlife refuges in the San Joaquin River Basin.

Numerous biological benefi ts have resulted from a 

reliable year-round water supply through CVPIA that 

adequately meets the delivery schedule for wetland 

management on CVPIA wildlife refuges. Habitat is 

now available during the months of August and early 

September which benefi ts early migrant waterfowl 

and shorebirds, and also provides habitat for resident 

wildlife and their young during a critical time of the year 

when wetland habitat can be particularly limited due by 

hydrology. 

Applying water for semi-permanent and permanent 

wetland habitat in the spring and summer directly 

benefi ts the recovery of special status species such as 

the giant garter snake, white-faced ibis, and tricolored 

blackbirds. Wintering wildlife also benefi t because this 

habitat type provides diversity in a landscape dominated 

by shallow wetland habitat. 

Seasonal wetlands are now maintained and de-watered 

to coincide with peak migration times of shorebirds 

and waterfowl. Timely de-watering also promotes the 

germination and irrigation of important moist-soil food 

plants, such as swamp timothy grass and watergrass. 

These plants provide a high-energy food source 

through both their seeds and associated invertebrate 

communities. The increase in supply reliability allows 

wetland managers to lower water depths to make seeds 

and invertebrates available without the fear of having 

wetlands completely evaporate.

Another signifi cant advantage is that the ability to 

battle avian disease outbreaks, such as botulism and 

cholera, is greatly assisted by applying additional water 

and creating a “fl ow through” system of water delivery 

and drainage. This “fl ow through” also helps deal with 

wetland areas high in salinity, which are often lower in 

productivity and diversity. CVPIA water allows wetland 

managers to “fl ush” salts from wetland basins and 

improve soil quality. 
78 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

CVPIA Section 3406(g)

“The Secretary, in cooperation with the State of 

California and other relevant interests and experts, 

shall develop readily usable and broadly available 

models and supporting data to evaluate the ecologic 

and hydrologic effects of existing and alternative 

operations of public and private water facilities and 

systems in the Sacramento, San Joaquin, and Trinity 

River watersheds.”

The goal of the Ecological/Water Systems Operations 

Models Program (EWSOM) is to develop broadly 

available and readily accessible models and 

supporting data to evaluate existing and alternative 

water management strategies. By demonstrating the 

effect of water operations on quality and quantity of 

various habitats, these models improve the scientifi c 

understanding of ecosystems in the Sacramento, San 

Joaquin and Trinity watersheds. 

As part of the model development process, the program 

has and will continue to support hydrologic and biologic 

data collection. Measures to determine the effectiveness 

of models and timeframes for this program have not yet 

been determined.

The program is an essential tool for Interior, and 

since 1998 has provided a high level of support for 

development of the integrated Central Valley Project/

State Water Project (CVP/SWP) model, CalSim 

II. The primary benefi t of CalSim II has been for 

planning investigations, including the most recent 

Ecological/Water Systems 

Operations Models Sacramento

San Francisco

Los Angeles

CVP Operations Criteria and Plan (OCAP). CalSim 

II has been utilized in many other studies, including 

the ongoing CALFED storage and conveyance 

investigations. CalSim II is available for public use and a 

new version of the model (CalSim III) is currently being 

developed jointly by Reclamation and the California 

Department of Water Resources (DWR). This version, 

scheduled for release in the fall of 2008, will have 

substantially improved spatial resolution and hydrology 

and groundwater simulation capabilities. 

In addition to CalSim, the program supports the 

development and application of other types of river 

management and ecological models including water 

quality, hydrology, groundwater, fi sh population and 

riparian habitat models used for support of operations 

and planning by Reclamation’s Division of Planning, the 

Service, federal and state water contractors and public 

interest organizations. 

This program also supports participation of Reclamation 

and Service staff in professional organizations as well as 

CalSim training conducted by Reclamation and the DWR.

Measuring Success

EWSOM continues to perform data collection activities 

to support modeling and improvement of scientifi c 

understanding of ecosystems in the Sacramento, San 

Joaquin and Trinity watersheds. To date, the program 

is operating the integrated CVP/SWP model (CalSim 

II) and six other models; two more are currently under 

development. 
3406(g) 79

Table 19. Ecological and Water Systems Operations Models (1996-2007)

Model

Initiation/

Operational Date

Agencies Involved in 

Development Description

CalSim II 1998/2002 Reclamation, DWR, Service, 

federal/state water contractors, 

Sacramento Valley Settlement 

contractors

Used for coordinated 

system-wide planning and 

operations of CVP and 

SWP water projects 

CalSim III 2007 Reclamation, DWR, Service, San 

Joaquin Exchange contractors 

and their consultants

Used for coordinated 

system-wide planning and 

operations of CVP and 

SWP water projects 

Upper Sacramento 

River Water Quality 

Model (USRWQM) 

2001/2003 Reclamation, Service, NOAA, 

NMFS, CALFED Integrated 

Storage Investigations (ISI)

Used for planning and 

operations of reservoirs 

for water temperature 

management in 

anadromous fi sh spawning 

and rearing habitats

Riparian Habitat 

Establishment Model 

(RHEM) 

2007 Reclamation, CALFED ISI Used for planning and 

operations of reservoirs for 

the recruitment and survival 

of cottonwood and other 

riparian vegetation

InSalmo 1996/2005

Beta version; 

awaiting calibration 

and validation

Service Evaluates andromous 

fi sh survival at various life 

stages and in a variety of 

aquatic environments

SALMOD 1996/2005 Developed by USGS and refi ned 

by USGS and Reclamation 

contractors; used by Reclamation, 

Service, CALFED ISI

Used in planning studies to 

evaluate effects of reservoir 

operations on anadromous 

fi sh spawning, incubation 

and rearing

Land Atmosphere 

Water Simulator 

(LAWS)

2002/2006 Reclamation Used to develop hydrologic 

budgets and water 

demands for CalSim model

HydroGeoSphere 

(HGS) 

2003/2005 Reclamation Used for planning of surface 

and subsurface hydrologic 

interactions related to water 

supply, water quality and 

ecosystem restoration

Ecologically Cogent 

Operations Suite of 

Integrated Models 

(ECOSIM) 

1998/1998 Service Used for analyses of 

changes to the macroscopic 

water resources for CVP/

SWP operations 
80 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Of the models listed in Table 19, the following are 

currently under development or undergoing signifi cant 

modifi cations: 

CalSim III San Joaquin QA/QC Review and 

Documentation

New hydrologic datasets for CalSim III in the Sacramento 

and San Joaquin valleys were developed jointly in 2007 

by Reclamation’s Reservoir Systems Analysis Branch 

staff, Reclamation’s Technical Service Center, and private 

contractors. The group also completed a detailed Quality 

Assurance/Quality Control review of the Sacramento 

Valley water budgets in collaboration with DWR 

modelers to help improve the model’s level of confi dence.

Additionally, in cooperation with DWR, Reclamation 

staff completed signifi cant improvements for the CalSim 

III model including enhanced methods for evaluating 

hydrologic inputs based on DWR’s Integrated Flow 

model, groundwater simulation capability based on 

the new California Central Valley Simulation model, 

and more consistent implementation of hydrology and 

groundwater in both the Sacramento and San Joaquin 

valleys.

RHEM Model Developments

Reclamation staff completed initial model development 

and fi eld data collection studies in 2007. Currently, a 

controlled fi eld study of cottonwood seedling growth is 

being performed to develop parameters for the Riparian 

Habitat Establishment Model (RHEM) and additional 

development of a two-dimensional version of the RHEM 

is underway. The RHEM will support maintenance of 

healthy riparian ecosystems – including anadromous 

fi sh – in the Central Valley.

Hydrogeosphere/CalSim Linkage – Literature 

Review and Methodology Development; 

HGS Temperature Module Planning

HydroGeoSphere (HGS) is used for planning of 

surface and subsurface hydrologic interactions 

related to water supply, water quality and ecosystem 

restoration. Testing activities related to HGS subtiming/

subgridding methodology (allowing for physically 

realistic simulations with shorter computation times) are 

currently ongoing. A conceptual model report including 

both Red Rock Ranch (small scale) and the San Joaquin 

Basin (large scale) has been written by HydroGeoLogic, 

Inc. and is under review by Reclamation and DWR staff. 

The report details the climate, topography, geology, 

hydrology and hydrogeology of the small and large 

scale systems, as well as a proposed approach to the 

accurate numerical modeling of the two systems and 

testing of the subtiming/subgridding implementation. 

HydroGeoLogic, Inc. is preparing the input fi les 

for the application, facilitated by means of GIS and 

visualization tools. Next steps will be to calibrate and 

test the baseline model and investigate appropriate 

applications.
3408 (h) 81

CVPIA Section 3408(h)

“The Secretary is authorized to purchase from 

willing sellers land and associated water rights and 

other property interests...which receives Central 

Valley Project water under a contract executed with 

the United States, and to target such purchases to 

areas deemed most benefi cial to the overall purchase 

program, including the purposes of this title.”

The Land Retirement Program (LRP) purchases land, 

water and other property interests from willing sellers 

who receive CVP water. By ceasing irrigation of these 

agricultural lands, the program reduces the volume 

of agricultural drainage, and protects and restores the 

retired land for wildlife habitat.

The long-term land retirement goal referenced in the Act 

is to retire 75,000 acres by 2040. The program has three 

targets that support this long-term goal: 

• Retire 15,000 acres of agricultural land by 2014 

for the Land Retirement Demonstration Project 

(LRDP)

• Restore appropriate habitat on 400 acres of retired 

lands per year on LRDP sites

• Reduce the production of agricultural drainage 

water annually by 6,000 acre-feet upon completion 

of the LRDP

The LRDP was implemented in 1999 at two sites in 

the western San Joaquin Valley (Tranquillity, managed 

by Reclamation) and the Tulare Lake Basin (Atwell 

Island, managed by BLM) to study the environmental 

impacts of land retirement and to evaluate cost-effective 

restoration strategies for retired lands. 

Mendota Pool

Atwell Island Site

Fresno Slough

Tule River

N.F. Kings River

Kings River

Murphy Slo ugh

FRESNO

Drainage impacted lands

Demonstration project sites

Tranquillity Site

5

Figure 22. Land Retirement Program Sites 

 Land Retirement Program Sacramento

San Francisco

Los Angeles
82 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2007 ANNUAL REPORT

Measuring Success

Retiring and Restoring Lands

Of the targeted 15,000 acres, Interior has acquired 

9,306 acres and retired (or removed from irrigated 

agriculture) 8,596 acres from agricultural production. In 

2007, the program acquired and retired 213 acres from 

agricultural production.

On average, the LRP has exceeded its land restoration 

performance goals of 400 acres per year. Since 1998, 

the LRP has restored 4,981 acres. Complete restoration 

to upland habitats found in the San Joaquin Valley can 

take many years to achieve, but the program has restored 

portions of upland habitat and continues to adapt 

techniques to achieve desired habitat values.

Restoration efforts on retired lands immediately 

increased biodiversity and abundance, including 

Special Status Species. Wildlife surveys of restored 

units observed important fi ndings of sensitive 

San Joaquin Valley wildlife species, including 

populations of endangered Tipton kangaroo rats, 

burrowing owls, coast horned lizards, San Joaquin 

Valley coachwhips, Swainson’s hawks and a sensitive 

plant called Hoover’s woolystar. The Atwell Island 

wildlife sightings database now contains more 

than 9,500 observations. Utilizing the database, 

BLM developed plant and animal lists and a photoillustrated fl ora for the Atwell Island Project Area.

Annual Acres Acquired

Acres Retired 

from Agriculture 

 (cumulative)

Acres 

Restored

(annual)

Atwell Island Tranquillity

1992 0 0 0 0

1993 0a 0 00

1994 0 0 0 0

1995 0 591 591

1996 0 0 591

1997 0 0 591

1998 0 995 1,585 1,220

1999 0 60 1,646 100

2000 2,645b 0 4,291 777

2001 1,414 444 4,977 702

2002 1,510 0 6,675 373

2003 616 0 6,925 261

2004 155 0 7,495 308

2005 625 0 8,345 349

2006 38 0 8,383 416

2007 213 0 8,596 475

TOTAL 7,216 2,090 8,596 4,981

a

 Prospect Island (1228 acres) was purchased in 1995 in Sacramento before the Demonstration Project 

was initiated and is not considered part of or counted toward the Land Retirement Demonstration Project 

acquisition total.

b

 455 acres of this purchase in AIWD was paid for by CVP Conservation Program.

Table 20. Land Acquired, Retired & Restored by Year at Tranquillity and Atwell Island Sites (1992-2007)
3408 (h) 83

At Atwell Island, BLM successes are being adapted to 

future plantings. In 2007, 475 acres were planted with 

three seed mixes in confi gurations that can be used for 

future kit fox artifi cial burrows.

At Tranquillity, the established San Joaquin Valley Native 

Plant Nursery worked to increase seed from more than 

100 plants species collected within a 50-mile radius. 

The USDA Natural Resources Conservation Service Plant 

Materials Center helped research agricultural production 

techniques to help determine species for restoration 

strategies and methods for cost-effi cient cultivation. 

Trials focusing on weed competition control, the major 

challenge in successful upland habitat restoration, were 

initiated in 2004 and continued through 2007.

Reducing Agricultural Drainage 

Five years of groundwater monitoring at the LRDP 

site near Tranquillity shows a declining shallow 

water table in response to land retirement. The 

water table response observed at the Tranquillity 

site is representative of conditions present at a high 

percentage of lands that are targeted for retirement 

in the western San Joaquin Valley. The declining 

shallow water table observed beneath demonstration 

project lands indicates the success of land retirement 

as a drainage reduction strategy. 

Total selenium concentrations, soluble selenium 

concentrations and salinity (EC) in the surface soil 

showed a decreasing trend over the fi ve-year monitoring 

period, as high salinity and selenium concentrations in 

the shallow groundwater are a result of leaching from 

irrigated soils. As long as the water table continues to 

decline as expected, the high concentrations of selenium 

in the groundwater should have no consequences to 

biota at the site. Decreasing selenium and salinity 

trends in the surface soil indicate that upward fl ux of 

salt and selenium from capillary rise and evaporation 

of shallow groundwater at the soil surface is minimal, 

and that some downward leaching of soluble selenium 

and salt from surface soils occurred during the fi ve-year 

study despite dryer than average conditions. Selenium 

concentrations in biota have not changed signifi cantly 

over the study period and are below concentrations of 

concern to EPA and the Service. 

Annuals restoration at Atwell Island Land Retirement Site
84 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2007 ANNUAL REPORT
APPENDIX A 85 

APPENDIX A: GLOSSARY OF TERMS

Acre-foot (AF): The quantity of water required 

to cover one acre to a depth of one foot. Equal to 

1,233.5 cubic meters (43,560 cubic feet)

Anadromous fi sh: Stocks of salmon, steelhead, 

striped bass, white and green sturgeon, and 

American shad that ascend the Sacramento and 

San Joaquin rivers and their tributaries and the 

Sacramento-San Joaquin Delta to reproduce after 

reaching maturity in the San Francisco Bay or the 

Pacifi c Ocean; fi sh species that spend most of their 

lives in the ocean but reproduce in fresh water

Anadromous Fish Restoration Program (AFRP): 

A program authorized by the CVPIA to address 

anadromous fi sh resource issues in Central Valley 

streams that are tributary to the Delta 

Biota: Total collection of organisms of a 

geographic region or a time period

CALFED Bay-Delta Program: A unique 

collaboration among 25 state and federal agencies 

that came together to improve California’s water 

supply and the ecological health of the San 

Francisco Bay/Sacramento-San Joaquin River Delta 

Capillary rise: Movement of water upwards from 

the watertable (the top of the groundwater) into 

the unsaturated soil above; can be likened to a dry 

sponge (the unsaturated soil) being placed on top of 

a wet surface (the watertable), the sponge sucking 

up water being similar to capillary rise in soils

Central Valley: Area in the central portion of 

California bounded by the Cascade Range to the 

north, the Sierra Nevada to the east, the Tehachapi 

Mountains to the south and the coast ranges and 

San Francisco Bay to the west

Central Valley Project (CVP): As defi ned 

by Section 3403(d) of the CVPIA, “all Federal 

reclamation projects located within or diverting water 

from or to the watershed of the Sacramento and San 

Joaquin rivers and their tributaries as authorized 

by the Act of August 26, 1937 (50 Stat. 850) and all 

Acts amendatory or supplemental thereto, ...”

Central Valley Project water: As defi ned by 

Section 3403(f) of the CVPIA, “all water that 

is developed, diverted, stored, or delivered by 

the Secretary in accordance with the statutes 

authorizing the Central Valley Project in 

accordance with the terms and conditions of water 

rights acquired pursuant to California law.”

Central Valley Project Improvement Act 

(CVPIA): Public Law 102-575, Title 34. This law 

was passed in 1992 for the following purposes: 

a) Protect, restore, and enhance fi sh, wildlife, 

and associated habitats in the Central Valley 

and Trinity River basins of California 

b) Address impacts of the Central Valley Project 

on fi sh, wildlife and associated habitats 

c) Improve the operational fl exibility of the 

Central Valley Project 

d) Increase water-related benefi ts provided 

by the Central Valley Project to the State 

of California through expanded use of 

voluntary water transfers and improved water 

conservation 

e) Contribute to the State of California’s interim 

and long-term efforts to protect the San 

Francisco Bay/Sacramento-San Joaquin 

Delta Estuary 

f) Achieve a reasonable balance among 

competing demands for use of Central Valley 

Project water, including the requirements of 

fi sh and wildlife, agricultural, municipal and 

industrial and power contractors
86 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2007 ANNUAL REPORT

Central Valley Habitat Joint Venture (CVHJV): 

The association of federal and state agencies 

and private parties established for the purpose of 

developing and implementing the North American 

Waterfowl Management Plan as it pertains to the 

Central Valley of California.

Constant Fractional Marking Program (CFM): 

When fi sh are counted for CVPIA monitoring, 

program managers differentiate between wild and 

hatchery fi sh; hatcheries mark a percentage of 

juveniles before they are released and when fi sh 

come back to spawn, the mark will indicate which 

were hatchery-born

Diversion: Area where river water is rerouted in a 

direction other than its natural course

Entrainment: When fi sh are diverted from their 

natural spawning course (e.g., caught in a water 

pump or diverted from the river into a canal)

Environmental Impact Statement (EIS): An 

analysis required by the National Environmental 

Policy Act (NEPA) for all major federal actions, 

which evaluates the environmental risks of 

alternative actions 

Escapement: Measurement of adult spawning 

anadromous fi sh (e.g., salmon) that manage to 

return to their spawning stream

Firm water supplies: Non-interruptible water 

supplies guaranteed by the supplier to be available 

at all times except for reasons of uncontrollable 

forces or continuity of service provisions 

Flow: The volume of water passing a given point 

per unit of time, usually measured in cubic feet per 

second (cfs)

Habitat: Area where a plant or animal lives

Level 2: A term used to refer to refuge water supply 

deliveries; the 1989 and 1992 Refuge Water Supply 

Studies defi ne Level 2 refuge water supplies as 

the average amount of water the refuges received 

between 1974 and 1983

Level 4: A term used to refer to refuge water 

supply deliveries; Level 4 refuge water supplies are 

defi ned in the 1989 and 1992 Refuge Water Supply 

Studies as the amount of water for full development 

of the refuges based upon management goals 

developed in the 1980s

Measure: A type of program activity defi ned by the 

provisions of CVPIA that includes specifi c physical 

or structural actions

Metric: The defi ned quantifi able measurement of 

outputs or outcomes

Mitigation: One or all of the following: (1) 

Avoiding an impact by not taking a certain action 

or parts of an action; (2) minimizing impacts by 

limiting the degree or magnitude of an action and 

its implementation; (3) rectifying an impact by 

repairing, rehabilitating, or restoring the affected 

environment; (4) reducing or eliminating an impact 

over time by preservation and maintenance 

operations during the life of an action; and (5) 

compensating for an impact by replacing or 

providing substitute resources or environments

Natural Production: As defi ned by Section 

3403(H) of the CVPIA, “fi sh produced to adulthood 

without direct human intervention in the spawning, 

rearing, or migration processes”

Outcome: The intended results or consequences 

to be achieved through implementing measures 

and programs described in the CVPIA 

Output: The specifi c actions, measures, programs 

and services produced by Reclamation and the 

Service and provided to the public or others; 

outputs are the activities of the CVPIA Program 

to achieve the outcomes defi ned by the Act or 

developed by Reclamation and the Service to 

achieve the environmental restoration purposes

Pelagic Organism Decline: A recent decline in 

both abundance and species richness of pelagic 

(living in water above the bottom) organisms 

within the Sacramanto-San Joaquin Delta; pelagic 

organisms include, most notably, the delta smelt 

and longfi n smelt, federally-listed endangered 

species of fi sh

Program: The overall effort to implement the 

provisions of CVPIA 

Program Activity: The individual provisions of 

CVPIA that are being implemented by “program 

managers” at Reclamation and the Service

Program Manager: The staff at Reclamation and 

the Service that oversees implementation of the 

CVPIA program activities; each active program 

activity has a program manager from its respective 

agency

Redd Dewatering: Occurs when redds (fi sh egg 

“nests”) are left exposed by receding water levels
APPENDIX A 87 

Restoration Fund: The fund established by 

Section 3407 of the CVPIA to contribute resources 

for the environmental restoration provisions of the 

Act; revenue comes into the fund primarily through 

surcharges on water and power contract rates

Restoration Fund Roundtable: A collective 

of stakeholders representing environmental 

organizations, federal and state resource agencies, 

water and power contractors, and other interested 

parties who meet as needed to discuss issues, 

news and activities related to the CVPIA and 

provide information to Reclamation and the Service

Riparian: Of or relating to or located on the banks 

of a river or stream

South Delta: Sacramento-San Joaquin Delta

Stranding: Stranding is a term used to describe 

fi sh that are trapped in pools of water that have 

no connectivity to the larger stream because of 

insuffi cient fl ow

Target: The quantifi able or otherwise measurable 

characteristics that tell how well a program must 

accomplish a performance measure

Taxa: designating an organism or group of 

organisms

Timeframe: The period of time when program 

activities occur (e.g. annual or long-term) that 

combine with a performance measure and target, 

establish a performance goal

Water Acquisition: The purchase of water from 

willing sellers

Weir: Type of fi sh ladder that utilizes a series of 

small dams and pools to create a long channel and 

allow spawning fi sh to get around an obstruction, 

like a dam