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 2008
TABLE OF CONTENTS i 

I. EXECUTIVE SUMMARY.................................................................. 1

II. INTRODUCTION .............................................................................. 5

III. 2008 PROGRAM ACTIVITIES AND ACCOMPLISHMENTS ..........17

Section 3406 Activities:

(b)(1) Anadromous Fish Restoration Program .............................................................. 18 

(b)(1) “other” Habitat Restoration Program ............................................................................... 26

(b)(1) “other” & (b)(23) Trinity River Restoration Program........................................................................ 32

(b)(1)(B) Modifi ed CVP Operations .................................................................................... 37

(b)(2) Dedicated 800,000 acre-feet Project Yield ......................................................... 40

(b)(3) & (g) Water Acquisition Program – Instream Water ..................................................... 44

(b)(4) Tracy (Jones) Pumping Plant Program ................................................................ 46

(b)(5) Contra Costa Canal Pumping Plant ..................................................................... 49

(b)(9) & (b)(19) Flow Fluctuations and Reservoir Storage ............................................................ 51

(b)(10) Red Bluff Diversion Dam ..................................................................................... 53

(b)(11) Coleman National Fish Hatchery ........................................................................ 56

(b)(12) Clear Creek Restoration Program ....................................................................... 59

(b)(13) Spawning and Rearing Habitat Restoration Program.......................................... 63

(b)(15) Head of Old River Barrier .................................................................................... 67

(b)(16) Comprehensive Assessment and Monitoring Program ....................................... 69

(b)(20) Glenn-Colusa Irrigation District Program ............................................................ 76

(b)(21) Anadromous Fish Screen Program ..................................................................... 78 

(c)(1) San Joaquin River Comprehensive Plan ............................................................. 82

(d) Introduction Introduction to the Refuge Water Supply Program .............................................. 84

(b)(3) & (d)(2) Water Acquisition Program – Refuge Water ........................................................ 88

(d)(5) Refuge Facilities Construction Program and San Joaquin Basin Action Plan ........90

 Lands Program

(d)(1), (2) & (5) Refuge Water Conveyance (Wheeling) ............................................................... 92

(g) Ecosystem and Water Systems Operations Models .......................................... 94

Section 3408 Activities:

(h) Land Retirement Program ................................................................................... 98

Appendices

Appendix A Glossary of Terms .............................................................................................. 102

Appendix B Acronyms ........................................................................................................... 106

Contents
ii CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2008 ANNUAL REPORT

List of Figures

Figure 1 Central Valley Project System .............................................................................................. 7

Figure 2 Central Valley Refuges Receiving CVPIA Water Supplies ................................................. 10

Figure 3 Total CVPIA Obligations by Action Category and Fund Source (1993-2008) .................... 13

Figure 4 Habitat Restoration Program Project Locations ................................................................. 28

Figure 5 Trinity River Restoration Program Map .............................................................................. 33

Figure 6 (b)(2) Use in WY 2008 in Thousand Acre-Feet (TAF) ........................................................ 41 

Figure 7 Tracy (Jones) Pumping Plant .................................................................................................. 47

Figure 8 Rock Slough Fish Screen (Proposed) ................................................................................ 50

Figure 9 Red Bluff Diversion Dam .................................................................................................... 54

Figure 10 Spawning Returns, Winter-Run Chinook, Sacramento River (1967-2006) ........................ 55 

Figure 11 Coleman Fish Hatchery ...................................................................................................... 57 

Figure 12 Gravel Injection and Channel Restoration Sites................................................................. 60 

Figure 13 Fall-Run Chinook Salmon Escapement, Clear Creek (2007) ............................................. 61 

Figure 14 Adult Spring-Run Chinook Salmon Population, Clear Creek (2001-2008) ........................ 61 

Figure 15 Juvenile Fall-Run Chinook Salmon Produced/Adult Female, ........................................... 61

 Clear Creek (1998-2007)

Figure 16 Clear Creek Channel Restoration Project Phases ............................................................. 62

Figure 17 Recent projects sites in the Sacramento, American, and Stanislaus rivers ....................... 64

Figure 18 Sacramento River project completed after adding 8,300 tons of gravel ............................ 65

Figure 19 Spawning locations (dots) within gravel injection sites on the Stanislaus River ................ 65

Figure 20 American River Upper Sailor Bar (Pre-Project) ................................................................. 66

Figure 21 American River Upper Sailor Bar (Post-Project) ............................................................... 66

Figure 22 Estimated Total Natural Chinook Production, Central Valley (1992-2007) ......................... 71

Figure 23 Estimated Abundance of 15-year-old White Sturgeon in San Pablo ................................. 72

 Bay and Suisun Bay, 1993-2005

Figure 24 Estimated Abundance of Adult Green Sturgeon in San Pablo Bay and ............................ 72

 Suisun Bay, 1993-2005

Figure 25 Estimated abundance of adult striped bass in the Sacramento-San Joaquin .................. 73

 River Delta, Sacramento River downstream from the town of Colusa, and 

 portion of the San Joaquin River downstream from the town of Mossdale, 1992-2005

Figure 26 Midwater trawl index for YOY American shad in the Sacramento-San ............................. 73

 Joaquin River Delta and San Pablo and Suisun Bays, 1992-2007

Figure 27 Glenn-Colusa Irrigation District Pumping Plant ................................................................. 77

Figure 28 CVPIA Fish Screens Constructed (1992-2008) .................................................................. 81 

Figure 29 Central Valley Refuges Receiving CVPIA Water Supplies ................................................. 85

Figure 30 Land Retirement Program Sites ......................................................................................... 99
TABLE OF CONTENTS iii 

List of Tables

Table 1 FY 2008 Funding Obligations by Provision ........................................................................ 12

Table 2 AFRP Fish Production Estimates in All Central Valley Streams (1992-2007) .................... 25 

Table 3 Chinook salmon AFRP production, in Battle, Butte and Clear creeks, and .......................... 25

Table 4 Acres of Habitat Protected & Restored per Year (1996-2008) for the ............................... 27

 Habitat Restoration Program

Table 5 FY 2008 Projects Funded by the Habitat Restoration Program ......................................... 30

Table 6 Annual Target Escapement, Trinity River ........................................................................... 34

Table 7 IFIM Studies Active as of 2008 ........................................................................................... 39

Table 8 Allocation vs. Use of (b)(2) Water (2001-2008) .................................................................. 42

Table 9 FY 2008 Use of (b)(2) Water ............................................................................................... 43 

Table 10 Annual (b)(3) Instream Water Acquisitions (1994-2008) .................................................... 45 

Table 11 Coleman NFH Facility Rehabilitation Phases (1991-2008) ................................................ 58

Table 12 Total Gravel Placed (1997-2008) ........................................................................................ 64 

Table 13 CAMP Recommended Monitoring Elements by Watershed .............................................. 74

Table 14 AFSP Projects and cfs Screened, Central Valley (1992-2008) .......................................... 79

Table 15 Refuge Water Type and Mandated Target .......................................................................... 87

Table 16 Water Allocations by Refuge from 1989 Reports ............................................................... 87

Table 17 Level 2 and Incremental Level 4 Water Deliveries by Water Year (2002-2008) ................. 89

Table 18 Cumulative Completed Construction Actions by Year (1997-2008) ................................... 91

Table 19 Ecosystem and Water Systems Operations Models (1996-2008)...................................... 96

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

 Island Sites (1992-2008) ................................................................................................... 100

EXECUTIVE SUMMARY 1

Since 1992, Reclamation and the Service have worked 

cooperatively to implement the Central Valley Project 

Improvement Act (CVPIA or Act), 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. 

The CVPIA program managers convened a series 

of meetings in Fiscal Year (FY) 2008 to discuss the 

effectiveness of past actions and to identify priority 

watersheds and opportunities for coordinated actions 

that will maximize the effectiveness of program dollars. 

The outcome of these discussions will form the basis 

of a long-term implementation plan that will guide the 

program over the next 10 years. The CVPIA program 

is also conducting independent reviews for the fi sheries 

program and the refuges water supply program. The 

independent review panels will provide programmatic 

recommendations to improve effectiveness and 

effi ciency of the programs; these recommendations will 

be considered as the program develops the long-term 

plan.

For FY 2008, $59.1 million was appropriated in the 

Restoration Fund. Payments in to the Restoration Fund 

were $52.9 million. Of the $52.9 million, $1.8 million 

was received on September 30, 2008, and was not 

available for execution in FY 2008. This, in conjunction 

with the drought and delta pumping restrictions, 

produced a budget shortfall total of $8 million. $52.8 

million was obligated from a combination of the 

Restoration Fund and Water and Related Resources 

account; approximately $41.4 million was obligated 

from the Restoration Fund and approximately $11.4 

I. Executive Summary

million was obligated from the Water and Related 

Resources account. Obligations in the Restoration Fund 

were offset by large recoveries in the Anadromous 

Fish Screen Program (AFSP) and Refuge Water Supply 

Program. The majority of these recoveries were not 

reobligated in FY 2008, but carried over into the next 

fi scal year. In FY 2009, an additional $4.4 million will 

be requested in restoration payments to make up the 

difference in 3407(d) offsets of FY 2008. To date, a total 

of $1.013 billion has been obligated to CVPIA since its 

implementation.

The enormity and complexity of the Central Valley 

ecosystem requires a comprehensive approach with 

Spring-run Chinook salmon in Butte Creek
2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

participation at all levels. The program must also 

contend with recent events such as drought and court 

ordered delta pumping restrictions. 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

Progress Towards Goals

The following paragraphs summarize progress toward 

the broad goals of the CVPIA program - anadromous 

fi sh doubling goal; habitat restoration; and refuge water 

supply:

Anadromous Fish Doubling Goal

As of 2007, the average natural production for all 

races of Chinook salmon is 477,337, or approximately 

48 percent of the doubling target. These numbers 

are the most recent numbers that have been through 

the Quality Assurance/Quality Control (QA/QC) 

process from the California Department of Fish and 

Game (DFG) Grand Tab. Updates and revisions are 

posted throughout the year on the Anadromous Fish 

Restoration Program (AFRP) website 

(www.delta.dfg.ca.gov/afrp/). 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 either nearly met or exceeded. 

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 AFRP 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 protected and 

restored nearly 100,000 acres since program inception, 

while the Land Retirement Program (LRP) has retired 

more than half of the 15,000 acres targeted as part of 

the pilot project. Of the 8,916 acres retired, the Land 

Retirement Program has restored more than 5,000 

acres towards sustainable uplands habitat. 

Refuge Water Supply

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. Purchasing 

permanent or long-term water, rather than spot market 

White-faced lbis
EXECUTIVE SUMMARY 3

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.

2008 ACCOMPLISHMENTS

The following section summarizes the specifi c FY 

2008 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 FY 

2008 activities included fl oodplain restoration on 

the Sacramento River National Wildlife Refuge 

(NWR), increasing spawning gravel on the 

Mokelumne River, and funding the permitting 

and environmental documentation for the Iron 

Canyon Fish Ladder on Big Chico Creek [(b)(1)]

• In water year 2008, which was critically dry, 

600,000 acre-feet of (b)(2) water was available for 

fi sh actions; the 600,000 acre-feet was managed 

for fi sh, wildlife and habitat restoration purposes 

[(b)(2)]

• The Water Acquisition Program acquired 106,490 

acre-feet of water (53 percent of the 200,000 acrefeet 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 and maintain fl ows on Central Valley 

Project (CVP) streams to minimize losses of 

anadromous fi sh due to fl ow fl uctuations

• The Clear Creek Restoration Program 

successfully met fl ow objectives related to 

controlling water temperature during critical 

seasons. Gravel was added at Whiskeytown Dam 

(1,000 tons), Placer Road Bridge (3,000 tons), 

Phase 3A (1,500 tons), and Phase 2A (3,000 tons) 

to increase spawning habitat [(b)(12)]

• The Spawning and Rearing Habitat Restoration 

Program purchased and placed approximately 

8,300 tons of gravel in the Sacramento River; 

mapped Chinook redds on added gravel on the 

Stanislaus River; and permitted for and placed 

7,000 tons of spawning gravel at Sailor Bar on the 

American River [(b)(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 (14 

actions have been completed as of 2008). FY 

2008 activities included continuing research and 

pilot studies for improved debris and predator 

management, collecting water quality data at the 

entrance to the Delta Mendota Canal (DMC), and 

beginning construction of a new onsite research 

building [(b)(4)]

• The Contra Costa Canal Pumping Plant program 

continued to conduct fi sh monitoring; consulted 

under ESA and the Coordination Act with the 

U.S. Fish and Wildlife Service (Service) on the 

Los Vaqueros Biological Opinion (BO) as it 

relates to the environmental commitment of the 

Rock Slough Fish Screen; continued discussions 

with the Service for operation beyond the year 

2008 in the absence of a screening facility; and 

continued to negotiate appropriate mitigation to 

the Service for the Sacramento-San Joaquin Delta 

Pelagic Organism Decline effort [(b)(5)]

• The Red Bluff Diversion Dam program 

implemented operational changes in 2007 to 

avoid further impacts to green sturgeon holding 

below the dam; no green sturgeon fatalities were 

observed in 2008. A Record of Decision was 

signed July 16, 2008, following completion of 

Endangered Species Act (ESA) consultation on 

the planned construction of the proposed new 

pumping plant; the plant will increase pumping 

capacity fourfold, providing a more reliable water 

supply [(b)(10)]

• The Head of Old River Barrier program installed 

a seasonal, temporary rock barrier at the head of 

Old River and continued additional planning and 

environmental compliance work on the permanent 

operable fi sh gate [(b)(15)]

• The Glenn-Colusa Irrigation District Program 

is 100 percent complete for related testing and 

monitoring for the project. The completed facility 

screens up to 105,000 acre-feet of fi rm annual 

water supply to 20,000 acres of Sacramento NWR 

lands. In 2008, the program completed hydraulic 
4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

testing and a set of underwater observations of 

predator distributions [(b)(20)]

• The AFSP completed construction on the 

Reclamation District (RD) 108 Poundstone 

Pumping Plant Fish Screen Project in Sutter 

County; this project consolidated three existing 

unscreened diversions into a new screened 

300 cubic feet per second (cfs) diversion on the 

Sacramento River. The program also initiated a 

four-year screening and monitoring program on 

the Sacramento River which includes collection 

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

[(b)(21)]

• The Trinity River Restoration Program released 

fl ows of 647,000 acre-feet, completed construction 

of eight channel rehabilitation sites associated 

with the Lewiston-Dark Gulch Site Rehabilitation 

Project, and placed 14,300 cubic yards of gravel 

[(b)(1) ”other” and (b)(23)]

Refuges and Waterfowl

• In 2008, the Refuge Water Supply Program 

(RWSP) delivered 400,362 acre-feet of Level 

2 and 37,066 acre-feet of Incremental Level 4 

water. The program also negotiated a fourth 

amendment to extend the groundwater pumping 

reimbursement agreement with the DFG to 

supplement Level 2 water at Gray Lodge Wildlife 

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

and (5)]

• Major construction and preliminary testing of 

the Phase I, East Bear Creek Pumping Plant and 

Pipeline at the San Luis NWR was completed in 

2008. 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 [(d)(5)]

Other Fish and Wildlife

• The Habitat Restoration Program protected an 

additional 1,787 acres of new habitat and restored 

1,908 acres of habitat. To date, the program has 

protected approximately 93,000 acres and restored 

approximately 7,400 acres [(b)(1) ”other”] 

• The San Joaquin River Comprehensive Plan 

Program made progress on the development 

of specifi c operational guidelines for releasing 

Restoration Flows and the framework for a 

Recovered Water Account and made progress on 

the development of a Fisheries Management Plan 

[(c)(1)]

• In 2008, the Land Retirement Program restored 

320 acres of former agricultural lands and 

eliminated the production of 3,500 acre-feet of 

poor quality agricultural drainage [3408(h)]

Studies, Investigations, and Modeling

• The Modifi ed CVP Operations program 

reoperated the system multiple times to provide 

benefi ts to anadromous fi sh on Clear Creek 

without impacting other CVP obligations or 

authorized purposes and also completed draft 

reports 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 on the Yuba River [(b)(1)(B)]

• The Comprehensive Assessment and Monitoring 

Program (CAMP) completed an annual report 

that synthesizes and analyzes anadromous fi sh 

monitoring data collected between 1992 and 

2007 on 21 watersheds; funded a cooperative 

agreement to develop statistical and structural 

design recommendations for a comprehensive 

database to document changes in the abundance 

of juvenile Chinook salmon in the Central Valley; 

and launched a program to develop watershedspecifi c documents that describe the relationship 

between restoration activities and the production 

of adult and juvenile Chinook salmon [(b)(16)]

• The Ecosystem and Water Systems Operations 

Models program currently operates the integrated 

CVP/State Water Project (SWP) model and 

seven other models – two more are currently 

under development. Reclamation and Service 

modelers continued the development and 

application of ecosystem models to evaluate the 

effects of reservoir operations and river fl ows 

on anadromous fi sh and riparian habitats on the 

Sacramento River. These activities included the 

use of several existing models including CalSim, 

Upper Sacramento River Water Quality Model 

(USRWQM) and Riparian Habitat Establishment 

Model (RHEM) [3406(g)]
INTRODUCTION 5

For the past 16 years, the CVPIA has guided the 

implementation of projects supporting the protection, 

restoration and enhancement of fi sh and wildlife 

associated with the 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 $1.013 billion 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 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 state’s economy. The CVPIA has afforded 

the Department of the Interior (DOI or Interior) a prime 

opportunity to help restore conditions favorable for fi sh 

and wildlife in the Central Valley, while providing for 

continuation of its rich agricultural heritage and service to 

municipal and industrial users throughout the state.

This Annual Report summarizes the actions taken by 

the Bureau of Reclamation (Reclamation) and Service 

personnel, working with other federal agencies, the State 

of California, and numerous partners and stakeholders 

during fi scal year FY 2008 (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. In some instances, 

FY 2008 accomplishments were completed with funds 

that were obligated in prior years.

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.

II. Introduction

FY 2008

Funding Obligation

$41.4 million (Restoration Fund)

$11.4 million (Water and Related Resources)

Total

$52.8 million

Sunset at Kern National Wildlife Refuge
6 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

BACKGROUND

The Central Valley Project’s Role in California’s Water Resources

For 73 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 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 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 

much so that the courts have intervened to ensure 

that adequate fresh water enters these ecosystems. 

Compliance with the 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 changed greatly 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 CVPIA. 

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 

CVP. 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 CVP’s operational fl exibility

(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 longterm 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, 
INTRODUCTION 7

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

Sacramento

San Francisco

Los Angeles

Figure 1. Central Valley Project System
8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 CVPIA 

provisions were implemented beginning in 1993, most 

were not initiated until after the ROD was signed 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.

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 on a three-year rolling average basis 

(adjusted for infl ation) in Restoration and Mitigation 

Payments from the CVP water and power users. A 

maximum of $50 million (adjusted for infl ation) in 

annual appropriations from the Restoration Fund is 

allowed in any year under the 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 AFRP, 

Dedicated Yield, and 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 Klamath River’s largest tributary, 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 AFRP (AFRP Restoration 

Plan). Actions contained within the AFRP Restoration 
INTRODUCTION 9

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 Program, 

(b)(17) Anderson-Cottonwood Irrigation District 

Diversion Dam, (b)(20) Glenn-Colusa Irrigation District 

Program, and (b)(21) AFSP; restoration activities such 

as (b)(12) Clear Creek Restoration Program and (b)(13) 

Spawning and Rearing Habitat Restoration 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) Ecosystem and 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 

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 in the Refuges sections 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 the CVP’s 

construction and operation, and the 3408(h) LRP, which 

purchases and retires land from agricultural production 

to improve water quality and provide for terrestrial 

habitat restoration.

FUNDING FOR ACTIVE 

PROVISIONS 

While there were no cost estimates associated with the 

CVPIA in 1992, Congress has provided substantial 

annual appropriations of Restoration Funds and Water 

and Related Resources funds. As of 2008, a total of 

$1.013 billion has been obligated to CVPIA since its 

implementation in 1993 (Figure 3). For FY 2008, $59.1 

million was appropriated in the Restoration Fund. 

Payments into the Restoration Fund were $52.9 million. 

Of the $52.9 million, $1.8 million was received on 

September 30, 2008, and was not available for execution 

in FY 2008. This, in conjunction with the drought and 

delta pumping restrictions, produced a budget shortfall 

total of $8 million. $52.8 million was obligated from 

a combination of the Restoration Fund and Water 

and Related Resources account; approximately $41.4 

million was obligated from the Restoration Fund, and 

approximately $11.4 million was obligated from the 

Water and Related Resources account. Obligations in 

the Restoration Fund were offset by large recoveries in 

the AFSP and RWSP. The majority of these recoveries 

were not reobligated in FY 2008, but carried over into 

the next fi scal year. In FY 2009, an additional $4.4 

million will be requested in restoration payments to 

make up the difference in 3407(d) offsets of FY 2008.

Several CVPIA provisions are now complete and/or 

otherwise not funded in the FY 2008 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)
10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

• 3406 (b)(17) Anderson-Cottonwood Irrigation 

District 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 were eligible to receive 

appropriations to support FY 2008 program activities. 

Table 1 lists each active provision and the amount of 

funding provided.

Figure 2. Central Valley Refuges Receiving CVPIA Water Supplies
INTRODUCTION 11

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 CVP’s ongoing operations.

Contract Renewals

Since the passage of CVPIA, Reclamation has 

completed interim and long-term contract renewals 

for the various CVP divisions and units. To date, 

Reclamation has executed 130 long-term renewal 

contracts with Sacramento River Water Right Settlement 

contractors; 95 long-term renewal contracts with 

contractors from the Tehama-Colusa, Delta-Mendota 

Canal, and Friant divisions; and 21 interim-renewal 

contracts with Cross Valley, San Luis, and other 

Delta-Mendota contractors. There are currently 15 

Sacramento River Water Right Settlement contractors 

that elected not to renew and two pending renewal. 

The eight Cross Valley contracts are currently 

conducting long-term renewal negotiations; Reclamation 

and the San Luis Unit contractors have completed 

negotiations for their long-term renewal contract, 

and are awaiting execution pending completion and 

acceptance of the Operations Criteria and Plan (OCAP) 

which is currently undergoing fi nal environmental 

consultations with the Fish and Wildlife Service and 

the National Oceanic and Atmospheric Administration 

(NOAA) Fisheries.

Upon completion and acceptance of OCAP, Reclamation 

will offer to enter into long-term negotiations with the 

eight remaining contractors whose contracts do not 

expire until between 2010 and 2022. It is anticipated 

that the OCAP will be completed in summer 2009, and 

long-term contract renewals can be fully completed by 

the beginning of water year 2011.

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.

As of mid-December 2008, Reclamation has approved 

the transfer of CVP water in the following categories for 

the 2008 water year:

• 328,187 acre-feet of CVP agricultural water was 

approved for agricultural purposes

• 1,200 acre-feet of CVP agricultural water was 

approved for municipal and industrial purposes

• 2,600 acre-feet of CVP municipal and industrial 

water was approved for agricultural purposes

• 3,250 acre-feet of CVP municipal and industrial 

water was approved for municipal and industrial 

purposes

• 26,425 acre-feet of CVP agricultural water 

approved to Reclamation’s Refuge Water 

Acquisition Program

RECENT DEVELOPMENTS 

The CVPIA Program faces several challenges. First, 

is the scope and overall complexity of the project 

which is a long-term effort to restore the Central 

Valley ecosystem that involves federal, state, local and 

tribal entities, as well as public and private interests. 

Compounding the program complexity are recent 

events on the regional, national, and international scale, 

such as court ordered delta pumping restrictions, west 

coast salmon fi shery closure, and climate change. The 

drought in California continued in Water Year (WY) 

2008 (October 1 – September 30) which was classifi ed 

as a critically-dry year. These conditions impact water 

deliveries for agriculture and municipal and industrial 

users as well as affecting the availability and cost 

of water to purchase on the open market for refuge 

water deliveries. Several recent developments will 

have a direct effect on the implementation of CVPIA 

actions, including the Pelagic Organism Decline 

(POD), litigation of BO, the OCAP BO’s, the Offi ce of 

Management and Budget (OMB) Program Assessment 

Rating Tool (PART) process, outcome of independent 
12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Table 1. FY 2008 Funding Obligations by Provision

Provision

Water & Related 

Funds* Restoration Funds* State*

3406(b)(1) Anadromous Fish Restoration 

Program

 0 $2,957,000

3406(b)(1) “other” - Habitat Restoration 

Program

 0 $1,346,000

3406(b)(1) “other - Trinity River Restoration 

Program

$ 5,176,000 $1,647,000

3406(b)(1)(B) Modifi ed CVP Operations 0 $509,000

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

Project Yield

 0 $817,000

3406(b)(3) Water Acquisition Program - 

Instream Water 

(includes 3408 (g) [Vernalis 

Adaptive Management Plan 

(VAMP)])

 0 $3,750,000

 $2,964,000

 $6,782,000

(VAMP)

Level 4

$1,332,000

3406(b)(4) Tracy (Jones) Pumping Plant 

Program

 $1,815,000 0 ($14,970)

3406(b)(5) Contra Costa Canal Pumping Plant $55,000 0 ($2,500)

3406(b)(9) Flow Fluctuations 0 $31,000

3406(b)(10) Red Bluff Diversion Dam $5,636,000 0 ($2,000)

3406(b)(11) Coleman National Fish Hatchery $826 0

3406(b)(12) Clear Creek Restoration Program $99,000 $611,000

3406(b)(13) Spawning and Rearing Habitat 

Restoration Program

 0 $883,000 $878

3406(b)(15) Head of Old River Barrier 0 0

3406(b)(16) Comprehensive Assessment and 

Monitoring Program

 0 $291,000

3406(b)(19) Reservoir Storage 0 0

3406(b)(20) Glenn-Colusa Irrigation District 

Program

 $71,000 0

3406(b)(21) Anadromous Fish Screen Program ($3,144,000) ($1,310,000) ($178,433)

3406(b)(23) Trinity River Restoration Program $1,685,000 $3,000

3406(c)(1) San Joaquin River Comprehensive 

Plan

 0 $7,733,000

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

 0 $10,264,000

 $137,000

(construction)

(wheeling)

3406(d)(5) San Joaquin Basin Action Plan 

Lands Program

 $42,000 $941,000

3406(g) Ecosystem and Water Systems 

Operations Models

 $735 $402,000

3408(h) Land Retirement Program 0 $630,000

TOTAL FUNDING OBLIGATED $11,436,561 $41,388,000 $1,134,975

* Rounded for presentation purposes

Amounts in ( ) = credit amount
INTRODUCTION 13

Figure 3. Total CVPIA Obligations by Action Category and Fund Source (1993-2008)

reviews, and the development of a long-term plan for 

CVPIA implementation.

Pelagic Organism Decline

Abundance indices calculated by the Interagency 

Ecological Program (IEP) through 2008 show continued 

marked declines in four pelagic fi shes in the upper 

San Francisco Estuary (the delta and Suisun Bay). 

These fi shes include two native species, delta smelt 

and longfi n smelt, and two non-native species, age-0 

striped bass, and threadfi n shad. Delta smelt has 

recently been uplisted to endangered under the state 

ESA and remains listed as threatened by the federal 

ESA. The state has also recently listed longfi n smelt 

as threatened. The abundance of both delta smelt and 

threadfi n shad dropped to new record lows in 2008, 

while the abundance of longfi n smelt and age-0 striped 

bass remained very low.

Several CVPIA provisions including (b)(4) Tracy (Jones) 

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

Pumping Plant, and (b)(15) Head of Old River Barrier 

have been affected as diverters reduced pumping in 

response to the decline in delta smelt. The decline has 

also heightened the need to improve fi sh protection in 

the south delta and at the intake to Contra Costa Canal 

to further minimize the loss of these pelagic fi sh species 

due to exports. Revised federal ESA BO’s are being 

issued or have been issued by the Service and National 

Marine Fisheries Service (NMFS) that specifi cally 

address the need for additional fi sh protection due to 

exports.

Litigation of Biological Opinions

On December 14, 2007 (FY 2008), a federal judge (U.S. 

District Court Judge Oliver Wanger) ordered state and 

federal water project managers to reduce the amount 

34%

Other Fish & Wildlife $114,184,792

Administrative $56,962

Anadromous Fish - Habitat Modification $258,837,104

Anadromous Fish - Structures $339,714,637

Refuges & Waterfowl $252,429,922

Studies/Investigations/Modeling $35,441,923

Monitoring $12,489,185

Action Category

Total obligations: $1,013,154,525

26%

25%

11%

3%

1%

0.01%

29%

1%

7%

63%

Fund Source

Total obligations: $1,013,154,525

0.10%

Water & Related Resources Fund $295,943,649

CVPIA Restoration Fund $636,255,357

State Cost Share $73,429,186

Bay-Delta Fund $6,526,333

Donation $1,000,000
14 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 

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.

Operations Criteria and Plan Biological 

Opinions 

The 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, 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 OCAP’s potential 

effects 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 

new OCAP Service BO was issued in December 2008. 

The court has directed NMFS to issue its BO March 

2009, but like the Service, the new BO will be issued 

June 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 revised OCAP BO issuance to ensure that 

future program activities comply with OCAP mitigation 

requirements. 

Program Assessment Rating Tool 

The OMB 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 extended 

into FY 2008. The major actions include completing 

program independent reviews by a panel of experts and 

completing a long-term plan to guide CVPIA actions 

over the next 10 years (2010 through 2019); these reports 

are due in FY 2008 and FY 2009. 

Independent Review 

An independent review is a process through which 

a panel of experts evaluates a program and makes 

recommendations to improve its effectiveness. Each 

panel is comprised of independent professionals and 

academics with expertise in relevant areas. The overall 

purpose of these independent reviews is to provide 

programmatic recommendations and guidance to the 

CVPIA program to improve effectiveness and effi ciency, 

understand how to organize the program, and maximize 

restoration progress in a time of limited resources.

Reclamation and the Service are sponsoring two 

independent reviews: one to evaluate the fi sheries 

program and one to evaluate the RWSP. The reviews 

are funded by the Bureau of Reclamation budget for the 

CVPIA Program. Reclamation and the Service decided 

to conduct the evaluations on the program elements 

related to fi sh restoration and refuges as these two 

elements represent a substantial portion of the annual 

Restoration Fund expenditures.
INTRODUCTION 15

The purpose of the fi sheries independent review is to 

seek recommendations on how to implement the CVPIA 

fi sheries programs more effi ciently and effectively 

to reach the fi sh doubling goals described in Section 

3406(b)(1) of the Act. The fi sheries independent review 

convened preparatory panel sessions where program 

managers presented the scientifi c, program management, 

and other background information used to support the 

fi shery restoration plans and activities. The six-member 

panel convened privately to review the program and 

develop draft recommendations. The preparatory 

panel sessions and the panel deliberation sessions were 

conducted May 2008 through October 2008. The fi nal 

report from the fi sheries independent review panel was 

submitted to Reclamation and the Service on December 

16, 2008. The independent review panel provided 

valuable recommendations for improving the CVPIA 

fi sh restoration program, including recommendations 

to improve the program’s science-based framework, 

reorganize the program structure and management, 

improve program implementation by making full use of 

CVPIA authorities, and improve collaboration. 

The purpose of the refuges independent review is 

to seek recommendations on how to implement the 

CVPIA RWSP more effi ciently and effectively to 

reach the goals of providing full Level 4 water. The 

independent refuges evaluation is focused on the Central 

Valley refuges goals described in Sections 3406(d)

(1 – 5) of the Act. The refuges independent review 

convened preparatory panel sessions in February 2009 

to present the scientifi c, program management, and 

other background information used to support the 

refuges restoration plans and activities. The fi vemember panel will convene privately to review the 

program and develop draft recommendations. The panel 

deliberation sessions will be conducted between March 

2009 and May 2009. The fi nal report from the refuges 

independent review panel will be produced by June 30, 

2009.

Reclamation and the Service will consider the 

recommendations of the panels as they develop the 

Long-term Plan that will guide program priorities and 

activities over the next 10 years.

Long-term Plan 

The CVPIA Program is developing a Long-term Plan 

(LTP) that will provide focus and direction for the 

CVPIA Program for the coming 10 years (2010-2019); 

it will provide the foundation for planning, budgeting, 

performance management, and accountability processes. 

The LTP focuses on providing objectives and strategies 

for the following areas: Fisheries, Refuges, Other 

Resources, and CVPIA Program Management.

The LTP will be developed through internal processes 

using independent review panel recommendations. The 

internal process includes participation by Reclamation 

and Service program managers, biologists, and 

engineers that are involved in the day-to-day work of 

Program implementation; these meetings will culminate 

with the development of prioritized activities in each 

of the resource areas. As stated above, independent 

review panels are reviewing Program accomplishments 

and preparing recommendations for Fisheries and 

Refuges regarding priorities and effi ciencies to 

maximize progress towards the restoration goals. As 

the independent review panels complete their work, the 

recommendations will be considered for incorporation 

into the priorities and strategies in the LTP. 

With priorities in place, the next steps will be to 

establish benchmarks for measuring progress in 

restoring the ecosystem. The Program needs to develop 

longer term or interim outcome oriented goals that 

will serve as a blueprint of how the restoration will 

occur. This process will come full circle as the Program 

evaluates these performance data to develop future 

LTP’s.

LOOKING AHEAD

Quantifying 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.
16 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 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 CVPIA’s 

long-term goals. 
2008 PROGRAM ACTIVITIES AND ACCOMPLISHMENTS 17 

III. 2008 Program Activities and 

Accomplishments

This section summarizes FY 2008 program 

accomplishments and funding obligations for each active 

provision. Wherever possible, each section includes 

quantifi ed goals and targets to measure progress towards 

the Act’s implementation. The following program 

activities are discussed in this section:

• 3406 (b)(1) AFRP

• 3406 (b)(1) “other” Habitat Restoration Program

• 3406 (b)(1) “other” & (b)(23) Trinity River 

Restoration Program

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

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

Yield

• 3406 (b)(3) & (g) Water Acquisition Program – 

Instream Water

• 3406 (b)(4) Tracy (Jones) Pumping Plant Program

• 3406 (b)(5) Contra Costa Canal Pumping Plant

• 3406 (b)(9) & (b)(19) Flow Fluctuations and 

Reservoir Storage

• 3406 (b)(10) Red Bluff Diversion Dam

• 3406 (b)(11) Coleman National Fish Hatchery

• 3406 (b)(12) Clear Creek Restoration Program

• 3406 (b)(13) Spawning and Rearing Habitat 

Restoration Program

• 3406 (b)(15) Head of Old River Barrier

• 3406 (b)(16) CAMP

• 3406 (b)(20) Glenn-Colusa Irrigation District 

Program

• 3406 (b)(21) AFSP 

• 3406 (c)(1) San Joaquin River Comprehensive Plan

• 3406 (b)(3) & (d)(2) Water Acquisition Program – 

Refuge Water

• 3406 (d)(5) Refuge Facilities Construction and San 

Joaquin Basin Action Plan Lands Programs

• 3406 (d)(1), (2) & (5) Refuge Water Conveyance 

(Wheeling)

• 3406 (g) Ecosystem and Water Systems Operations 

Models

• 3408 (h) LRP

Hocker Flat Rehabilitation Site, Trinity River

Tule Elk, San Luis National Wildlife Refuge
18 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 Act’s language, Interior developed 

the AFRP as the overarching program to address 

anadromous fish doubling in the Central Valley. The 

CVPIA goal is to at least double the natural production 

of anadromous fish on a long-term, sustainable basis. 

The specific system-wide doubling targets for natural 

production of anadromous fish are categorized by fish 

run/species, per year:

Anadromous Fish Restoration 

Program Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$2,957,000 (Restoration Fund)

Accomplishments

• The program conducted several activities to 

improve habitat for anadromous fi sh by providing 

fl ows and improved physical habitat including: 

fl oodplain restoration on the Sacramento River 

NWR; increasing spawning gravel on the 

Mokelumne River; channel reconstruction and 

gravel augmentation in the Cosumnes River; 

and funding proposals for fl oodplain and sidechannel enhancement projects on the Stanislaus, 

Tuolumne, and Merced rivers

• The program worked to improve survival rates 

of juveniles at diversions by funding a feasibility 

study to construct a bypass for out-migrating 

salmonids at two screened diversions in Antelope 

Creek

• The program continued to improve the opportunity 

for adult fi sh to reach their spawning habitats 

by funding the permitting and environmental 

documentation for the Iron Canyon Fish Ladder 

on Big Chico Creek and the Lower Calaveras 

River Anadromous Fish Barrier Project 

• The program conducted several activities 

to collect fi sh data to facilitate evaluation of 

restoration actions by conducting an experimental 

gravel injection at Englebright Dam and video 

weir monitoring for Bear, Cottonwood, and Cow 

creeks 
3406(b)(1) 19

Measuring Success

Key actions and evaluations undertaken or completed 

in 2008 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

Deer Creek – In order to address Deer Creek’s Final 

Restoration Plan Actions 1 and 3, critical riffl es 

identifi ed by the California Department of Fish and 

Game (DFG) on Deer Creek were assessed to identify 

a range of critical fl ows needed for upstream passage 

of adult salmonids. In addition to the fl ow analysis, 

recommendations of potential solutions to correct 

passage problems at the critical riffl es were also 

identifi ed. AFRP provided FY 2004 funds for this 

project and reports are available on the AFRP website 

(www.delta.dfg.ca.gov/afrp/).

Sacramento River – On the mainstem Sacramento 

River, phase II of the La Barranca unit of the 

Sacramento River NWR was funded to remove the 116 

acre orchard, prepare the site and write a vegetation 

restoration plan (Final Restoration Plan Action 9 and 

Evaluations 1,5). The restoration plan will develop two 

options for planting designs based on the hydrologic, 

geologic, edaphic (soil), biologic (baseline special 

status species, migratory birds, plants and vegetation) 

and historic conditions at the site, and outline the 

implementation strategies for the site. The plan will 

include a fully irrigated restoration design option and 

a dry land restoration option for native grasses, forbs, 

and valley oak acorns. The plan will specify targeted 

wildlife species that will benefi t from the future 

restoration of the site and identify the numbers of plants 

and seeds required for the full restoration of the site. 

Mokelumne River – During FY 2008, funds were 

provided to purchase spawning gravel materials used 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. This gravel replenishment project 

is in partnership with the East Bay Municipal Utility 

District (EBMUD) and addresses Actions 2 and 7 of 

the Final Restoration Plan for this watershed. Gravel 

was purchased and placed in channel, and the enhanced 

habitat continues to provide opportunity for increased 

• 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 Act’s passage, the AFRP developed 

a series of planning reports that culminated in the 

Final AFRP Restoration Plan (Plan) in 2001. As 

acknowledged in the CVPIA 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:

1) Improve habitat for all life stages of anadromous 

fish through provision of flows 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 fish to reach 

their spawning habitats in a timely manner 

4) Collect fish population, health, and habitat data to 

facilitate restoration actions evaluation

5) Integrate habitat restoration efforts with harvest 

and hatchery management 

6) Involve partners in implementing and evaluating 

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 scientific 

core group composed of experts from state and federal 

agencies, private industry, and academia with specific 

knowledge of anadromous fish species in Central Valley 

rivers and streams. It lists potential factors or stressors 

that may limit natural production of anadromous fish 

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

natural production of Chinook salmon and steelhead. 

This project area is rigorously characterized each year 

for spawning use, bed form and function, and provides a 

foundation project for the Spawning Habitat Integrated 

Rehabilitation Approach (SHIRA) as conducted by the 

University of California (UC) Davis. Final reports are 

available on the AFRP website. 

Cosumnes River – Permitting and fi nal phases of project 

planning were completed in time to begin the channel 

reconstruction and gravel stockpiling and placement 

for the Cosumnes Passage and Habitat Improvement 

Project (Final Restoration Plan Action 6, Evaluation 2). 

The project will improve adult salmonid passage and 

enhance habitat by reconfi guring the channel and adding 

spawning gravel for both immediate use and subsequent 

year recruitment resulting in overall improved survival 

and reproduction for Chinook salmon. This project 

will reconfi gure the channel bed to provide more and 

higher quality spawning gravel as well as place gravel 

upstream for continual gravel recruitment with fl ow 

events over the course of several years. Gravel has been 

stockpiled on site and is readily available for placement 

over consecutive years. AFRP is collaborating with 

Fishery Foundation of California, Omochumne-Hartnell 

Water District, Robertson-Bryan, Inc., and DFG and has 

leveraged $232,500 in cost share and in-kind services to 

date for this effort.

Stanislaus River – Two new fl oodplain and side-channel 

enhancement projects were funded (Honolulu Bar and 

Lancaster Road) to increase juvenile salmonid rearing 

habitat and decrease predation (Final Restoration Plan 

Action 2). Tours of restoration sites on the river were 

provided to attendees of the Salmonid Restoration 

Federation annual meeting and to the CVPIA Fisheries 

Independent Review Panel. Community outreach 

activities were also initiated during 2008 as well as 

the development of a draft Outreach Plan and a draft 

Fisheries Restoration Plan. 

Objective 2: Improve survival rates by reducing or 

eliminating entrainment of juveniles at diversions 

Antelope Creek – Currently there are two diversions at 

Edwards Dam that are screened; however no bypass was 

constructed due to the site’s complexity. The screens 

are a fair distance down the irrigation canals. During 

dry years, irrigation starts earlier in the spring and 

juvenile salmonids get stranded in the canals. FY 2008 

funds were awarded to the Tehama County Resource 

Conservation District to conduct a feasibility study 

to determine the best solution to get out-migrating 

salmonids back into Antelope Creek. This project is a 

cooperative effort between the U.S. Fish and Wildlife 

Service (FWS), DFG, National Marine Fisheries Service 

(NMFS), Los Molinos Mutual Water Company, and the 

landowner. The feasibility study and environmental 

compliance should be complete in FY 2009.

Battle Creek – The Orwick fi sh screen improvement 

project was completed. This project was funded 

in FY 2006 by AFRP. The fi sh screen will prevent 

entrainment of juvenile salmonids and straying of adult 

Chinook salmon at Battle Creek (Final Restoration Plan 

Action 4). 

Butte Creek – Review of the draft report for the Five 

Points/Avis Channel Fish Passage and Entrainment 

Assessment was completed in June 2008. Comments 

on the draft report for the Butte Slough/Sutter Bypass 

Fish Entrainment Study are under way. Both of these 

evaluation projects were funded with FY 2006 AFRP 

funds and address Evaluations 1-9 for Butte Creek in 

the Final Restoration Plan. Preliminary results for 

both reports show that implementing the potential 

Cosumnes River Habitat Improvement Project - Before 

(Top) and After (Bottom)
3406(b)(1) 21

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 an 

estimated 8 miles of quality spring-run Chinook salmon 

habitat (Final Restoration Plan Action 2). The final 

phases (phases 3 and 4) are expected to be completed in 

2009.

Butte Creek – Final Restoration Plan Action 18 was 

completed during this reporting period with the 

construction of the White Mallard Dam and fi sh ladder. 

The White Mallard Dam project was funded in FY 2003 

by AFRP to facilitate passage and reduce entrainment 

at this facility, benefi ting salmonid survival and 

production. 

Cow Creek – Clover Creek, tributary to Cow Creek, 

has an agricultural dam and exposed siphon, both of 

which are complete barriers. AFRP provided FY 2007 

funds to the Western Shasta Resource Conservation 

District for the Millville Diversion Environmental 

Compliance Project to complete all environmental 

compliance documents necessary to obtain permits to 

modify the diversion dam and siphon for fi sh passage, as 

designed. This project will open up 10 miles of historic 

habitat to fall-run Chinook and Central Valley steelhead 

trout, a federally-listed Threatened species. This is 

an interagency effort with California Department of 

Water Resources (DWR), DFG, CALFED Ecosystem 

Restoration Program (ERP), and the Natural Resource 

Conservation Service (NRCS). The DWR Fish Passage 

Improvement Program is providing initial engineering 

design. CALFED ERP is providing implementation 

funds. The project consists of removing the dam 

and siphon, installing agricultural grade pumps, and 

constructing a solar array to offset pumping costs. The 

environmental compliance effort is ongoing and should 

be completed in FY 2009. This project is but one of 

many steps required to address Cow Creek’s Final 

Restoration Plan Action 3.

Calaveras River – The fi nal report for the Lower 

Calaveras River Chinook Salmon and Steelhead 

Limiting Factors Analysis was completed and will 

be available on the AFRP website. This project, 

working with the Fishery Foundation of California, 

was conducted to fi ll existing information gaps to 

assist in managing the Calaveras River to support 

anadromous salmonid populations. In particular, this 

project quantifi ed fl ows required to pass fi sh upstream of 

actions (screens) would reduce entrainment and 

contribute to increases in juvenile-to-adult survival of 

Butte Creek spring-run Chinook salmon, though the 

individual benefi ts of the potential actions on population 

performance appears to be small due to other diversions 

in the system that still need to be addressed.

Objective 3: Improve the opportunity for adult fish to 

reach their spawning habitats in a timely manner 

Antelope Creek – Antelope Creek is an eastside 

tributary to the upper Sacramento River in Tehama 

County. The DFG has operated a fi sh ladder at the 

Antelope Creek Edwards Dam since 1981. The ladder 

and dam had been damaged on a number of occasions, 

most recently in the January 1997 fl ood event, and it did 

not adequately pass upstream migrating anadromous 

salmonids. A DFG fi sh passage engineer designed 

an improved ladder, and the DFG Red Bluff Screen 

Shop constructed the ladder in the fall of 2007, with 

AFRP FY 2005 funds. DFG monitors adult spring 

run Chinook escapement in the watershed and data is 

reported in the DFG Grantab that is available on the 

AFRP website. This was a cooperative effort with FWS, 

DFG, NMFS, the Los Molinos Mutual Water Company, 

and the landowner.

Antelope Creek Edwards Dam Fish Ladder – Before 

(Top) and After (Bottom)
22 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

current barriers. A hydrologic model of the system was 

developed to assist with future fl ow recommendations 

and identify the required fl ows needed for successful 

immigration and out-migration of Chinook salmon 

and steelhead. This analysis was designed to provide 

additional information by evaluating various channel 

bed and substrate confi gurations occurring in the 

migration corridor and to quantify the amount of 

fl ow required to provide upstream passage in the Old 

Calaveras River channel and Mormon Slough/Diverting 

Canal from tidewater to Bellota Weir. Fish passage of 

adult and juvenile salmonids at existing diversion dams 

and barriers (Action 3) and evaluating instream fl ow 

(Evaluation 2) are activities in the Final Restoration Plan 

that are currently being addressed by this project.

Objective 4: Collect fish population, health and habitat 

data to facilitate evaluation of restoration actions 

Bear, Cottonwood, and Cow creeks – The video weir 

monitoring project for Bear, Cottonwood, and Cow 

creeks was a cooperative project funded by AFRP 

and the Sport Fish Restoration Act. The work was 

completed through a cooperative effort of FWS, DFG, 

Western Shasta Resource Conservation District, and the 

Cottonwood Creek Watershed Group. Although 2007 

was a record low fall-run Chinook escapement year, the 

information provided by these efforts was scientifi cally 

valid and economically effi cient. Continued monitoring 

at these sites will be benefi cial to guide AFRP 

restoration efforts. In addition, the information is 

valuable for DFG’s Grandtab of Central Valley total 

Chinook returns. The fi nal reports for all three creeks 

are available on the AFRP website.

Mill Creek – Determining escapement in Mill Creek 

requires an ability to accurately count adult spring-run 

Chinook salmon during the spring high fl ow season, in 

turbid waters and without handling the fi sh or potentially 

impeding upstream migration using weirs or traps. To 

address these sampling conditions, a fi xed-location 

hydroacoustic array using split-beam (DTx) and a 

Dual-frequency Identifi cation Sonar (DIDSON) was 

chosen for evaluation. The AFRP provided FY 2007 

funding to implement a second year of a pilot study 

to assess the feasibility of counting adult Chinook 

salmon escapement in Mill Creek using fi xed-location 

hydroacoustic techniques. Sampling occurred between 

April 15, 2008, and June 27, 2008. The fi nal report for 

this project is forthcoming.

Yuba River – On the Yuba River a baseline hydrologic, 

geomorphic, and ecologic research project was 

conducted between Englebright Dam and the Highway 

20 bridge in support of management of anadromous fi sh 

populations (Final Restoration Plan Evaluation 4). Much 

of this work involved ongoing analyses of 2D models. 

A completely new activity conducted in FY 2008 was 

an experimental gravel injection at Englebright Dam. 

Grain size measurements were made of pre-existing 

angular gravel and gravel-sized shotrock in this reach. 

However, no signifi cant fl ows occurred on the river this 

winter; so, limited gravel fate monitoring took place in 

FY 2008. Also, at the Garcia Gravel Pit reference site 

an effort was made to locate any painted or magnetized 

tracer stones placed before the 2006 New Years fl ood, 

but none were found. The fi nal report is available on the 

AFRP website. 

A peer-reviewed journal article was also published in 

the journal Geomorphology- Moir, H. J. and Pasternack, 

G. B. 2008. Relationships between mesoscale 

morphological units, stream hydraulics, and Chinook 

salmon (Oncorhynchus tshawytscha) spawning habitat 

on the Lower Yuba River, California. Geomorphology. 

doi:10.1016/j.geomorph.2008.02.001. Also, a journal 

manuscript evaluating the “elasticity” of salmon 

selection of substrates at this site as a function of local 

fl ow velocity was written and submitted to the Canadian 

Journal of Fisheries and Aquatic Sciences for peer 

review. The manuscript focuses on a comparison of 

substrate availability with utilization and shows that 

salmon actually spawn on the Yuba River in a wider 

range of substrates than previously thought, depending 

on the local velocity. Three additional journal 

manuscripts or reports about the hydrogeomorphic 

response of different sites in the Yuba River to the May 

2005 fl ood and 2006 New Years fl ood were drafted, and 

a manuscript also was drafted on the role of valley width 

in controlling riffl e location and persistence over the last 

century. 

A topographic/bathymetric map of the Englebright Dam 

reach was also developed. This map will be valuable 

for evaluating the fate of gravel injected at the base of 

the dam. A map of the geomorphic units throughout 

Timbuctoo Bend was made, and photographic images 

of Parks Bar obtained from a blimp were compiled 

to produce a mosaic image of the glide-riffl e-islandchute complex, including locations of salmon redds. 

All these activities were part of the SHIRA-based 
3406(b)(1) 23

river analysis and fi eld based manipulative sediment 

transport experiments for the Lower Yuba River and 

funded entirely with FY 2003-FY 2007 AFRP funds at 

a total project cost of $299,998. Partners for this project 

include Pacifi c Gas & Electric (PG&E), Yuba County 

Water Agency, UC Davis, South Yuba River Citizens 

League, DFG, United States Army Corp of Engineers 

(USCOE), and NMFS.

Two VAKI Riverwatcher fi sh counting systems that 

were installed in 2005 continued operation in 2008 and 

were used to count the number of fi sh passing upstream 

of the North and South fi sh ladders at the Daguerre Point 

Dam as a demonstration project. This data was collected 

to better understand the timing, abundance, population 

trends, and response to changing fl ow and temperature 

conditions of adult spring and fall-run Chinook salmon, 

and Central Valley steelhead in the Lower Yuba River 

(Final Restoration Plan Action 7). This information will 

help improve management of these species in the Lower 

Yuba River, including actions such as salmonid habitat 

restoration projects and providing appropriate in-stream 

fl ow regimes. AFRP purchased these monitoring 

systems in FY 2005; the California Department of Fish 

and Game operates them with oversight by the South 

Yuba River Citizens League.

Calaveras River – Data was collected on steelhead 

and fall-run Chinook salmon passage and stranding 

to provide information to improve flow management 

and inform prioritization and evaluation of passage 

impediments. These assessments were done in 

partnership with the Fishery Foundation of California 

and address the Final Restoration Plan Action 3 and 

Evaluation 2 for this watershed.

Stanislaus River – FY 2008 accomplishments included 

the collection of both juvenile and adult passage data 

via rotary screw trapping (juveniles) and a fi sh counting 

weir (adults) operated in partnership with Tri-Dam 

(Final Restoration Plan Action 1). The rotary screw 

trapping was funded with FY 2007 (b)(16) CAMP and 

(b)(2) Dedicated Project Yield funds. These studies 

assist with evaluating benefi ts resulting from habitat 

restoration actions, and summary reports are available in 

the AFRP website. 

Merced River – Rotary screw trapping to track juvenile 

salmonid outmigration was conducted in FY 2008. The 

data will be used to assist in evaluating the benefi ts of 

habitat restoration actions. The project used FY 2007 

CAMP funds and FWS staff to offset a budget shortfall 

that would have prevented the project from occurring. 

A summary report for this activity is available on the 

AFRP website.

Objective 5: Integrate habitat restoration efforts with 

harvest and hatchery management

Mokelumne River – Conducted analyses of fall-run 

Chinook salmon otoliths to determine the ratio of 

hatchery to wild fi sh. Data will be used to develop new 

methodologies that can measure hatchery contribution 

and derive more accurate estimates of natural 

production. The pilot study was funded with FY 2007 

funds and will conclude in 2009. 

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 Fishery Foundation of California 

to form various diverse partnerships with multiple 

stakeholders that are interested in improving salmonid 

habitat and fi sh passage in the Cosumnes and Lower 

Calaveras rivers. AFRP is also collaborating with 

the Friends of the Tuolumne to restore fl oodplain and 

riparian habitats in the Tuolumne River. These efforts 

can potentially leverage about $4 million in additional 

funding that can be used to address restoration activities 

in these watersheds. Since 2001, AFRP has been 

successful in leveraging more than $12 million in the 

Yuba River, $4.8 million in the Merced River, and more 

than $9.8 million in the Tuolumne River through various 

funding sources such as CALFED ERP, DWR 4-Pumps, 

Tuolumne Irrigation District (ID), Merced ID, Yuba 

County Water Agency, and NRCS for anadromous fi sh 

restoration activities. These are just some examples of 

the many partners and programs AFRP collaborates 

with in many of its restoration projects.

Natural Production Doubling 

In addition to assessing progress by implementing 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 
24 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

anadromous fish, the program’s restoration actions 

and evaluations have focused on Chinook salmon, 

as, in general, AFRP restoration activities benefit all 

anadromous fi sh. Table 2 summarizes the status of 

Central Valley-wide natural production of Chinook 

salmon, steelhead, and sturgeon in relation to the 

doubling goals and the baseline period. Reporting 

on PART, the average natural production of Central 

Valley-wide Chinook salmon in the doubling period 

(1992-2007) is currently 477,337 and below the 2009 

target of 625,000 total anadromous fi sh. These numbers 

are the most recent numbers that have been through the 

QA/QC process from the DFG Grand Tab. Updates and 

revisions are posted throughout the year on the AFRP 

website. The natural production average has been 

decreasing in the last couple of years due to low adult 

escapement estimates in 2006 and 2007 resulting from 

poor ocean returns.

The Final Restoration Plan also provides doubling goals 

for specific 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 sufficient investment has been made in flow and 

passage (Butte and Clear creeks) and habitat restoration 

(Clear Creek). Average Chinook salmon production for 

the period of 1992-2007 has exceeded the doubling goal 

target on Battle, Butte, and Clear creeks, and has been 

met on the Mokelumne River, as seen in Table 3. 

In order to more accurately assess natural production, 

AFRP is demonstrating new escapement counting 

technologies, Alaskan weir (Stanislaus River), Vakiinfra-red counting systems (Stanislaus and Yuba rivers), 

video weir monitoring (Bear, Cottonwood, and Cow 

creeks), and hydroacoustics (Mill Creek). The AFRP 

is also supporting a study which should better define 

the percentage of hatchery-origin fish in escapement 

by looking at sulfur isotope (S32:S34) ratios in otoliths 

taken from natural spawning Chinook salmon from 

the Mokelumne River and comparing these to ratios 

observed in hatchery produced stocks. This information 

will provide methods to derive more accurate estimates 

of natural production. 
3406(b)(1) 25

Table 2. AFRP Fish Production Estimates in All Central Valley Streams (1992-2007)

1 Only streams and rivers with complete salmon production data sets (1992-2007) are shown.

2 Annual 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].”

3 Baseline 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.

4 Grand 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 2007.

5 The percent of increased natural production over baseline for each watershed was calculated by subtracting baseline 

natural production (1967-1991) from natural production (1992-2007) and dividing the result by baseline natural production 

(1967-1991) and multiplying by 100.

6 Data is through 2005.

Chinook Salmon 

Species and 

Watershed1

AFRP Annual 

Doubling 

Goals2

Average 

Baselines

(1967-1991)3

Average Natural 

Production 

(1992-2007)4

Average % Natural 

Production Difference 

From Baseline5

All Chinook runs, all 

Central Valley streams

990,000 497,240 477,337 -4

Fall-run, all Central 

Valley streams

750,000 374,217 432,096 15

Winter-run, all Central 

Valley streams

110,000 54,417 8,086 -85

Spring-run, all Central 

Valley streams

 68,000 34,425 16,383 -52

Late fall-run, all Central 

Valley streams

 68,000 34,182 20,772 -39

Steelhead, all Central 

Valley streams

 13,000 6,574 1,127 -83

Green sturgeon, all 

Central Valley streams

 1,966 983 2,2466 128

White sturgeon, all 

Central Valley streams

 11,000 5,571 5,5076 -1

Table 3. Chinook salmon AFRP production, in Battle, Butte and Clear creeks, and Mokelumne River (1992-

2007)

Chinook Salmon 

Species and 

Watershed1

AFRP Annual 

Doubling 

Goals2

Average 

Baselines 

(1967-1991)3

Average Natural 

Production 

(1992-2007)4

Average % Natural 

Production Difference 

From Baseline5

Battle Creek, fall-run 10,000 5,012 20,935 318

Battle Creek, late fallrun 550 273 681 149

Butte Creek, fall-run 1,500 763 3,141 312

Butte Creek, spring-run 2,000 1,017 11,382 1,019

Clear Creek, fall-run 7,100 3,574 11,946 234

Mokelumne River, fallrun 9,300 4,679 9,079 94
26 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 identified adverse 

environmental impacts of the CVP not specifically 

enumerated in this section.”

The Habitat Restoration Program (HRP), under section 

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

species and their habitats that were adversely impacted 

by operation and construction of the CVP and are not 

specifically addressed in CVPIA’s Fish and Wildlife 

Restoration section. Habitat loss and fragmentation due 

to urbanization and agriculture conversion occurred 

on an estimated 2.7 million acres as a result of CVP 

construction and operation (Interim Contract Renewals, 

February 1995). 

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 significant; targeted restoration of 

CVP-impacted habitats where actions will markedly 

improve conditions; research to facilitate species 

recovery; and public outreach, education, planning, 

and management. These actions support the program’s 

output goal of contributing to restoring the 2.7 million 

acres impacted by the CVP construction and operation. 

To help direct conservation actions into high-priority 

areas and assist applicants in developing competitive 

proposals, the HRP developed a Geographic 

Information System (GIS)-based “Project Area Map” 

Sacramento

San Francisco

Los Angeles

Habitat Restoration Program 

FY 2008

Funding Obligation

$1,346,000 (Restoration Fund)

Accomplishments

• Protected 1,787 acres of habitat

• Restored 1,908 acres of habitat

• Funded seven projects that focused on high 

priority species and habitats impacted by the CVP

Snake Marsh Pilot Restoration - Before (Top) and 

After (Bottom). The new pond replaced the existing 

invasive yellow water primrose in a 1-acre area.
3406(b)(1) “other” 27

that defines the program’s geographic focus area. The 

HRP also developed a “High Priority Species List” that 

defines species identified in various recovery plans (both 

resources are available on the HRP Web site: http://

www.usbr.gov/mp/cvpcp).

High Priority Species and Habitats

To date, the HRP has allocated about $24 million to fund 

about 90 projects supporting the recovery of federally 

listed 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 butterfly 

• Valley elderberry longhorn beetle 

• Riparian brush rabbit 

• Riparian woodrat 

• Lange’s metalmark butterfly 

• Vernal pools species (plants and invertebrates) 

• Gabbro soil plants

Figure 4 maps the HRP project locations from 1996-

2008

Since 1996, HRP funds have been used to acquire 

(protect) more than 93,000 acres and restore more than 

7,300 acres, for a total of more than 100,000 acres; this 

contributes towards one of the HRP’s performance 

goals. The 100,000 acres is almost 4 percent of the 2.7 

million acres restoration goal to restore habitat impacted 

by the CVP. As shown in table 4, the bulk of the acreage 

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

Newman and Romero Ranches) project. 

Acres of habitat that have been protected and restored 

can also be calculated based on the percentage of 

funding from the HRP and from contributing partners. 

Of the 100,000 acres, almost 11,000 acres have been 

Table 4. Acres of Habitat Protected & Restored per Year (1996-2008) for the Habitat Restoration Program

Year

Total Acres of Habitat Protected and 

Restored for Projects that the HRP 

Contributed Towards with Partners

Acres of Habitat Protected and 

Restored Based on Percentage the HRP 

Contributed Towards the Total Acres

Habitat Protection 

(acres protected via 

fee title acquisition 

and conservation 

easements)

Habitat Restoration 

(acres restored)

Habitat Protection 

(acres protected via 

fee title acquisition 

and conservation 

easements)

Habitat Restoration 

(acres restored)

1996 3,018 0 362 0

1997 284 617 149 485

1998 74,146 0 4,399 0

1999 1,180 0 554 0

2000 1,426 206 366 78

2001 2,831 0 529 0

2002 2,211 0 122 0

2003 2,866 0 459 0

2004 719 432 129 106

2005 755 3,370 5 2,352

2006 193 731 21 364

2007 1,603 122 16 48

2008 1,787 1,908 1 446

SUBTOTAL 93,019 7,386 7,112 3,879

TOTAL 100,405 10,991

GOAL/TARGET 2.7 million
28 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Figure 4. Habitat Restoration Program Project Locations
3406(b)(1) “other” 29

Since 1996, 67 surveys and studies and 12 planning, 

management, and outreach actions have been funded by 

the HRP. These actions also contribute to the overall 

goal of species recovery. 

Measuring Success

In fi scal year 2008, HRP funds ($1,346,000) were 

used to fund a balanced set of actions that focused on 

high-priority species and habitats impacted by the CVP 

(Table 5). Progress reports are available for all projects 

and may be requested from the HRP program managers. 

Table 5 summarizes the FY 2008 projects.

California Red-legged Frog – A Species that has 

Benefi tted from Restoring Spivey Pond

acquired or restored with contributions solely from 

the HRP (Table 4). This represents about 11 percent 

of funding contributed by the HRP towards important 

protection and restoration actions. Partners have 

contributed about 89 percent of the funding. By joining 

with partners, the HRP program is able to expand its 

ability to meet program goals. 

Acquisition only covers the purchase of the land; 

further effort is required to restore the desired habitat. 

Habitats protected and restored include vernal pool, 

riparian, alkali scrub, foothill chaparral, valley-foothill 

hardwood and grassland (Table 5). Post-monitoring 

certain project sites has revealed high rates of success 

with restoration activities. For example, riparian 

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

experienced an approximately 80 percent survival 

rate. Another example is the new pond construction 

downstream of known California red-legged frog 

populations at Spivey Pond in El Dorado County which 

helped expand populations of this species. The HRP 

partnered with the American River Conservancy and 

the Bureau of Land Management to help purchase 

Spivey Pond. The pond supports one of the few known 

populations of California red-legged frogs. In 2005, 

the HRP funded construction of a pond downstream 

of Spivey Pond, where occurrence of the species has 

recently been recorded. 

Acquiring and Restoring Red-Legged Frog Habitat at 

Spivey Pond - Before (Top) and After (Bottom)
30 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Table 5. FY 2008 Projects Funded by the Habitat Restoration Program

Project Status Signifi cance

National Audubon Society - Fee 

title acquisition of 1,787-acres of 

Charter Ranch in Yolo County, and 

development of Best Management 

Practices for managing 587acres 

of rice land for listed species, 

shorebirds, and waterfowl. HRP 

funded $258,220.

On-going

Property appraisal approved by 

DOI in October 2008. Audubon 

in continued negotiations with 

landowner. Acquisition will result in 

permanent protection of giant garter 

snake habitat in the Central Valley.

Supports species and habitat 

protection: Charter Ranch is 

contiguous with other restored 

wetland, riparian, and upland 

habitats, and provides the 

opportunity to protect and restore 

lands for listed species including 

valley elderberry longhorn beetle, 

giant garter snake, and Swainson’s 

hawk.

River Partners - Riparian habitat 

restoration for endangered species 

on 223 acres at the Arambel Unit 

of the San Joaquin River NWR in 

Stanislaus County. Restoration of 

high quality riparian habitat will occur 

over a 3-year period. HRP funded 

$200,000.

On-going

Restoration plan approved in 

October 2008. Site preparation and 

planting begun on fi eld A-1. Cultural 

resources survey needed on fi eld 

A-2; restoration activities to begin 

in spring 2009. Restoration to be 

completed by spring 2010.

Supports species and habitat 

protection: Restoration will continue 

efforts already begun at the site, and 

provide benefi ts for several listed 

species, including riparian brush 

rabbit, riparian woodrat, least Bell’s 

vireo, and valley elderberry longhorn 

beetle, as well as dozens of other 

species as the site matures.

Service, Sacramento Field 

Offi ce - Restoration of 22.5 acres 

of riparian habitat for special status 

species at Vino Farms along 0.6 

mile of the lower Mokelumne River 

in San Joaquin County. HRP funded 

$186,114.

On-going

Interagency agreement signed 

in September 2008. Landowner 

coordination complete; preliminary 

site preparation to begin in October/ 

November 2008. Restoration to be 

completed by spring 2010.

Supports species and habitat 

protection: The Mokelumne River 

watershed is under threat of losing 

its remaining native riparian habitats 

to vineyards, orchards and other 

agricultural uses and residential 

development. This project will 

benefi t riparian-dependent species 

including valley elderberry longhorn 

beetle, least Bell’s vireo, western 

yellow-billed cuckoo, willow 

fl ycatcher, and Swainson’s hawk.

Bureau of Land Management 

(BLM) - Fuels Management at the 

Cameron Park Unit of the Pine Hill 

Preserve will decrease the number, 

size, and intensity of wildfi res at 

the 454-acre Cameron Park Unit of 

the Pine Hill Preserve in El Dorado 

County, which will improve habitat 

for seven rare plant species. HRP 

funded $70,000.

On-going

Under three different contractors, 

BLM has removed shrubs and 

trimmed trees in about 6 acres along 

the urban-wildland-interface at the 

Cameron Park unit of the Pine Hill 

Preserve. The six acres include 

fi ve different sites where fuels have 

been reduced along more than 0.5 

mile of the Preserve boundaries and 

up to 100 feet into Preserve lands. 

BLM will continue to improve habitat 

for rare plants; monitor response of 

habitat and rare plants; implement 

fuels load reduction techniques; 

provide fi re defensible space around 

structures adjacent to the Preserve; 

and prepare and submit Progress 

Reports, Draft Report, and a Final 

Report to the HRP (due 2010). 

Supports species and habitat 

protection: The project will improve 

habitat for seven rare plant species 

(Stebbin’s morning glory, Pine Hill 

ceanothus, El Dorado bedstraw, 

Layne’s butterweed, El Dorado muleears, Bisbee-Peak rush-rose, and 

Red Hills soaproot); contribute to the 

safety of Cameron Park and Shingle 

Springs communities by providing 

defensible space around structures 

adjacent to the Preserve; and set up 

a program to monitor fuels reduction 

effects on rare plants by developing a 

Monitoring Plan.
3406(b)(1) “other” 31

Table 5. FY 2008 Projects Funded by the Habitat Restoration Program (Continued)

Project Status Signifi cance

Service, Antioch Dunes NWR - 

Continuation of captive propagation 

of the Lange’s metalmark butterfl y 

at Moorpark College in the Exotic 

Animal Training and Management 

Program facility, and continuation 

of restoration of dune habitat for the 

butterfl y, Contra Costa wallfl ower, 

and Antioch Dunes evening 

primrose at Antioch Dunes NWR in 

Contra Costa County. HRP funded 

$112,069.

On-going

Captive propagation is going very 

well. Over 115 adult butterfl ies were 

counted at Antioch Dunes NWR in 

2008. Additionally, more than 

8 acres of dunes habitat have been 

cleared and planted with native 

buckwheat. The NWR submitted 

another proposal to the HRP 

for FY 2009 to continue funding 

the propagation and restoration 

activities. Funding decisions were 

made in April 2009.

Supports habitat and species 

protection: The Lange’s metalmark 

butterfl y is on the verge of extinction 

and is found only at Antioch Dunes 

NWR; restoration of dunes habitat 

will enhance native buckwheat host 

plant survivability and recovery of 

the wallfl ower and primrose, two 

federally endangered species.

Carol Witham, Sole Proprietor 

Consultant - Status surveys for 

seven federally listed vernal pool 

grasses and Chamaesyce hooveri 

(Hoover’s spurge) in the Sacramento 

and San Joaquin Valleys. The 

last comprehensive survey for 

these species was conducted in 

1986-1987. These new surveys 

will contribute towards determining 

the current status of all California 

Natural Diversity Database (CNDDB) 

occurrences in the Central Valley 

for these important species. HRP 

funded $147,800.

On-going

The consultant began work on the 

project in 2008. Data was collected 

at two sites in Sacramento County, 

which helped test the methodology 

to be used, especially the data 

dictionary for the Global Positioning 

System (GPS). The dictionary was 

revised to make the data entry 

order more logical, based upon 

the sequence of fi eld steps that 

are most effi cient. The consultant 

is continuing to work on the GIS 

database; aerial photography 

analysis of presumed extirpated 

sites; and landowner contacts and 

access issues. Field work may need 

to be delayed if drought continues. 

Supports species and habitat 

protection: Project is urgent in terms 

of gathering information in order 

to make better-informed decisions 

related to prioritizing recovery 

actions for the species. The project 

specifi cally targets eight listed plant 

species: Hoover’s spurge, Colusa 

grass, SJ Valley orcutt grass, Hairy 

orcutt grass, Slender orcutt grass, 

Sacramento orcutt grass, Greene’s 

tuctoria, and Solano grass.

Bureau of Land Management, 

Folsom Field Offi ce – Research 

and restoration of priority wetlands 

for giant garter snake at Snake 

Marsh located at the Cosumnes 

River Preserve in Sacramento 

County. This project will contribute 

towards determining how rapidly 

changing hydrology and invasive 

water primrose on and adjacent to 

the Cosumnes River Preserve are 

impacting the giant garter snake 

population located on the Badger 

Creek sub-unit of the Preserve. HRP 

funded $142,225.

On-going

Project tasks have begun. Traps 

were placed to determine baseline 

giant garter snake presence, 

distribution, and relative density 

prior to and after conducting the pilot 

restoration project. A 1-acre pond 

was excavated to create open-water 

habitat for the giant garter snake. 

Excavated material (invasive water 

primrose and soil) was dumped 

within a designated stockpiling area, 

leveled, and contoured to create 

a new 1-2-acre high-ground area 

that could eventually be used by 

burrowing rodents, thereby creating 

additional aestivation and, possibly, 

over-wintering habitat for the giant 

garter snake. Giant garter snakes 

will continue to be monitored during 

the 2009 active season to evaluate 

the species’ immediate response 

to the pilot restoration effort, and 

formulate a long-term management 

strategy for the marsh.

Supports species and habitat 

protection: The project is urgent 

because the Snake Marsh population 

represents the most genetically 

distinct population of giant garter 

snakes known to date. A signifi cant 

portion of Snake Marsh goes 

completely dry in summer as a 

result of the primrose and altered 

hydrology of the marsh and creek. 

It is anticipated that if primrose 

continues to grow and expand into 

the last remaining limits of Snake 

Marsh and Badger Creek, the habitat 

will no longer support the snake or 

prey species for the snake, and thus 

cause the likelihood of localized 

extinction.
32 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

CVPIA Section 3406(b)(1) “other” and 

3406(b)(23)

“...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”; 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 program uses 

Sacramento

San Francisco

Los Angeles

Weaverville

Redding

Trinity River Restoration 

Program

FY 2008

Funding Obligation

$1,647,000 - 3406(b)(1) “other” - (Restoration Fund)

$5,176,000 - 3406(b)(1) “other” - (Water & Related)

$3,000 - 3406(b)(23) - (Restoration Fund)

$1,685,000 - 3406(b)(23) - (Water & Related)

Accomplishments

• Released fl ows of 647,000 acre-feet

• Completed construction of eight channel 

rehabilitation sites associated with the LewistonDark Gulch Site Rehabilitation Project

• Placed 14,300 cubic yards of gravel: 12,000 

cubic yards in the mainstem of the Trinity River 

and 2,300 cubic yards directly injected to the river 

by mechanical conveyor 

• Completed or initiated nine priority watershed 

projects that prevented between 30,000 and 

60,000 cubic yards of sediment from being 

produced in upland source areas and its potential 

delivery to the Trinity River

Conveyer Gravel Injection in Lewiston during the May 

2008 High Flow Event
3406(b)(1) “other” and 3406(b)(23) 33

two authorities: CVPIA section 3406 (b)(1) “other” for 

river restoration and CVPIA section 3406 (b)(23) for 

delivering fl ows. 

The Trinity River Mainstem Fishery Restoration 

Environmental Impact Report/Environmental Impact 

Statement (EIR/EIS) and its accompanying Record 

of Decision (ROD) were 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.

Since 2001, the CVPIA Restoration Fund has 

allocated $11.1 million to the TRRP. The program has 

implemented 16 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. Signifi cant accomplishments made by TRRP 

include:

• Construction of 16 channel rehabilitation projects 

(Hocker Flat, four sites near Canyon Creek, three 

sites near Indian Creek, and eight sites in the 

Lewiston area)

• Construction of three replacement bridges and 

upgrade of an approach road/culvert allowing full 

implementation of the ROD fl ow regime

• 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 78 domestic water or sewer systems 

• Processing environmental documentation, 

regulatory permits, and engineering designs to 

allow a construction contract award for up to eight 

additional channel rehabilitation projects in 2009 

and 2010

Reclamation and TRRP partners have implemented 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 

Extremely Wet, Dry, and Normal with volumes ranging 

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

implementation of ROD releases are now possible based 

on water year type. Approximately 1.8 million acre-feet 

more water has been released to the river over the past 

eight years than would have occurred without the ROD.

Working in partnership with Native American tribes, 

other federal agencies, the State of California, Trinity 

County, and a broad cross-section of stakeholders, 

Reclamation plans and implements restoration 

activities and adaptively manages the program based on 

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 6. The 1983 EIS for 

the Trinity River Basin Fish and Wildlife Management 

Program documented the in-river spawner escapement 

goals and the Trinity River Salmon and Steelhead 

Hatchery production goals developed by DFG. The 

goals were subsequently adopted by the TRRP as 

escapement numbers. The in-river goals represent the 

Figure 5. Trinity River Restoration Program Map

Lewiston Dam

Trinity Dam

Lewiston Reservoir

Trinity River Grass Valley Creek

Trinity River Restoration Area

North Folk Trinity River North Fork Trinity River
34 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Target Trinity River Natural Adult Spawner 

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 6. Annual Target Escapement, Trinity River

total number of naturally produced adult spawners 

for the Trinity River Basin below Lewiston Dam and 

exclude fi sh caught by the fi sheries.

The output-based goals are indicated by four criteria:

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; the 

target fl ow release is between 369,000 and 815,000 acrefeet per year (varies by water year type), with potential 

peak fl ows to 11,000 cfs by 2008 and annually thereafter.

Implementing construction projects – Measured by 

progress toward completion of 47 mechanical channel 

rehabilitation projects and all necessary infrastructure 

improvements. The channel rehabilitation target is to 

complete 24 channel rehabilitation projects by the end of 

2008, with the remainder by 2012. The infrastructure 

improvements target is to complete the infrastructure 

improvements to allow fi shery fl ow releases of up to 

11,000 cfs by 2008.

Coarse sediment management – Goals for coarse 

sediment management are to increase the total quantity 

of coarse sediment stored in the Trinity River, and to 

reduce bed surface grain sizes to facilitate bed mobility 

and salmonid spawning. Progress toward these goals 

is assessed by measuring coarse sediment transport 

through a bedload sampling program, documenting the 

quantities of coarse sediment added to the river through 

rehabilitation site construction and gravel augmentation, 

and mapping of bed sediment characteristics. Specifi c 

targets are to place 7,000 cubic yards of gravel in the 

upper river per year, to verify that gravel augmentation 

volumes equal or exceed the fl ux of gravel transported 

out of the upper river, and to reduce reach-averaged 

median bed surface grain sizes to approximately 3-inch 

diameter particles. 

Watershed restoration – Watershed restoration and 

associated activities are intended to reduce the quantity 

of fi ne sediment (particles less than about 1/4 inch in 

diameter) in the Trinity River by reducing fi ne sediment 

production and delivery from tributary watersheds, and 

by increasing fi ne sediment transport rates in the Trinity 

River. Quantitative targets include achieving a long-term 

reduction in the total quantity of fi ne sediment stored 

in the Trinity River between Lewiston Dam and the 

North Fork Trinity River by at least 250,000 cubic yards, 

to reduce fi ne sediment delivery to the upper river by 

10,000 to 20,000 cubic yards per year, and to annually 

transport as much or more fi ne sediment downstream as 

is delivered to the upper river from tributary watersheds. 

Measuring Success

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. Data suggest an upward trend in 

coho salmon and steelhead run size over the last 12 

years, along with decreased prevalence of disease and 

improved egg/sperm viability of spawners of all species.

The DFG responded to increases in 2006 and 2007 

record fi sh runs in steelhead numbers by instituting 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 

and runs. The variable nature of these populations is 

demonstrated in preliminary 2008 weir counts, which 
3406(b)(1) “other” and 3406(b)(23) 35

suggests a smaller steelhead run than the past two years, 

but with a somewhat higher percentage of wild fi sh. 

Output-based Targets 

Increasing Minimum Flow Releases

Water Year 2008 was classifi ed as a normal water year 

in accordance with the ROD resulting in 647,000 acrefeet being released from the Lewiston Reservoir, which 

met the target fl ow release of between 369,000 and 

815,000 acre-feet per year. 

Implementing Construction Projects

In FY 2008, the program completed construction of 

eight channel rehabilitation sites covering a project area 

of three miles in length associated with the LewistonDark Gulch Site Rehabilitation Project. This will 

provide increased geomorphic and hydraulic complexity 

to this high priority area of the river and provide greater 

diversity of fi sh habitats, supporting a wide range of life 

stages. Completion of these eight sites in 2008 brings 

the total number of mechanical channel rehabilitation 

projects to 16, which is eight sites short of the goal of 

completing 24 sites by 2008. In addition, the TRRP 

has only enough funding to complete two sites in 

2009, which will make it diffi cult to meet the goal of 

constructing 47 sites by 2012. 

Coarse Sediment Management

In 2008, the program placed a total of 12,000 cubic 

yards of gravel in the mainstem of the Trinity River as 

part of the Lewiston-Dark Gulch channel rehabilitation 

construction contract to improve spawning and rearing 

habitat, as well as facilitate the creation of needed 

geomorphic features farther downstream. An additional 

2,300 cubic yards was directly injected to the river by 

mechanical conveyor during peak fi shery restoration 

fl ows in May 2008. In total, the program placed about 

14,300 cubic yards of coarse sediment in the river during 

2008, doubling the annual target of 7,000 cubic yards. 

This quantity greatly exceeded the quantity of coarse 

sediment transport transported out of the upper river 

in 2008, which is estimated at approximately 520 cubic 

yards.

The program has made substantial progress toward 

restoring the total quantity of coarse sediment stored in 

the upper river to pre-dam levels. A total of more than 

54,400 cubic yards of coarse sediment has been added 

to the upper river since dam closure, with about 22,300 

cubic yards of that total being placed since 2003. A 

current update of sediment budgets previously computed 

through WY 2000 that incorporates recent augmentation 

quantities and recent estimates of the coarse sediment 

loads transported downstream suggests that the total 

quantity of coarse sediment stored in the upper river is 

within about 7,000 cubic yards of pre-dam levels. 

Watershed Restoration

In 2008, TRRP completed or initiated nine priority 

watershed projects, and leveraged more than $300,000 in 

matching funds for watershed implementation. Projects 

under construction in 2008 were road upgrades in the 

Indian Creek, Browns Mountain, Little Browns Creek, 

and Union Hill areas, revegetation/soil stabilization 

projects in Grub Gulch and the Oregon/Junction Fire 

area, landowner outreach for mitigation in the Lowden 

Fire area, a culvert replacement in Union Gulch, and 

excavation of a sediment detention basin at Dark Gulch. 

Constructed Gravel Bars in the Lewiston-Dark Gulch 

Project - Before (Top) and After (Bottom)
36 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

These projects prevented between 30,000 and 60,000 

cubic yards of sediment from being produced in upland 

source areas and its potential delivery to the Trinity 

River. Ten additional projects were identifi ed and 

funded for implementation in 2009. Also in 2008, about 

10,000 cubic yards of fi ne sediment was transported 

downstream past the sediment transport sampling 

location near Douglas City.

Constructed side channel from the Indian Creek project 

in October 2007 (Top) and June 2008 (Bottom)
3406(b)(1)(B) 37

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 

Sacramento

San Francisco

Los Angeles

Modifi ed CVP Operations

FY 2008

Funding Obligation

$509,000 (Restoration Fund)

Accomplishments

• Reoperated the system multiple times to provide 

benefi ts to anadromous fi sh on Clear Creek

• Completed draft reports for spring- and fall-run 

Chinook salmon and steelhead fry and juvenile 

rearing and redd dewatering and juvenile chinook 

and steelhead stranding on the Yuba River 

• Completed monitoring for fall-run Chinook salmon 

and steelhead spawning on Clear Creek

• Completed fi nal report for fl oodplain inundation on 

the Tuolumne River
38 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 PG&E during 

development of the annual operating plan. Establishing 

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 

recommended 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 

2008, the data from this IFIM study were used to justify 

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

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 habitatbased 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, and Stanislaus 

rivers 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 

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 the 

Sacramento, American, and Merced rivers and Butte 

Creek; 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 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 

Collecting IFIM Field Data in Clear Creek
3406(b)(1)(B) 39

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, from 2001 to 2008 the Service 

added the Yuba and Tuolumne rivers and Clear and 

South Cow creeks to the priority list of rivers to be 

modeled over the next fi ve years.

Measuring Success

In FY 2008, the CVP reoperated the system multiple 

times to provide benefi ts to anadromous fi sh on Clear 

Creek without impacting other CVP obligations or 

authorized purposes. These reoperations improved 

conditions on Clear Creek without changing the total 

amount of CVP water being released. 

Since 1995, the program has completed 12 IFIM studies 

meeting the program goal to provide up to nine IFIM 

studies. Table 7 illustrates progress on the studies that 

were active in 2008. (Dates indicate completion of an 

activity.)

As shown in Table 7, the major accomplishments for 

2008 include the following:

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

juvenile rearing and completion of draft report for 

redd dewatering and juvenile Chinook and steelhead 

stranding.

Clear Creek – Completion of monitoring for fall-run 

Chinook salmon and steelhead lower reach spawning.

Tuolumne River – Completion of fi nal report for 

fl oodplain inundation as a function of fl ow.

Table 7. IFIM Studies Active as of 2008

River IFIM Modeling Project Monitoring Modeling Peer Review Final Report

Yuba Spring and fall-run Chinook 

salmon and steelhead fry and 

juvenile rearing

FY 2007 FY 2008 FY 2009 Expected 

FY 2009

Redd dewatering and juvenile 

Chinook and steelhead stranding

FY 2007 FY 2008 FY 2009 Expected 

FY 2009

Spring- and fall-run Chinook 

salmon and steelhead spawning

FY 2004 FY 2006 FY2006 Expected 

FY 2009

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

FY 2008 FY 2009 Expected 

FY 2009-10

Expected 

FY 2009-10

Juvenile spring-run Chinook 

salmon and steelhead upper 

reach rearing

FY 2007 FY 2009 Expected 

FY 2009-10

Expected 

FY 2009-10

Juvenile spring-run and fall-run 

Chinook salmon and steelhead 

lower reach rearing

FY 2009 FY 2009 Expected 

FY 2009-10

Expected 

FY 2009-10

Tuolumne Floodplain inundation as a 

function of fl ow (La Grange Dam 

to river mile 22)

N/A FY 2007 FY 2008 FY 2008
40 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 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 fish, 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 accounted as CVP releases and decreased CVP 

export pumping, relative to a hypothetical pre-CVPIA 

baseline operation. The accounting specifi cally looks at 

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 6 for location 

map). 

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

reductions and CVP reservoir release increases 

relative to a hypothetical base case of 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:

Sacramento

San Francisco

Los Angeles

Dedicated 800,000 acre-feet 

Project Yield

FY 2008

Funding Obligation

$817,000 (Restoration Fund)

Accomplishments

• Managed 600,000 acre-feet of CVP (b)(2) water 

for fi sh, wildlife and habitat restoration purposes 

• Augmented low base fl ows on the American 

River, Sacramento River, Stanislaus River, and 

Clear Creek

• Assisted in meeting WQCP requirements with 

water from the Sacramento, American, and 

Stanislaus rivers

• Used (b)(2) water in conjunction with acquired (b)

(3) water to provide pulse fl ows for adult Chinook 

migration and spawning and juvenile salmonid 

outmigration on the Stanislaus River

• Curtailed exports to assist in meeting WQCP 

delta requirements, to comply with Interim 

Remedial order (delta smelt entrainment 

concerns), and to meet VAMP export target
3406(b)(2) 41

1. Instream fl ow augmentations on CVP-controlled 

streams to protect salmon and steelhead and contribute toward meeting AFRP fl ow objectives

2. Increase releases from Goodwin Reservoir to 

help meet the 1995 Water Quality Control Plan 

(WQCP) requirements for San Joaquin River 

fl ows at Vernalis

3. Increase releases from Keswick and/or Nimbus 

reservoirs to help meet the WQCP fi sh and wildlife standards

4. Export reductions at the CVP Jones pumps to 

protect at-risk fi sh species (notably salmon, steelhead, and delta smelt) and to help meet the WQCP 

delta standards

Figure 6. (b)(2) Use in WY 2008 in Thousand AcreFeet (TAF)

Water Management 

Related to the management of (b)(2) water, the 2000 

CALFED Programmatic Record of Decision established 

an Environmental Water Account (EWA) program with 

the purpose of providing assurances to contractors and 

protection (supplemental to a hypothetical pre-EWA 

baseline level of protection) to the endangered fish in 

the Bay-Delta Estuary. Although accounted differently, 

the management of (b)(2) water is usually coordinated 

with the management of CALFED’s EWA, since the use 

of both (b)(2) and EWA often contribute concurrently 

to the CVPIA’s goal of doubling natural production 

of anadromous fish and protection of other fi sh and 

wildlife, including endangered fi sh species. However, in 

2008 there was very little EWA water to manage. 

In the 2008 water year, both the Sacramento and San 

Joaquin River Basins were classifi ed as “critically dry,” 

which resulted in reduced deliveries of CVP water to 

certain users within the CVP. For that reason, and 

consistent with Section 3406(b)(2) of the CVPIA and 

the Department of the Interior’s (Interior) May 2003 (b)

(2) Policy, total (b)(2) assets were ultimately limited to 

600,000 acre feet during the 2008 water year. Further 

complicating CVP operations during the 2008 water 

year was the issuance of an Interim Remedial Order 

on December 14, 2007 in Natural Resource Defense 

Council v. Kempthorne, 1:05-CV-1207 OWW GSA 

(E.D. Cal.), for the protection of the federally-listed delta 

smelt. 

Throughout the 2008 water year, Interior managed (b)

(2) assets consistent with the Ninth Circuit’s decision 

in Bay Inst. of San Francisco v. United States, 87 Fed. 

Appx 637 (2004), confi rming Interior’s discretion to give 

effect to the “hierarchy of purposes” in Section 3406(b)

(2), Interior’s May 9, 2003 (b)(2) Policy, and Interior’s 

December 17, 2003 (b)(2) Guidance. At the end of 

the 2008 water year, however, Judge Wanger issued a 

memorandum opinion in San Luis & Delta Mendota 

Water Authority v. Department of the Interior, 1:97-

cv-6140, 1:98-cv-5261 OWW DLB (E.D. Cal. Sept. 19, 

2008), concerning Interior’s (b)(2) accounting for the 

2004 water year.1

 Thus, Interior accounted for fi shery 

actions, including Endangered Species Act (ESA) and 

WQCP actions during the 2008 water year consistent 

with that opinion, as well as, the Ninth Circuit’s decision 

in Bay Inst. of San Francisco, Interior’s 2003 (b)(2) 

Policy, and 2003 (b)(2) Guidance.

1 In that opinion, Judge Wanger stated that the “primary 

purpose” of CVPIA Section 3406(b)(2) “includes all those 

fi sh and wildlife restoration activities specifi cally described in 

section 3406(b),” including “water dedicated to accomplish the 

anadromous fi sh doubling goal set forth in section 3406(b)(1)” 

and “water needed to accomplish any of the other specifi cally 

enumerated programs listed in section 3406(b)(2). SLDMWA, 

at 43 (underline in original). Thus, “if an action taken under 

the WQCP and/or ESA predominantly contributes to one of 

the primary purpose programs (e.g., fi sh doubling), it must be 

counted toward the 800,000 AF limit.” Id. at 48. In so doing, 

Judge Wanger recognized that there may be some “primacy” 

to section 3406(b)(1) in relation to other stated purposes of 

section 3406(b), but he did not rule on that question. Id. at 45.
42 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Monitoring and Evaluation

The (b)(2) program includes monitoring and evaluation 

to assess the effectiveness of the use of the (b)(2) water.

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.

Measuring Success 

The 800,000 acre-feet annual allocation has been fully 

utilized each water year since 2000 when the (b)(2) 

accounting began, with three notable exceptions: 

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 water year 

2008, which was critically dry, only 600,000 acre-feet of 

(b)(2) was available for fi sh actions (Table 8).

In addition to other restoration activities, the increased 

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

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.

Uses of (b)(2) water in 2008 are listed in Table 9.

Table 8. Allocation vs. Use of (b)(2) Water (2001-2008)

Use of Dedicated Water (Approximate)

Year

(b)(2) allocated 

(acre-feet)

Fisheries 

(acre-feet)

Unused* 

(acre-feet)

Banked 

(acre-feet)

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 800,000 422,000 183,000 195,000

2007 800,000 798,000

2008 600,000 600,000

* Section 3406 (b)(2)(D): If the quantity of water dedicated under this paragraph, or any portion thereof, is not needed for the purposes of this section, based on a fi nding by the Secretary, the Secretary is authorized to make such water available for other project 

purposes.
3406(b)(2) 43

Table 9. FY 2008 Use of (b)(2) Water

River Action Timeframe Results

American Augmented low base 

fl ows

December 2007 – 

April 2008

Contributed to meet AFRP fl ow objectives 

and improved instream conditions for fall-run 

Chinook and steelhead during spawning, 

incubation, rearing, and downstream migration

Assisted in meeting 

WQCP delta requirements

May 2008 Contributed to AFRP fl ow objectives in May, 

benefi tted fall-run Chinook and steelhead 

smolts, and predominantly contributed to the 

primary purpose of CVPIA Section 3406(b)(2)

Sacramento Augmented low base 

fl ows

December 2007 – 

January 2008

Contributed to AFRP fl ow objectives and 

improved instream conditions for spring-run 

Chinook fry, fall-run Chinook, late fall-run 

Chinook, and steelhead during spawning, 

incubation, and rearing periods, and assisted 

in meeting WQCP delta standards

Clear Creek Augmented low base 

fl ows throughout water 

year 2008

December 2007 – 

September 2008

Contributed to AFRP fl ow objectives and 

improved instream conditions for fall-run 

Chinook, spring-run Chinook, and steelhead 

during spawning, incubation, rearing, and 

downstream migration

Stanislaus (b)(2) water used in 

conjunction with acquired 

(b)(3) water to provide 

pulse fl ow for adult 

Chinook migration and 

spawning

October 2007 Provided fall attraction fl ow for adult Chinook 

migration and spawning

Augmented low base 

fl ows

November 2007 - 

January 2008

Contributed to AFRP fl ow objectives and 

improved instream conditions for fall-run 

Chinook and steelhead during spawning, 

incubation, and rearing periods

(b)(2) water used in 

conjunction with acquired 

(b)(3) water to provide 

pulse in spring 2008 

for juvenile salmonid 

outmigration (pursuant to 

VAMP)

April – May 2008 Improved survival of salmon smolts emigrating 

down the San Joaquin River and improved 

habitat conditions in the central and southern 

delta for numerous aquatic species

CVP Jones 

Pumping Plant

Export curtailments to 

assist in meeting WQCP 

delta requirements

November 2007 – 

January 2008 and 

March 2008

Protected estuarine habitat for anadromous 

fi shes and other estuarine-dependent species

Export curtailment related 

to delta Cross channel 

gate closure

December 2007 Benefi tted winter-run and spring-run Chinook 

salmon outmigrants and other species

Export curtailments 

to comply with Interim 

Remedial order (delta 

smelt entrainment 

concerns)

December 2007 - 

March 2008 and 

June 2008

Provided increased protection for delta smelt 

(ESA Threatened) and addressed entrainment 

at the CVP pumps

Export curtailment to 

meet VAMP export target

May 2008 Benefi tted San Joaquin Basin fall-run Chinook 

outmigration, contributed to AFRP fl ow 

objectives, and predominantly contributed to 

the primary purpose of CVPIA Section 

3406(b)(2)
44 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 fish 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 modifications 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) is charged 

to acquire water to supplement the 800,000 acre-feet 

of dedicated CVP yield for fisheries. The target for 

instream 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 CVPIAdesignated refuges and wildlife management areas. 

WAP activities for refuge water acquisitions are 

discussed in Section (d)(2) Water Acquisition ProgramRefuge 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 flows for fall-, winter- and 

spring-run Chinook salmon and steelhead

Water Acquisition Program – 

Instream Water Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$3,750,000 – Instream Water (Restoration Fund)

$2,964,000 – VAMP (Restoration Fund)

$1,332,000 (State)

Accomplishments

• Acquired 106,490 acre-feet for San Joaquin River 

Agreement/Vernalis Adaptive Management Plan
3406(b)(3) and 3406(g) 45

To date as noted below, very little water, and none 

in Water Year 2008, has been acquired for instream 

purposes north of the Delta.

Managing Flows Pursuant to San Joaquin 

River Agreement and Vernalis Adaptive 

Management Plan

In support of the second objective, WAP acquires 

instream flows 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 fishery flows 

on the Stanislaus, Tuolumne, Merced, and lower San 

Joaquin rivers.

VAMP is a scientifically-based fishery management plan 

that determines the relationships between flows, exports, 

and other factors on fish survival in the SacramentoSan Joaquin Delta. The SJRA and VAMP govern the 

operation of water in the lower San Joaquin River to 

ensure that pulse flows and other flows are provided 

to support restoration of anadromous fish in the river. 

Specifically, the spring flows assist in the outmigration 

of juvenile salmonids and can help meet water quality 

requirements. Fall flows 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 

fishery flows on the Stanislaus, Tuolumne, Merced and 

lower San Joaquin rivers. The increased flows primarily 

benefit Chinook salmon, which can account for more 

than 70 percent of the statewide commercial harvest, as 

well as numerous resident and anadromous fish species.

Measuring Success 

Since 2001, the program has acquired an average of 

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

target almost exclusively on the lower San Joaquin. The 

actual volume of water acquired each year fluctuates 

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 fixed by the SJRA.

As noted above, Reclamation has not been able to 

acquire the full 200,000 acre-feet of target flows, due to 

a lack of willing sellers as well as the high cost of water 

on the open market. In addition to the water identified 

in the SJRA, on occasion WAP has been able to acquire 

instream flows in the Sacramento Valley by entering 

into one-year transfers with local water agencies that 

have transferable water to sell. 

In 2008, the program acquired 106,490 acre-feet for 

SJRA/VAMP. Table 10 shows the volume of water 

purchased for the years 1994 through 2008. 

Table 10. Annual (b)(3) Instream Water Acquisitions 

(1994-2008)

Year

Annual Water Acquisitions in Acre-Feet 

(Percentage of 200,000 Acre-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%)

2008 106,490 (53%)
46 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

CVPIA Section 3406(b)(4)

“Develop and implement a program to mitigate for 

fishery impacts associated with operations of the 

Tracy Pumping Plant. Such program shall include, 

but is not limited to improvement or replacement 

of the fish screens and fish 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 program’s primary 

purpose is to mitigate for South Delta fi shery impacts 

at the federal JPP. The program’s current primary 

objective 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 presentday operations and effi ciencies for TFCF, as well as 

assisting the Department of Water Resources (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 DFG, DWR, the Service, and NMFS. 

Tracy (Jones) Pumping Plant 

Program 

Clifton Court

Forebay

Tracy Fish Collection Facility

Suisun

Bay

San

Francisco

Bay

FY 2008

Funding Obligation

$1,815,000 (Water & Related)

($14,970) (State)

Amounts in ( ) = credit amount

Accomplishments

• Continued study efforts to determine the Tracy 

Fish Collection Facility’s present-day fi sh salvage 

effi ciency

• Continued reassessment of the outdated Bates 

Table used for establishing fi sh hauling densities 

during transport

• Continued research and pilot studies for improved 

debris and predator management

• Continued recessed holding tank stress tests

• Collected water quality data at the entrance to the 

Delta Mendota Canal 

• Distributed various Tracy Research Volume 

Series and publications

• Updated the Tracy Research Web site

• Completed replacement of fi sh transfer buckets, 

fi sh haul trucks and tanks

• Began construction of a new onsite research 

building
3406(b)(4) 47

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 procedures) to reduce fi sh losses and 

improve fi sh salvage success while meeting the 

CVPIA’s goal. 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 National Oceanic and 

Atmospheric Administration (NOAA) Fisheries and 

Service CVP OCAP BO’s.

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 fi ve to seven 

years to fully assess the existing TFCF and implement 

and evaluate all remaining physical and operational 

improvements presently identifi ed at TFCF. 

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 signifi cant increase in fi sh mortality during 

the salvage process, prior to and including fi sh 

holding and hauling

Tracy (Jones)

Pumping Plant

Delta-Mendota Canal

Figure 7. Tracy (Jones) Pumping Plant
48 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Measuring Success

Program Actions

To date, the program has completed 14 of 23 actions, 

or 61 percent of the program’s present goal. Actions 

in 2008 included continued study efforts to determine 

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

continued reassessment of the outdated Bates Table 

used for establishing fi sh hauling densities during 

transport, ongoing improvement to debris and predator 

management as well as hydraulic control of the 

facility, continuation of recessed holding tank stress 

tests, collection of water quality data at the entrance 

to the DMC, distribution of various Tracy Research 

Volume Series and publications, and updating the 

Tracy Research Web site. Also, Reclamation completed 

replacement of fi sh transfer buckets, fi sh haul trucks 

and tanks, and began constructing a new onsite research 

building.

Program Research

The program has published 41 volumes of researchrelated activities to date. The information from the Tracy 

Research Volume Series includes Technical Publications 

and a PhD Dissertation and 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 2008, the 

program completed distribution of Tracy Research 

Volume Series Nos. 34, 35, 37, & 41, distribution 

of Tracy Technical Bulletins 2008-1, -2 and -3, and 

facilitated ongoing development of the Tracy Research 

technical website and enhanced data accessibility. The 

program also published a PhD Dissertation related to 

fi sh holding stress on Chinook salmon.

The information contained on the website is used by 

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

affects and concerns. 

In 2009, 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
3406(b)(5) 49

CVPIA Section 3406(b)(5)

“...Develop and implement a program to mitigate 

for fishery impacts resulting from operations of 

the Contra Costa Canal Pumping Plant No. 1. 

Such a program shall provide for construction and 

operation of fish screening and recovery facilities, 

and for modified 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, then gravity propels the 

water to its terminus in Martinez. 

Operation of the Contra Costa Pumping Plant No. 1, 

without adequate screening or alternative mitigation, 

results in fish mortality. In addition to the CVPIA 

mandate, the 2004 Los Vaqueros BO extension, requires 

that a fish screen be built at Rock Slough. This program 

is focused on improving operation of the Rock Slough 

Intake to minimize loss of fish through three main 

activities: 

• Design and construct a fish screen for CCWD’s 

Pump #1 and one or more new intake structures 

• Work with CCWD to modify operations (change 

the pumping schedule) 

• Make interim annual mitigation payments to the 

Service to compensate for presumed losses of delta 

smelt during continued Contra Costa Pumping 

Plant operation in the absence of a fish screen 

Contra Costa Canal Pumping 

Plant Contra Costa

Canal Pump

Suisun

Bay

San

Francisco

Bay

FY 2008

Funding Obligation

$55,000 (Water & Related)

($2,500) (State)

Amounts in ( ) = credit amount

Accomplishments

• Conducted fi sh monitoring

• Continued discussions with the Service for 

operation beyond the year 2008 in the absence of 

a screening facility 

• Consulted under ESA and the Coordination Act 

with the Service on the Los Vaqueros BO as it 

relates to the environmental commitment of the 

Rock Slough Fish Screen

• Continued to negotiate appropriate mitigation 

to the Service for the Sacramento-San Joaquin 

Delta Pelagic Organism Decline effort

Rock Slough
50 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Because fish losses at pumping stations, dams and 

diversions are of concern throughout the CVP system, 

currently several CALFED Stage 1 studies are under 

way, including the Los Vaqueros Reservoir Expansion 

Study, Rock Slough Water Quality Improvement Study, 

and various ecosystem restoration projects and studies. 

These studies may benefit other agencies, including the 

Tracy (Jones) Pumping Plant Program (b)(4), the AFSP 

(b)(21), and other Central Valley actions for endangered 

species. 

These studies have the potential to significantly alter 

the currently designed fish screen facility at Rock 

Slough or to eliminate the need for a screened diversion 

altogether. In anticipation of this more rigorous and 

elaborate analysis, alternative short-term, lower-cost 

fisheries mitigation measures are being investigated and 

developed, including short-term operational flexibility, 

alternative exclusionary measures, and 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 fish 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 National Environmental Policy Act (NEPA) 

documentation. This document presents the potential 

effects of the currently identified potential fish screen 

alternatives. Fish monitoring continued through 2008 

according to the monitoring plan. 

1 The team is made up of representatives from DFG, DWR, 

Service, Reclamation, NOAA Fisheries, and the Contra Costa 

Water District (CCWD)

Figure 8. Rock Slough Fish Screen (Proposed)

Contra Costa Canal

Rock Slough

Rock Slough 

Fish Screen 

(Proposed)

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 fish screen until 2008. 

The program continued discussions with the Service 

for operation beyond the year 2008 in the absence of 

a screening facility. This includes mitigation for each 

year that Reclamation extends or surveys actions related 

to listed species impacted by the CVP. Currently, no 

conclusions have been reached.

The program is currently consulting under ESA and the 

Coordination Act with the Service on the Los Vaqueros 

BO as it relates to the environmental commitment of the 

Rock Slough Fish Screen. 

Mitigation Payments 

In 2008, the program continued to negotiate appropriate 

mitigation 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.
3406(b)(9) and 3406(b)(19) 51

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 mortality of holding and spawning adults, 

decreased egg viability in redds due to thermal distress, 

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 

Flow Fluctuations and Reservoir 

Storage Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$31,000 (Restoration Fund)

Accomplishments

Minimized losses of anadromous fi sh due to fl ow 

fl uctuations by:

• Maintaining Clear Creek fl ows using a 

combination of (b)(2) water and (b)(1)B 

reoperation 

• Augmenting Sacramento River fl ows in December 

2007 and January 2008 with (b)(2) water to 

minimize dewatering fall-run Chinook redds

• Augmenting American River fl ows from December 

2007 through mid-April 2008 using (b)(2) water

• Augmenting Stanislaus River fl ows from midOctober 2007 through early March 2008 using a 

combination of (b)(2) and (b)(3) water 

The American River from Guy West Bridge
52 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 water year 2008 (October 

2007 through September 2008), 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.

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 water year 2008 to determine how to 

minimize damaging fl ow fl uctuations on the Sacramento 

River to the extent possible. In December 2007 and 

January 2008, Sacramento River fl ows were augmented 

with (b)(2) water to try to minimize dewatering fallrun Chinook redds, which had been constructed in 

October and November 2007 at fl ows greater than 5,700 

cfs. Absent the (b)(2) augmentation, base fl ows on the 

Sacramento River would have dropped to 3,250 cfs 

beginning in mid-December. Interior used (b)(2) water 

to maintain moderate fl ows (i.e., 4,000 – 4,500 cfs) 

through the emergence period and gradually reduced 

fl ows to 3,250 cfs by late January 2008.

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 2008, 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. In water year 2008, American River 

fl ows were augmented using (b)(2) water from 

December 2007 through mid-April 2008. 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 2009. 

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 water year 2008, Stanislaus River fl ows 

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

(3) water from mid-October 2007 through early March 

2008. Large fl ow fl uctuations during critical fi sh 

periods did not occur.
3406(b)(10) 53

CVPIA Section 3406(b)(10)

“Develop and implement measures to minimize 

fish passage problems for adult and juvenile 

anadromous fish at Red Bluff Diversion Dam...”

The Red Bluff Diversion Dam (RBDD) is located on 

the Sacramento River about 2.5 miles 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 sturgeon (ESAlisted) and white sturgeon were also blocked and losses 

of out-migrating juvenile salmon were also 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. 

A 1993 biological opinion (BO) required that the gates 

remain out of the river or “open” for eight months of the 

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

FY 2008

Funding Obligation

$5,636,000 (Water & Related)

($2,000) (State)

Amounts in ( ) = credit amount

Accomplishments

• Achieved unimpeded passage for approximately 

20 percent of the adult spring-run Chinook and 

approximately 50 percent of the green sturgeon 

based on the current operation of the facility (fourmonth closure of the gates)

• Observed no further green sturgeon fatalities 

after operational changes were implemented by 

Reclamation at RBDD in 2007 (gates are kept 

“open” or raised a minimum of one foot from the 

river fl oor)

• Signed a Record of Decision on July 16, 2008, 

following completion of ESA consultation on the 

planned construction of a new pumping plant.

Open gates at Red Bluff Diversion Dam
54 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

year (from September 15 through May 15); as a result of 

this and complementary CVPIA actions, the population 

index for the winter-run Chinook dramatically increased 

and juvenile predation dropped.

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 10).

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 

gates operations at Red Bluff based on the presence of 

an unusually large number of green sturgeon “holding” 

in the vicinity of the dam, the nature of the injuries seen 

on carcasses, and the location of some carcasses. It was 

inferred 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 now kept “open” 

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

Reclamation and the Tehama Colusa Canal Authority 

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 

to improve fi sh passage. Delays resulted from the then 

Red Bluff

Diversion Dam

Corning Canal

Lake Red Bluff

Sacramento River

Tehama-Colusa Cana

potential listing of the green sturgeon as a threatened 

and endangered species. Following listing, it was 

decided to recirculate the EIS/EIR in 2006 to include 

discussion of the Operations Criteria and Plan (OCAP) 

BO then in effect and its requirements, as well as to 

make it clear the assessment of the potential impacts 

to the green sturgeon was unchanged. 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 OCAP ESA 

consultation and the BO which is expected to be issued 

in 2009. Also, full 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.

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:

• Outcome target: achieve annual passage of 80 to 

100 percent of adult spring-run salmon and 50 to 

100 percent of adult green sturgeon

• Output target: supply Full Level 4 water to the 

SNWR

• Output target: complete RBDD infrastructure 

improvements as necessary to achieve annual 

fi sh passage targets and to be capable of full time 

operation, if needed

One of the program goals has been met:

Refuge Water Conveyance Capacity

The mandated goal to supply Full Level 4 water to the 

SNWR has been met. The goal was met after evaluation 

of eight options by installation of a siphon on the GlennColusa Irrigation District (GCID) Canal at Stony Creek 

to allow year-round deliveries. Use of the RBDD for 

this purpose was therefore abandoned, although the 

planned changes at Red Bluff will provide a back-up to 

conveyance via GCID’s facilities.

Figure 9. Red Bluff Diversion Dam
3406(b)(10) 55

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

Measuring Success

Fish Passage

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 unimpeded 

passage. 

No further green sturgeon fatalities were observed 

in 2008 in response to the operational changes 

implemented by Reclamation at RBDD in 2007 (gates 

are kept “open” or raised a minimum of one foot from 

the river fl oor).

Infrastructure Improvements

A Record of Decision was signed July 16, 2008, 

following completion of ESA consultation on the 

planned construction. Alternative 2b of the EIS/EIR 

was identifi ed as the preferred alternative; it 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-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.) 

Decisions concerning operation, however, 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. Design of a new pumping facility 

is in progress.

Figure 10. Spawning Returns, Winter-Run Chinook, Sacramento River (1967-2006)
56 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 

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

FY 2008

Funding Obligation

$826 (Water & Related)

Accomplishments

• Completed the design of a visitor kiosk at the 

Coleman NFH

Modifi cations to Keswick Fish Trap
3406(b)(11) 57

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.

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 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 CALFED-funded Salmon 

and Steelhead Restoration Project’s efforts to restore 42 

miles of habitat in upper Battle Creek by promoting and 

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. 

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.

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 constructing 

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

Coleman Fish

Battle Creek

Hatchery

Figure 11. Coleman Fish Hatchery
58 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Domestic Water System and Visitor Facility 

Improvements

In 2005 and 2006, the CVPIA implemented a program 

to rehabilitate the domestic water system to ensure 

high-quality treated drinking water for station staff and 

the tens of thousands of visiting public. 

In 2006, the program began design of a visitor kiosk 

and informational panels at the Coleman NFH; design 

was completed in FY 2008. Construction is expected 

to be initiated in FY 2009. Construction cost overruns 

have precluded the ability to purchase information 

panels.

Table 11. Coleman NFH Facility Rehabilitation Phases (1991-2008)

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 capacity in 

2000 and 45,000 gpm capacity in 2002; 

no plans to further build out ozone facility 

to full capacity as prescribed by Phase 6 of 

the SDP

Reclamation

7. Construction of 20 additional 

5-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)(12) 59

The original construction of McCormick-Saeltzer Dam 

in 1903, modifi cations to McCormick-Saeltzer Dam 

in 1912, continued operation of McCormick-Saeltzer 

Dam, construction of Whiskeytown Dam in the 1960s 

and aggregate and gold mining in Clear Creek, caused 

widespread degradation of the creek habitat. This 

led to precipitous drops in Chinook and Steelhead 

salmon spawning and juvenile production. 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: Use approximately 80,000 acrefeet of (b)(2) water dedicated annually; variable 

target dependant on hydrology and biological 

conditions

 - Allow provision of at least 90 percent of the 

maximum possible habitat

 - Meet temperature targets at least 98 percent 

of days with no more than two consecutive 

temperature exceedence days

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 McCormickSaeltzer Dam...”

Clear Creek Restoration 

Program Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$611,000 (Restoration Fund)

$99,000 (Water & Related)

Accomplishments

• 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 were met 

99 percent of the time

• Gravel was added at Whiskeytown Dam (1,000 

tons), Placer Road Bridge (3,000 tons), Phase 3A 

(1,500 tons), and Phase 2A (3,000 tons)

• Phase 3B channel relocation and fl oodplain 

reconstruction was completed

• Fall Chinook escapement was 4,129 compared 

to the average baseline escapement of 1,689 

between 1967 and 1991

• Adult spring-run Chinook increased from a low of 

zero in 2001 to 200 in 2008

• Adult steelhead populations increased, as 

indicated by redd counts, from approximately 38 

in 2001 to 159 in 2008

• Initiated monitoring for benthic macro-invertebrate 

sampling to compare the effectiveness of the 

restoration projects 

• Initiated monitoring for mercury sampling during 

storms to evaluate the impact of Phase 3B on 

total mercury in Clear Creek
60 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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

Legend

by cooperators from the Western Shasta Resource 

Conservation District, the Service, National Park 

Service (NPS), and the Bureau of Land Management 

(BLM). All feasible and cost-effective projects were 

fi nished by 2001 and no further work is expected.

Measuring Success

Progress against the remaining program goals is 

summarized in the following sections.

Instream Flow

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

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

temperature objectives, and the instream habitat goal. 

Pre-CVPIA 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 99 percent of the time in 

2008. 

Lastly, the program has met the instream habitat goal of 

90 percent weighted useable area for the last six years 

including in FY 2008.

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. In 2008, gravel was 

added at Whiskeytown Dam (1,000 tons), Placer Road 

Bridge (3,000 tons), Phase 3A (1,500 tons), and Phase 2A 

(3,000 tons).

Securing a long-term gravel supply is critical for reestablishing sediment transport processes that create 

and maintain fi sh habitat. In FY 2008, a feasibility study 

was completed and a contract for design and permitting 

was initiated for the Cloverview long-term gravel supply 

project that could supply 23 years worth of gravel for 

Clear Creek at a fraction of the current cost. 

2) Fish passage: Obtain unimpeded fi sh passage provided past McCormick-Saeltzer Dam site through 

its removal

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

usable spawning habitat that existed before construction of Whiskeytown Dam by 2020 by adding 

17,000 tons of gravel annually

4) Channel restoration: Restore two stream miles by 

2010

5) Erosion control: Implement highest priority and 

cost effective erosion control projects by 2003

Two of the program goals have been met:

Fish 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. 

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 

Figure 12. Gravel Injection and Channel 

Restoration Sites
3406(b)(12) 61

from about 3,000 in 1998 to a low of 300 in 2005, as 

shown in Figure 15. 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) Water Acquisition 

Program to remove fi ne sediment from the stream 

channel. The pilot project would target fl ows of 3,250 

cfs from the Whiskeytown gloryhole for one day.

Channel Restoration

The two-mile stream channel is 80 percent restored 

(Figure 16). Phases 1, 2A, 2B, and 3A are complete. 

Phase 3B channel relocation and fl oodplain 

reconstruction was completed November 2007 (FY 

2008). Phase 3B fl oodplain revegetation began in 

September 2007 and will continue through April 2009. 

Phase 3C is not complete. An inventory of future 

channel restoration needs was initiated but canceled 

due to the shortfall in Restoration funding in 2008. 

Adaptive Management and Monitoring

Through addressing the program goals, the Clear 

Creek Restoration Program has increased fall-run 

Chinook escapement, and steelhead and spring-run 

Chinook populations. In 2007 (FY 2008), fall Chinook 

escapement was 4,129 compared to the average 

baseline escapement of 1,689 between 1967 and 1991, 

as shown in Figure 13. Similarly, adult steelhead 

populations also continued to increase, as indicated by 

redd counts, increasing from approximately 38 in 2001 

to 159 in 2008. Figure 14 depicts the increase of adult 

spring-run Chinook from a low of zero in 2001 to 200 

in 2008.

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 

1967-1991 2007

5000

4000

3000

2000

1000

0

Figure 13. Fall–Run Chinook Salmon Escapement, 

Clear Creek (2007)

2001 2002 2003 2004 2005 2006 2007 2008

200

180

160

140

120

100

80

60

40

20

0

AUGUST SNORKEL COUNT

Figure 14. Adult Spring-Run Chinook Salmon 

Population, Clear Creek (2001-2008)

1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

3500

3000

2500

2000

1500

1000

500

0

JUVENILE CHINOOK PER ADULT FEMALE

Figure 15. Juvenile Fall-Run Chinook Salmon 

Produced/Adult Female, Clear Creek (1998-2007) 
62 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Direct observation studies of the Phase 3A and Phase 

3B restoration projects continued to indicate that 

overall both projects performed well at providing 

juvenile Chinook rearing habitat, although boulder 

clusters and one type of rootwad structure performed 

poorly. 

New monitoring initiated in FY 2008 included 

benthic macro-invertebrate sampling to compare the 

effectiveness of the restoration projects, mercury 

sampling during storms to evaluate the impact of 

Phase 3B on total mercury in Clear Creek, and a 

riparian encroachment and restoration opportunity 

inventory that was later put on hold due to a shortage 

of Restoration Funds. This inventory will provide 

information to evaluate the need for further physical 

habitat restoration in Clear Creek.

Figure 16. Clear Creek Channel Restoration Project Phases
3406(b)(13) 63

CVPIA Section 3406(b)(13) 

“Develop and implement a continuing program...

to restore and replenish spawning gravel...and 

rearing habitat... on the American, Stanislaus 

and Sacramento Rivers...shall include preventive 

measures...”

The construction of Central Valley Project dams has had 

dramatic effects on the rivers in which they are placed; 

one effect is the prevention of rocks, gravel, dirt and 

other substrates from passing through them. Absent the 

dams, these materials would move into the river providing 

habitat needed for successful spawning and juvenile 

rearing. The (b)(13) program represents a continuous 

effort to restore spawning and rearing habitat, in the 

Upper Sacramento River from Keswick Dam to the Red 

Bluff Diversion Dam, in the American River downstream 

of Nimbus Dam and in the Stanislaus River downstream 

from Goodwin Dam. 

The average annual gravel defi cits on CVP streams are 

based on scientifi cally developed estimates for the amount 

of gravel that the dams retain: 

• Sacramento River–50,000 cubic yards (65,000 

tons) 

• Stanislaus River–20,000 cubic yards (26,000 tons) 

• American River–57,200 cubic yards (74,000 tons)

With gravel defi cits of this magnitude and the cost of 

acquiring gravel, the program focuses on sites that are 

thought to have the most benefi t to increase the quality 

and quantity of spawning and rearing habitat. The 

program goals are to annually place 10,000 tons in the 

Sacramento River, 3,000 tons in the Stanislaus River, and 

Spawning and Rearing Habitat 

Restoration Program Sacramento

San Francisco

Los Angeles

Weaverville

Redding

FY 2008

Funding Obligation

$883,000 (Restoration Fund)

$878 (State)

Accomplishments

Sacramento River

• Purchased and placed approximately 8,300 tons 

of gravel

Stanislaus River

• Approximately 50% of spawning was in the 

Goodwin Canyon gravel placement area 

exceeding the program goal of 10% of spawning 

salmonids using the gravel placement

• Mapped Chinook redds on added gravel

• Surveyed topography of the three riffl es created 

at Knights Ferry

• Mapped bathymetry of the river for planning 

future gravel projects

American River

• Redd density for Chinook and steelhead 

combined on the 2008 placed gravel was about 

0.015 redds per square meter, near the program 

goal of 0.03 redds per square meter

• Egg retention in 2008 was ten percent, meeting 

the program goal

• Permitted for and placed 7,000 tons of spawning 

gravel at Sailor Bar

• Completed a gravel budget describing the amount 

of gravel blocked by Nimbus and Folsom Dams

• Completed gravel permeability studies

• Acquired aerial photography documenting 

Chinook spawning throughout the river

• Began testing and permitting to use gravel from 

historic mining operations along the river for 

future cost effective gravel enhancement

• Started testing and permitting of side channel 

restoration to improve rearing conditions for 

juvenile salmon and steelhead
64 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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

7,000 tons in the American River. 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 to deliver the gravel. All gravel 

is placed according to criteria developed by the DFG 

and NMFS. Figure 17 shows recent gravel placement 

locations.

Assessing Need

Aerial photos, redd surveys, snorkel surveys, and boat 

surveys are utilized to identify areas for augmentation. 

Spawning densities show that there are more 

anadromous fi sh than available spawning habitat. Future 

gravel placements are based on data from these surveys.

Once the gravel is placed, Reclamation and the Service 

monitor the spawning and rearing occurring at and 

near the restored sites to determine the program’s 

effectiveness. The program monitors fi sh use, habitat 

suitability, and several other variables to help determine 

success.

Fish Use

The goal for the Sacramento River gravel placement 

areas is 25 percent of spawning salmonids using the 

gravel placement reach; the goal for the Stanislaus 

River gravel placement areas is 10 percent of spawning 

salmonids using the gravel placement sites. The goal for 

the American River is 0.03 redds per square meter on 

emplaced gravel and less than 10 percent egg retention.1

Since the program’s implementation, monitoring has 

shown improvement (see below under measuring 

success) 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. 

Habitat Suitability

The suitability of gravel for spawning is an important 

indicator used to determine future gravel placement 

actions. Ongoing gravel studies examine areas with new 

and old gravel to determine if the gravel has suitable; 

permeability for egg survival, size of gravel for making 

redds, depth for fi sh to utilize it and for redds to be fully 

submerged, and velocity to provide oxygen and other 

nutrients.

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 study compared man made riffl es created with 

Table 12. Total Gravel Placed (1997-2008)

River

Total Gravel Placed 

Since 1997 (Tons)

Gravel Placed in 

2008 (Tons)

Annual Target 

(Tons)

Percent of Annual 

Target for 2008

Sacramento 168,300 8,300 10,000 83%

Stanislaus 14,100 0 3,000 0%

American 13,000 7,000 7,000 100%

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).

Figure 17. Recent projects sites in the Sacramento, 

American, and Stanislaus rivers
3406(b)(13) 65

varying sizes of gravel and determined that survival 

(egg to fry) was best in the mixture with a smaller sized 

gravel component.

Measuring Success

Sacramento River 

In the Sacramento River, salmon spawning increased 

from an average percentage of 6.9 percent of the 

Chinook population spawning in the gravel placement 

reach prior to CVPIA to an average percentage of 15.6 

percent spawning in the area that gravel was added 

since CVPIA was enacted (1993-2005). These numbers 

mean that now a greater proportion of fi sh use the gravel 

placement area near the dam where water temperature is 

coolest. The ability of fi sh to spawn in areas with cooler 

water should enhance survival of the listed runs. River 

conditions were unsuitable for collecting spawning 

surveys in 2006 and 2007; therefore, redd survey data 

is not available. The program goal of 25 percent of 

spawning salmonids using the gravel placement reach 

has not been attained.

In 2008, approximately 8,300 tons of gravel (83% 

of annual target) were purchased and placed in the 

Sacramento River (Figure 18). The gravel was placed 

on the side of the river channel at the Salt Creek site.

The gravel will be distributed naturally as high fl ow 

events occur in the river. Other accomplishments on 

the Sacramento River include: conducting substrate 

mapping of the river bottom, doing cross sections to 

examine channel evolution, and preparing a gravel 

budget for the river using a sediment transport model.

Stanislaus River 

Accomplishments in the Stanislaus River included 

mapping Chinook redds on gravel added in past projects 

(Figure 19), topographic survey of three riffl es created 

at Knights Ferry, and bathymetric mapping of the river 

(in cooperation with the Reclamation Central California 

Area Offi ce) for planning future gravel projects. 

Chinook salmon escapement in the Stanislaus River was 

low in 2007. During November and December 2007 

(FY 2008) approximately 50 percent of spawning was 

in the Goodwin Canyon gravel placement area so the 

program goal of 10 percent of spawning salmonids using 

the gravel placement was exceeded. Seven redds were 

mapped on the placement sites downstream at Knights 

Ferry. Data for 2008 is not yet available but use did not 

appear to be as high as in 2007.

Figure 18. Sacramento River project completed 

after adding 8,300 tons of gravel

Figure 19. Spawning locations (dots) within gravel 

injection sites on the Stanislaus River
66 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

American River

Studies in the American River conducted in 2007 

identifi ed existing areas of overly high-density spawning 

by salmonids, indicating spawning habitat area 

limitations. The program used this data in FY 2008 to 

prioritize gravel placement to improve these conditions. 

Accomplishments in 2008 on the American River 

included the permitting and placement of 7,000 tons of 

spawning gravel (100 percent of annual target) at Sailor 

Bar (Figures 20 and 21), completion of a gravel budget 

describing the amount of gravel blocked by Nimbus 

and Folsom Dams, completion of gravel permeability 

studies, and acquisition of aerial photography 

documenting Chinook spawning throughout the river. 

Redd density for Chinook and steelhead combined 

on the 2008 placed gravel was about 0.015 redds per 

square meter (110 redds in 6,800 square meters of placed 

gravel), near the goal of 0.03 redds per square meter. 

Egg retention in 2008 was 10 percent, meeting the goal, 

although total Chinook escapement was the lowest ever 

recorded. 

In 2008, the program began testing and permitting to 

use gravel from historic mining operations along the 

river for future cost effective gravel enhancement. 

Local gravel availability is low so utilizing on-site gravel 

sources can reduce the cost of projects. In 2008, the 

program also started testing and permitting side channel 

restoration to improve rearing conditions for juvenile 

salmon and steelhead. 

Figure 20. American River Upper Sailor Bar (Pre-Project) note that the site is relatively fl at water

Figure 21. American River Upper Sailor Bar (Post-Project) note the light gravel and the site formed a riffl e, 

which is desirable spawning habitat
3406(b)(15) 67

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, 

protect salmon in the San Joaquin River, and improve 

water supply reliability for south of delta contractors and 

environmental uses.

In support of SDIP, to reduce the number of fall- and 

late fall-run Chinook salmon that enter the Old River 

and to reduce entrainment at the CVP and SWP export 

facilities, the 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 three agricultural 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 

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

FY 2008

Funding Obligation

None

Accomplishments

• Installed a seasonal, temporary rock barrier at the 

head of Old River

• Continued additional planning and environmental 

compliance work on the permanent operable fi sh 

gate

 

Temporary Head of Old River Barrier
68 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

BO’s by the Service and NMFS must occur prior to 

construction. The OCAP BO’s cover the gate operations 

only; a separate BO for the construction effects is also 

required. The Service issued a BO on OCAP that 

includes gate operations. NMFS will issue a BO on 

OCAP in June 2009. As the NMFS BO is delayed, the 

construction target is now 2010.

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

A seasonal, temporary rock barrier at the head of Old 

River has been installed for 12 of the 16 CVPIA years 

(1992-2008), helping to keep fi sh in the San Joaquin 

River. The temporary barrier was not installed in four 

years (1995, 1998, 1999, and 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 delta smelt. Success of 

the permanent gates is measured based on completing 

three key stages, namely (1) planning and environmental 

compliance, (2) design, and (3) construction. The project 

completed most of the fi rst stage in 2006 with the 

issuance of the Final EIS/EIR; additional planning and 

environmental compliance work is expected to continue 

through 2009. 

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 be prepared to consider 

an increased permitted limit in the diversion rate at 

Clifton Court Forebay. This would 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 export 

facilities. 

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 for salmon and can be in 

place and operable when San Joaquin River fl ows are 

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

implementation, in 2007 Reclamation 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. This model 

could be used in future funding appropriation decisions. 

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 the OCAP 
3406(b)(16) 69

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....”

CAMP assesses progress toward the AFRP fi sh 

doubling goals, stated in section 3406 (b)(1), by 

monitoring natural production of adult anadromous 

fi sh in the Central Valley and comparing these data to 

AFRP production targets. CAMP activities focus on 

nine anadromous fi sh taxa: Chinook salmon (fall-, latefall-, winter-, and spring-run), steelhead, striped bass, 

American shad, white sturgeon and green sturgeon. 

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. 

In 1997, a CAMP Implementation Plan was developed, 

and describes methods and procedures for: (1) 

monitoring anadromous fi sh species in California’s 

Central Valley, and (2) assessing the biological results 

and effectiveness of different categories of restoration 

activities. The plan identifi es 82 monitoring elements 

that are required to assess progress toward the AFRP 

fi sh doubling goals. Currently, 62 of these activities are 

being conducted, generally by entities outside of the 

program, such as the state and water districts (table 13).

In 2004, the CAMP issued a contract to evaluate 

Comprehensive Assessment 

and Monitoring Program Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$291,000 (Restoration Fund)

Accomplishments

• Produced an annual report that quantifi es the 

production of anadromous fi sh from the Central 

Valley and assesses progress toward the AFRP 

fi sh production targets

• Funded a cooperative agreement to develop 

statistical and structural design recommendations 

for a comprehensive database to document 

changes in the abundance of juvenile Chinook 

salmon in the Central Valley

• Updated the CAMP web site (www.fws.gov/

sacramento/CAMP/index.htm) which 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

Weir installation for fi sh monitoring on the Stanislaus 

River
70 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

statistical procedures for assessing progress toward 

the fi sh doubling goals and determining sustainability 

of production increases. The report resulting from 

the contract cited a need for better data, including 

watershed-specifi c escapement estimates for naturally 

spawned and hatchery fi sh; watershed-specifi c 

juvenile production estimates; and ocean, mainstem 

and tributary angler catches. Implementation of these 

recommendations is frequently constrained by the 

budgetary limitations of entities that collect data. 

The CAMP has a single performance measure, which 

is to develop an annual report. Toward that end, the 

CAMP has produced several reports quantifying the 

abundance of anadromous fi sh species and tracking 

progress toward the AFRP fi sh doubling goals.

Measuring Success

CAMP has produced six annual reports since program 

inception. These documents were fi nalized in 1998, 

1999, 2001, 2002, 2007, and 2008. Each report monitors 

the production of anadromous fi sh and assesses progress 

toward the AFRP fi sh production targets during 

different periods.

The 2008 annual report synthesizes and analyzes 

anadromous fi sh monitoring data collected between 

1992 and 2007 on 21 watersheds. Because the process 

of collecting and reporting data is time consuming, 

data are only available for American shad and the four 

runs of Chinook salmon through 2007; and striped 

bass, green sturgeon, and white sturgeon through 

2005. Figure 22 provides a graph depicting the natural 

production of four runs of Chinook salmon from 21 

watersheds in the Central Valley; fi gures 23 and 24 show 

estimated abundance of white and green sturgeon in San 

Pablo Bay and Suisun Bay; fi gure 25 shows estimated 

abundance of adult striped bass in the Sacramento-San 

Joaquin River Delta; and fi gure 26 provides a graph 

depicting the midwater trawl index for young-of-theyear (YOY) American shad in the Sacramento-San 

Joaquin River Delta and San Pablo and Suisun Bays. 

Additional fi gures and data for striped bass, American 

shad, white sturgeon, green sturgeon, and individual 

runs of Chinook salmon from 1992 to 2007 are 

contained in the 2008 CAMP annual report posted on 

the CAMP web site. At the present time, a coordinated 

and comprehensive program for monitoring steelhead 

does not exist; however, a variety of entities are working 

to develop such a program. 

Overall, the 2008 annual report 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. 

Concerns about low Chinook salmon numbers prompted 

an unprecedented closure of the ocean harvest of Central 

Valley Chinook salmon in 2008. The inland harvest of 

fall-run Chinook salmon in the Central Valley was also 

dramatically curtailed in 2008 to improve the likelihood 

that the number of salmon will increase in the future. 

In FY 2008, CAMP funded a $45,341 cooperative 

agreement to develop statistical and structural design 

recommendations for a comprehensive database to 

document and understand changes in the abundance of 

juvenile Chinook salmon in the Central Valley.

In FY 2008, two of the 82 CAMP-recommended 

monitoring elements were completed with the assistance 

of CVPIA funds or staff. These include: (1) operation 

of a rotary screw trap in the Stanislaus River via a 

contract that was funded with CAMP and the Dedicated 

Project Yield program (3406(b)(2)) funds, and (2) 

operation of a rotary screw trap in the Merced River 

that was facilitated with AFRP (3406(b)(1)) staff and 

an AFRP-funded contract. Of the 80 other CAMPrecommended monitoring elements in FY 2008, 15 did 

not occur and the remaining 65 were conducted by other 

entities, e.g., DFG.

Program Planning & Evaluation

The CAMP currently is conducting an internal 

evaluation to determine the program’s future scope, 

direction, and costs. The internal evaluation will: 

• Review past and ongoing monitoring projects to 

identify data gaps;

• Quantify the cost for completing critical 

monitoring activities between 2008 and 2012;

• Identify partnerships CAMP should pursue to 

cooperatively fund projects where a partner may 

share a common interest; and
3406(b)(16) 71

• Identify mechanisms for providing monitoring 

information to interested parties.

The results from the internal evaluation 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.

Figure 22. 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
72 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Figure 23. Estimated Abundance of 15-year-old White Sturgeon in San Pablo Bay and Suisun Bay, 1993-2005

Figure 24. Estimated Abundance of Adult Green Sturgeon in San Pablo Bay and Suisun Bay, 1993-2005
3406(b)(16) 73

Figure 25. Estimated abundance of adult striped bass in the Sacramento-San Joaquin River Delta, 

Sacramento River downstream from the town of Colusa, and portion of the San Joaquin River downstream 

from the town of Mossdale, 1992-2005. 2002-2005 estimates only include male fi sh.

Figure 26. Midwater trawl index for YOY American shad in the Sacramento-San Joaquin River Delta and San 

Pablo and Suisun Bays, 1992-2007
74 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Table 13. CAMP Recommended Monitoring Elements by Watershed

CAMP 

Element Monitoring Method Watershed Species Lead Agency

 1 Carcass survey American River Fall-run Chinook salmon DFG

 2 Hatchery count American River Fall-run Chinook salmon DFG

 3 Hatchery marking American River Fall-run Chinook salmon DFG

 4 Angler survey American River Fall-run Chinook salmon DFG

76 Rotary screw trap American River Fall-run Chinook salmon DFG

65 Rotary screw trap Battle Creek Fall-run Chinook salmon FWS

 5 Video camera Battle Creek Fall-run Chinook salmon FWS/DFG

 6 Hatchery count Battle Creek Fall-run Chinook salmon FWS

 7 Hatchery marking Battle Creek Fall-run Chinook salmon FWS

34 Carcass survey Battle Creek Late fall-run Chinook salmon FWS/DFG

35 Hatchery count Battle Creek Late fall-run Chinook salmon FWS

36 Hatchery marking Battle Creek Late fall-run Chinook salmon FWS

51 Hatchery count Battle Creek Steelhead FWS

52 Hatchery marking Battle Creek Steelhead FWS

70 Rotary screw trap Big Chico Creek Fall-run Chinook salmon DFG

71 Rotary screw trap Big Chico Creek Spring-run Chinook salmon DFG

 8 Carcass survey Butte Creek Fall-run Chinook salmon DFG

72 Rotary screw trap Butte Creek Fall-run Chinook salmon DFG

45 Snorkel survey Butte Creek Spring-run Chinook salmon DFG

73 Rotary screw trap Butte Creek Spring-run Chinook salmon DFG

 9 Carcass survey Clear Creek Fall-run Chinook salmon DFG

64 Rotary screw trap Clear Creek Fall-run Chinook salmon FWS

10 Carcass survey Deer Creek Fall-run Chinook salmon DFG

68 Rotary screw trap Deer Creek Fall-run Chinook salmon DFG

46 Snorkel survey Deer Creek Spring-run Chinook salmon DFG

69 Rotary screw trap Deer Creek Spring-run Chinook salmon DFG

11 Carcass survey Feather River Fall-run Chinook salmon DWR

12 Hatchery count Feather River Fall-run Chinook salmon DFG

13 Hatchery marking Feather River Fall-run Chinook salmon DWR

14 Angler survey Feather River Fall-run Chinook salmon DFG

74 Rotary screw trap Feather River Fall-run Chinook salmon DWR

82 Hatchery marking Feather River Spring-run Chinook salmon DWR

15 Carcass survey Merced River Fall-run Chinook salmon DFG

16 Hatchery count Merced River Fall-run Chinook salmon DFG

17 Hatchery marking Merced River Fall-run Chinook salmon DFG

81 Angler survey Merced River Fall-run Chinook salmon DFG

80 Rotary screw trap Merced River-Hagaman 

County Park

Fall-run Chinook salmon FWS

18 Carcass survey Mill Creek Fall-run Chinook salmon DFG

66 Rotary screw trap Mill Creek Fall-run Chinook salmon DFG

47 Redd survey Mill Creek Spring-run Chinook salmon DFG

67 Rotary screw trap Mill Creek Spring-run Chinook salmon DFG

19 Ladder count Mokelumne River Fall-run Chinook salmon EBMUD

20 Hatchery count Mokelumne River Fall-run Chinook salmon DFG

21 Hatchery marking Mokelumne River Fall-run Chinook salmon DFG/EBMUD

22 Angler survey Mokelumne River Fall-run Chinook salmon DFG

77 Rotary screw trap Mokelumne River Fall-run Chinook salmon EBMUD
3406(b)(16) 75

CAMP 

Element Monitoring Method Watershed Species Lead Agency

23 Ocean harvest Pacifi c Ocean Fall-run Chinook salmon DFG

39 Ocean harvest Pacifi c Ocean Late fall-run Chinook salmon DFG

50 Ocean harvest Pacifi c Ocean Spring-run Chinook salmon DFG

44 Ocean harvest Pacifi c Ocean Winter-run Chinook salmon DFG

55 Midwater trawl survey Sacramento-San Joaquin 

River Delta

American shad DFG

57 Mark-recapture Sacramento-San Joaquin 

River Delta

Green sturgeon DFG

54 Mark-recapture Sacramento-San Joaquin 

River Delta

Striped bass DFG

56 Mark-recapture Sacramento-San Joaquin 

River Delta

White sturgeon DFG

25 Carcass survey Sacramento River Fall-run Chinook salmon DFG

26 Aerial redd count Sacramento River Fall-run Chinook salmon DFG

27 Angler survey Sacramento River Fall-run Chinook salmon DFG

37 Aerial redd count Sacramento River Late fall-run Chinook salmon DFG

38 Angler survey Sacramento River Late fall-run Chinook salmon DFG

49 Angler survey Sacramento River Spring-run Chinook salmon DFG

53 Angler survey Sacramento River Steelhead DFG

40 Hatchery marking Sacramento River Winter-run Chinook salmon FWS

41 Carcass survey Sacramento River Winter-run Chinook salmon DFG

42 Aerial redd count Sacramento River Winter-run Chinook salmon DFG

62 Rotary screw trap Sacramento River/GlennColusa Irrigation DiversionFall-run Chinook salmon DFG

63 Rotary screw trap Sacramento River/GlennColusa Irrigation DiversionSpring-run Chinook salmon DFG

61 Rotary screw trap Sacramento River/GlennColusa Irrigation DiversionWinter-run Chinook salmon DFG

24 Ladder count Sacramento River-Red 

Bluff Diversion Dam

Fall-run Chinook salmon FWS

59 Rotary screw trap Sacramento River-Red 

Bluff Diversion Dam

Fall-run Chinook salmon FWS

48 Ladder count Sacramento River-Red 

Bluff Diversion Dam

Spring-run Chinook salmon FWS

60 Rotary screw trap Sacramento River-Red 

Bluff Diversion Dam

Spring-run Chinook salmon FWS

43 Ladder count Sacramento River-Red 

Bluff Diversion Dam

Winter-run Chinook salmon FWS

58 Rotary screw trap Sacramento River-Red 

Bluff Diversion Dam

Winter-run Chinook salmon FWS

28 Angler survey San Joaquin River Fall-run Chinook salmon DFG

29 Carcass survey Stanislaus River Fall-run Chinook salmon DFG

30 Angler survey Stanislaus River Fall-run Chinook salmon DFG

78 Rotary screw trap Stanislaus River-Caswell 

State Park

Fall-run Chinook salmon FWS

31 Carcass survey Tuolumne River Fall-run Chinook salmon DFG

79 Rotary screw trap Tuolumne River - lower 

river

Fall-run Chinook salmon Turlock Irrigation 

District

32 Carcass survey Yuba River Fall-run Chinook salmon DFG

33 Angler survey Yuba River Fall-run Chinook salmon DFG

75 Rotary screw trap Yuba River Fall-run Chinook salmon DFG

Table 13. CAMP Recommended Monitoring Elements by Watershed (continued)
76 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 in the spring of 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 spring 

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

FY 2008

Funding Obligation

$71,000 (Water & Related)

Accomplishments

• Completed the biological and hydraulic testing 

and monitoring program that began in 2001

• Completed hydraulic testing and a set of 

underwater observations of predator distributions

• The project and related testing and monitoring is 

100 percent complete

Glenn-Colusa Irrigation District Fish Screen
3406(b)(20) 77

Measuring Success

Mitigating Project Impacts

The biological and hydraulic testing and monitoring 

program of the screen system started in summer 2001. 

To date, the testing program has not found any fi sh loss 

attributed to the operation of the fi sh screen system. 

The primary impact on terrestrial species involved 

the federally–listed valley elderberry longhorn beetle. 

Beetle habitat existed adjacent to the pumping plant and 

GCID Hamilton City

Pumping Plant

Glenn-Colusa Canal

Oxbow Outlet Channel

Sacramento River

Figure 27. Glenn-Colusa Irrigation District 

Pumping Plant

would likely have been 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. 

2008 Accomplishments

The principal effort in 2008 was completing 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; distinguishing between losses 

due to predators and any losses due to the new fi sh 

screen and bypass system; and measuring the approach 

velocity at the screen face. 

As of FY 2008, the project and related testing and 

monitoring is 100 percent complete. Hydraulic testing 

and a set of underwater observations of predator 

distributions were 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.
78 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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...measures shall include but 

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 sherysensitive areas.”

The 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 water diversions 

throughout the Central Valley and Sacramento-San 

Joaquin Delta. The AFSP actions contribute to the goal 

defi ned in CVPIA Section 3406(b)(1), which requires 

Interior to make all reasonable efforts to double natural 

production of anadromous fi sh in the Central Valley 

streams.

To date, the AFSP has assisted the state in screening 

24 diversions ranging from 17 cfs to 960 cfs for a 

cumulative total of more than 4,500 cfs (Table 14).

Currently, there are approximately 4,560 remaining 

unscreened diversions, including:

• Approximately 750 in the Sacramento River 

system 

• Approximately 950 in the San Joaquin River 

system

Anadromous Fish Screen 

Program Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

($1,310,000) (Restoration Fund)

($3,144,000) (Water & Related)

($178,433) (State)

Amounts in ( ) = credit amount

Credit amounts are due to deobligations being larger than 

current year obligations

Accomplishments

• Completed construction of the RD 108 Emery 

Poundstone Pumping Plant Fish screen 

Project consolidating three existing unscreened 

diversions totaling 377 cfs into a new screened 

300 cfs diversion on the Sacramento River

• Initiated construction of the Phase I Meridian 

Farms Fish Screen Project to screen 35 cfs at 

the New Grimes Diversion

• Initiated a four-year screening and monitoring 

program on the Sacramento River in partnership 

with CALFED ERP and the Family Water Alliance. 

Activities included conducted public outreach, site 

selection and permitting activities.

• Continued to provide technical assistance for ongoing AFSP projects including Natomas Mutual, 

RD 2035, Patterson ID and Yuba City fi sh screens

RD 108 Emery Poundstone Pumping Plant Fish 

Screen Project
3406(b)(21) 79

Table 14. AFSP Projects and cfs Screened, Central Valley (1992-2008)

Project Completed Project Location*

CFS Screened 

(Annual)

Number of Projects 

(Annual)

1992-1995 N/A N/A 0 0

1996 Pelger Mutual Water Company Sacramento River 40 1

Wilson Ranch Sacramento River 40 1

1997

Suisun Resource Conservation 

District

Suisun Marsh 93 5

Maxwell ID Sacramento River 100 1

Parrot-Phelan (M&T) Sacramento River 150 1

1998 Western Canal Butte Creek siphon 1

1999

Browns Valley ID Yuba River 65 1

Gorrill Land Company Butte Creek 122 1

Adams Ranch (Rancho Esquon) Butte Creek 135 1

RD 1004 Sacramento River 290 1

Princeton-Cordora Glenn & 

Provident ID

Sacramento River 605 1

2000 Dayly Lee Steamboat Slough 20 1

RD 108 (Wilkins Slough) Sacramento River 832 1

2001 N/A N/A 0 0

2002 N/A N/A 0 0

2003 Lower Butte Creek (Wier #3) Butte Creek (Sutter 

Bypass)

fi sh ladders & 

barriers

1

2004 Fairbairn (City of Sacramento) American River 210 1

Banta Carbona San Joaquin River 260 1

2005 Sacramento River WTP 

(City of Sacramento)

Sacramento River 245 1

2006 RD 999 Sacramento River 100 1

2007 Sutter Mutual Sacramento River 960 1

2008 RD 108 (Emery Poundstone) Sacramento River 300 1

TOTAL 4,567 24

* See Figure 28
80 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

• Approximately 2,500 in the Sacramento-San 

Joaquin Delta 

• Approximately 360 in the Suisun Marsh basin

Currently a long-term implementation plan is being 

developed for CVPIA that will identify priority 

restoration actions including fi sh screens; therefore, the 

exact number of screens to be constructed in the future 

has not yet been defi ned. 

The AFSP provides assistance to the state by matching 

state funding. The AFSP can provide up to 50 percent 

of the cost of a fi sh screen project. In recent years, 

state funding for fi sh screens has come through the 

CALFED Ecosystem Restoration Program. The AFSP 

also provides technical support to a diverter during 

the planning, design, and construction phases of a fi sh 

screen project. 

Measuring Success

In 2008, construction was completed on the Reclamation 

District (RD) 108 Emery Poundstone Pumping Plant 

Fish Screen Project in Sutter County. This project 

consolidated three existing unscreened diversions 

totaling 377 cfs into a new screened 300 cfs diversion 

on the Sacramento River. The AFSP provided a total of 

$15 million over the life of the project. This fi sh screen 

project protects out-migrating spring-, fall- and winterrun Chinook salmon and Central Valley steelhead 

as well as resident game and non-game fi sh from 

entrainment. Operation and maintenance of the fi sh 

screen is the responsibility of RD 108. 

In 2008, construction was initiated on the Phase I 

Meridian Farms Fish Screen Project consisting of the 

screening of a 35 cfs diversion at the New Grimes 

Diversion. 

In 2008, the AFSP continued to provide technical 

assistance (design, environmental and/or permitting) 

for several large fi sh screen projects which have not yet 

secured full construction funding, including:

• Natomas Mutual: Project to consolidate fi ve 

diversions totaling 630 cfs into two screened 

diversions on 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

In 2008, the AFSP initiated a four-year screening and 

monitoring program in partnership with CALFED 

ERP and the Family Water Alliance. The AFSP is 

implementing this program to assess the biological 

benefi ts of fi sh screening and to help prioritize future 

fi sh screening efforts. This program, which includes 

collection of fi sh loss data prior to installing fi sh 

screens, is focused on the Sacramento River. Activities 

conducted for this monitoring program in 2008 included 

public outreach, site selection, and permitting.
3406(b)(21) 81

Figure 28. CVPIA Fish Screens Constructed (1992-2008)

Wilson

Ranch

Parrot-Phelan

(M&T Ranch)

Adams Ranch

Gorrill

Land Co.

Western Canal Princeton-CordoraRD1004

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

Sacramento River WTP Fairbairn

2008 Projects 

Glenn & Provident ID

Legend
82 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 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. 

The San Joaquin River Restoration 

Program

Federal Authorization and Legislation 

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.

Authorizing legislation to fully implement the SJRRP, 

known as the San Joaquin River Restoration Settlement 

Act (Act), passed the full Senate on January 15, 2009, 

San Joaquin River 

Comprehensive Plan 

Friant Dam

Suisan

Bay

San

Francisco

Bay

Monterey

Bay Mendota Pool

S a n Joa quin Riv er

FY 2008

Funding Obligation

$7,733,000 (Restoration Fund)

Accomplishments

• Began development of specifi c operational 

guidelines for releasing Restoration Flows and 

the framework for a Recovered Water Account

• Began development of a plan to recirculate water 

back to the Friant Division long-term contractors

• Began development of a Fisheries Management 

Plan that incorporates an adaptive management 

approach

San Joaquin River
3406(c)(1) 83

and is headed to the House of Representatives for 

a vote before being submitted to the President for 

signature. The legislation was reintroduced as part of 

the Omnibus Public Land Management Act, Senate 

Bill 22, by Senator Jiff Bingaman (NM) on January 

7, 2009. Revised in late 2008 to include further water 

management and landowner protections, the Act is 

supported by the parties to the Settlement (Settling 

Parties) and downstream water and land interests 

(referred to as Third Parties). 

While authorization is still pending at the time of this 

2008 Annual Report, the Department of the Interior 

is proceeding with environmental review based on 

current authorities and funding, although timely 

passage of Congressional legislation will be critical 

to implementing provisions in the Settlement and 

maintaining the schedule. 

Measuring Success

In 2007, many organizational and managerial actions 

were completed to form the long-term structure for 

the SJRRP. In 2008, signifi cant progress was made 

towards supporting the development of the Program 

Environmental Impact Statement/Report (PEIS/R). 

Specifi c accomplishments in 2008 include:

• Progress on the development of specifi c 

operational guidelines for releasing Restoration 

Flows and the framework for a Recovered Water 

Account

• Progress on development of a plan to recirculate 

water back to the Friant Division long-term 

contractors

• Planning, coordinating, and implementing 

monitoring activities

• Completion and public release of draft Technical 

Memoranda 

• Providing public access to Program activities 

through the web, quarterly Program Updates 

mailed to a broad distribution list, public meetings, 

and briefi ngs at local forums

• Providing an on-the-ground tour from Friant Dam 

to the confl uence of the Merced River through the 

Water Education Foundation specifi c to the SJRRP

• Substantial progress on the development of 

a Fisheries Management Plan (FMP) that 

incorporates an adaptive management approach. 

Specifi c accomplishments on the FMP include:

- Draft documents completed during 2008 that 

form the basis of the integrated FMP include 

temporal occurrence and environmental 

requirements tables that are used to identify 

habitat suitability and physical requirements 

of the various Chinook salmon life stages, 

and conceptual models of spring-run and 

fall-run Chinook salmon that identify 

the groups conceptual understanding of 

the factors expected to limit the Chinook 

salmon population in the San Joaquin River. 

- Selection of a quantitative modeling tool 

(Ecosystem Diagnosis and Treatment) to 

assist with the development of the FMP and 

initial work in constructing the model. 

- Collaboration between a public Technical 

Feedback group and the Fisheries 

Management Work Group to gather 

comments and receive feedback from 

technical experts regarding the FMP.
84 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Introduction to the Refuge 

Water Supply Program Sacramento

San Francisco

Los Angeles

CVPIA Section 3406(d)(1), (2), and (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...”

“(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...”

The Refuge Water Supply Program (RWSP) 

encompasses several CVPIA provisions such as Water 

Acquisition, Conveyance, and Construction: 

Water Acquisition

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

acquisition of Incremental Level 4 quantities 

specifi ed in (d)(2) 

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; 

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 RWSP’s goal 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 29. The RWSP provisions (acquisition, 

conveyance, and construction) work together to 

implement these CVPIA provisions. 
3406(d) Introduction 85

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 before 1989. 

Reclamation is required to provide full Level 2 water 

annually, either from the CVP yield 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 

Figure 29. Central Valley Refuges Receiving CVPIA Water Supplies
86 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 used groundwater 

in supplementing some of their Level 2 supplies, 

and will continue to use groundwater. Reclamation 

is participating in additional studies and projects 

that may result in further increases in groundwater 

usage as part of long-term refuge water supplies. For 

example, Reclamation is funding a three year project to 

examine the utility of integrating groundwater into the 

Grasslands Level 4 water supply.

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 GWD, and 

DFG refuge lands and FWS lands. The data generated 

will be used to manage wetlands more effi ciently and 

monitor the quality of water leaving the refuges. 

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 

Reclamation must acquire this Incremental Level 4 

water supply through voluntary measures such as 

water conservation, conjunctive use, purchase, lease, 

donation, or similar activities.

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 

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 Tables 15 and 16. However, the total Level 4 

allocations for each refuge remains the same.

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: DFG, the 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, 
3406(d) Introduction 87

Table 16. Water Allocations by Refuge from 1989 Reports

Refuge Name - Region

Full Level 4 

Water (AcreFeet)

Level 2 

Water (AcreFeet)

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 Wildlife 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

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.

Table 15. Refuge Water Type and Mandated Target

Water Type

Volume Required by the Act 

(Acre-Feet Per Year)

Level 2 water 396,244a

Incremental Level 4 water 159,271a

Full Level 4 water 555,515

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.

Joaquin River. The fi nal report was issued in 2008 

and its conclusions 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.
88 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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

Per the Act, Full Level 4 water supplies were to be 

delivered to all CVPIA refuges on an annual basis 

by 2002. From 2002 to 2008, the Water Acquisition 

Program (WAP) acquired between 45,000 and 85,000 

acre-feet each year of Incremental Level 4 water. 

These acquisitions relied 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 average of this volume represents 

approximately 40 percent of the mandated quantity 

(159,271 acre-feet).

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. 

Measuring Success

The recent history of very dry conditions explains the 

program’s inability to come anywhere near the target 

acquisition volume of 159,271 acre-feet of water, and 

when coupled with current lower storage conditions in 

the Central Valley Project, also presents the very real 

possibility that these shortfalls may continue into the 

future.

Water Acquisition Program – 

Refuge Water Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$6,782,000 (Restoration Fund)

Accomplishments

• Acquired 30,308 acre-feet of water for 

Incremental Level 4 deliveries

Ross’s Geese, Merced National Wildlife Refuge
3406(b)(3) and (d)(2) 89

Water Year 2008 was much the same story. Critically 

dry conditions throughout the state meant a paucity of 

willing sellers, and consequently the WAP was able to 

purchase only 30,308 acre-feet for Incremental Level 4 

purposes.

Approximately 24,132 acre-feet was obtained from 

the Exchange Contractors, as well as 3,222 acre-feet 

from Stevinson Water District and 2,954 acre-feet from 

a groundwater project operated by Grassland Water 

District. Table 17 shows the actual water deliveries for 

Level 2 and Incremental Level 4.

Table 17. Level 2 and Incremental Level 4 Water Deliveries by Water Year (2002-2008)

a Water Year is defi ned as beginning on the fi rst day of March through the last day of February of the following year. b 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. c Delivery amounts do not include Pixley or Merced.

Water Yeara

Level 2 - Actual Deliveries and 

Percent of Target 422,251b

(Acre-Feet)

Incremental Level 4 – Actual 

Deliveries and Percent of Target 

133,264b (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%)

2008 386,181c (91%) 35,566c (27%)
90 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

CVPIA Section 3406(d)(5)

As of 2008, 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 – 

2008 Accomplishments

Reclamation completed the Final Conveyance of Refuge 

Water Supply South San Joaquin Valley Study Area 

Mendota Wildlife Area Environmental Assessment/

Refuge Facilities Construction 

Program and San Joaquin Basin 

Action Plan Lands Program 

Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$10,264,000 (Facilities Construction – Restoration 

Fund)

$941,000 (San Joaquin Basin Action Plan Lands – 

Restoration Fund)

$42,000 (San Joaquin Basin Action Plan Lands – 

Water & Related)

Accomplishments

• Completed the Final Conveyance of Refuge 

Water Supply South San Joaquin Valley Study 

Area Mendota Wildlife Area Environmental 

Assessment/Impact Statement 

• Continued 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

• Completed two HEC-RAS model alternatives for 

the conveyance facilities of the BWGWD

• Completed major construction and preliminary 

testing of the Phase I, East Bear Creek Pumping 

Plant and Pipeline at the San Luis NWR in Los 

Banos, CA

East Bear Creek Unit, Phase 1, Water Regulating 

Tank
3406 (d)(5) 91

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 Final Mendota WA EA/IS was released 

in May 2008 and is available on the Reclamation web 

site.

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%)

2008 31 actions (67%)

Table 18. Cumulative Completed Construction 

Actions by Year (1997-2008)

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. This report analyzes 

several aspects of the proposed conveyance facility 

including canal water levels, fl ow through the facility, 

and seepage; the report also provides a list of system 

improvements and cost estimates. The program 

completed two HEC-RAS model alternatives for the 

conveyance facilities of the BWGWD. The alternatives 

study the extent of conveyance system improvements 

needed to satisfy the delivery of Full Level 4 water 

supplies to the Gray Lodge WA.

San Joaquin Basin Action Plan - 2008 

Accomplishments

Work in FY 2008 consisted of the completion of major 

construction and preliminary testing of the Phase I, East 

Bear Creek Pumping Plant and Pipeline at the San Luis 

NWR in Los Banos, CA. Final testing and training 

exercises are expected to occur in the fi rst quarter of FY 

2009 and the project will be substantially complete the 

second quarter of FY 2009.

East Bear Creek Unit, Phase 1, Pumping Plant and Surge Tank
92 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Refuge Water Conveyance 

(Wheeling) Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$137,000 (Restoration Fund)

Accomplishments

• Delivered approximately 400,362 acre-feet of 

Level 2 water to the refuges; 41,111 acre-feet 

from diverse sources such as groundwater, water 

rights water, and mitigation water. 

• Delivered approximately 37,066 acre-feet of 

Incremental Level 4 water. 

• Finalized negotiations with Biggs West Gridley 

Water District and the California Department of 

Fish and Game resulting in a water accounting 

methodology for deliveries to the Gray Lodge WA 

• Negotiated a fourth amendment to extend the 

groundwater pumping reimbursement agreement 

with DFG. Groundwater combined with limited 

surface water deliveries provides Full Level 2 

allocation at Gray Lodge WA 

• Continued the cost share development process 

to determine current cost share apportionment 

for the State of California related to Incremental 

Level 4 water supplies

• Continued management of a conservation 

easement of 113 acres of giant garter snake 

mitigation habitat

Colusa NWR, Giant Garter Snake Habitat 

Increased

CVPIA Sections 3406(d)(1), (2), and (5)

Reclamation delivered approximately 92 percent of the 

mandated Level 2 water on average, between Water Year 

(WY) 2002 and WY 2008. This includes water from 

sources other than CVP yield. 

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 that benefi ts early migrant waterfowl and 

shorebirds; habitat is also provided for resident wildlife 

and their young during a critical time of the year when 

wetland habitat can be particularly limited 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 from this 

habitat diversity. 

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.
3406 (d)(1), (d)(2) and (d)(5) (Wheeling) 93

Reliable water supply has signifi cantly improved the 

battle against avian disease outbreaks, such as botulism 

and cholera by creating a “fl ow through” system of water 

delivery and drainage. This “fl ow through” reduces the 

stagnant conditions under which avian diseases thrive. 

It 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. 

Measuring Success

In WY 2008, approximately 400,362 acre-feet of Level 

2 water was delivered to the refuges. Of that number, 

41,111 acre-feet were from diverse sources other than 

Project water, such as water rights water, groundwater 

and mitigation water from a Federal Energy Regulatory 

Commission (FERC) licensing agreement. In addition, 

approximately 37,066 acre-feet of Incremental Level 4 

water was delivered to the refuges.

In Fiscal Year 2008, Reclamation fi nalized negotiations 

with Biggs West Gridley Water District (BWGWD) 

and DFG resulting in a water accounting methodology 

that provides for equitable accounting of DFG water 

rights water, Project water, and Reclamation acquired 

water delivered to the Gray Lodge WA through the 

BWGWD facilities. Reclamation also negotiated a 

fourth amendment to extend the groundwater pumping 

reimbursement agreement with DFG. Groundwater 

is combined with limited surface water deliveries to 

provide full Level 2 allocation at Gray Lodge WA until 

facilities improvements to BWGWD are complete. 

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 seven federal 

fi scal years, and efforts are coordinated with the 

Service, DFG, and DWR. The resulting task order will 

culminate with an invoice to DFG for their cost share. 

Reclamation and the Service continued management of a 

conservation easement of 113 acres of giant garter snake 

habitat from May 1 through September 30, 2008, on a 

privately-owned site in Glenn County. This habitat was 

restored in 2002 and is maintained annually to satisfy 

the mitigation requirements made necessary by refuge 

conveyance construction activities in the Sacramento 

Valley. 

Kern NWR, Tri-colored Blackbird Habitat and Nest Success Improved
94 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 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 Ecosystem and Water Systems 

Operations Models Program (EWSOMP) 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 

continues to support hydrologic and biologic data 

collection. Measures to determine the effectiveness of 

the models and timeframes for this program have not yet 

been determined.

The program is an essential tool for Interior. Since 

1998 EWSOMP has provided a high level of support 

for the development of the integrated CVP/SWP model, 

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

for planning investigations, including the 2008 CVP 

OCAP. CalSim II has been used in many other studies, 

including the ongoing CALFED storage and conveyance 

investigations. CalSim II is available for public review 

and use. A new version of the model, CalSim III and a 

Ecosystem and Water Systems 

Operations Models Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$402,000 (Restoration Fund)

$735 (Water & Related)

Accomplishments

• Completed a QA/QC review of the Sacramento 

Valley hydrology –CalSim III 

• Implemented a QA/QC review of the San Joaquin 

Valley – CalSim III

• Developed a GIS based interface to increase user 

accessibility – CalSim II

• Used modeling in support of the 2008 OCAP 

Biological Assessments - CalSim II, SALMOD and 

various temperature models

• Continued testing the model and added climate 

change impacts and sea level rise capability – 

CalLite

• Applied the upper Sacramento River Water 

Quality model (USRWQM) and the San Joaquin 

temperature model that provide simulations of 

water temperature 

• Continued the development and application 

of ecosystem models to evaluate the effects 

of reservoir operations and river fl ows on 

anadromous fi sh and riparian habitats on the 

Sacramento River - CalSim, USRWQM and 

RHEM

• Continued the development of surface and subsurface watershed and operations model linkage 

– HGS and CalSim
3406(g) 95

water management screening tool, CalLite, are currently 

being developed jointly by Reclamation and DWR. The 

CalSim III model, scheduled for release in summer 

2009, will have substantially improved spatial resolution, 

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

EWSOMP 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 seven other models; two additional models are 

currently under development (Table 19).

The program goal is to complete at least nine models. 

Currently, the Upper Sacramento River Water Quality 

Model (USRWQM) is complete; six models are 

complete, but are being updated (CalSim II, RHEM, 

LAWS, ECOSIM, InSalmo, and SALMOD); and four 

models are not complete (CalSim III, San Joaquin Basin 

Temperature Model, HydroGeoSphere, and CalLite).

Of the models listed in Table 19, the following are 

currently under development or undergoing signifi cant 

modifi cations: 

Water Operations Tools – CalSim II/III Model

The major accomplishments for the CalSim II model in 

FY 2008 included: a GIS based interface was developed 

that allowed the CalSim II model to be more readily 

accessible to users and the 2008 OCAP Biological 

Assessments modeling relied heavily on CalSim II, the 

salmon habitat suitability model (SALMOD) and various 

temperature models.

New hydrologic datasets for CalSim III in the 

Sacramento and San Joaquin valleys were developed in 

2007. Additionally, the program completed signifi cant 

improvements for the CalSim III model including 

enhanced methods for evaluating hydrologic inputs, 

groundwater simulation capabilities, and more consistent 

implementation of hydrology and groundwater in both 

the Sacramento and San Joaquin Valleys. In FY 2008, 

Reclamation, DWR and Service modelers continued 

the development and applications of water operations 

and water management tools. These activities included 

participation in a multi-agency effort to review and 

improve the CalSim III model for the Sacramento and 

San Joaquin Valleys. FY 2008 CalSim III activities 

also included completion of a quality assurance/quality 

control (QA/QC) review of the Sacramento Valley 

hydrology to improve the simulation of agricultural, 

environmental and municipal water supplies and 

demands and implementation of a QA/QC review of the 

San Joaquin Valley. 

Water Management Tool – CalLite Model

The CalLite model is under development and can 

simulate water conditions in the Central Valley over 

an 82-year planning period in under fi ve minutes 

and can be used to modify a variety of interactive 

water management actions including new conveyance 

facilities, off-stream storage reservoirs, groundwater 

management programs, and river and Delta channel 

fl ow and salinity targets. In addition, it can be used to 

simulate observed or possible future hydrologic regimes 

to represent climate change impacts and sea level 

rise. This tool will provide more rapid and interactive 

policy evaluation. In FY 2008, Reclamation and DWR 

continued testing the model, in addition to the base 

model; the climate change impacts and sea level rise 

capability were added to the model. The base model is 

planned for public release in spring 2009.

Ecosystem Modeling Tools Development

The program continued developing and applying 

ecosystem models to evaluate the effects of reservoir 

operations and river fl ows on anadromous fi sh and 

riparian habitats on the Sacramento River. These 

activities included the use of several existing models 

including CalSim, Upper Sacramento River Water 

Quality Model (USRWQM), and Riparian Habitat 

Establishment Model (RHEM). 
96 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

Table 19. Ecosystem and Water Systems Operations Models (1996-2008)

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, 

federal/state water contractors, 

Sacramento Valley Settlement 

contractors and San Joaquin Valley 

Exchange Contractors

Used for coordinated system-wide 

planning and operations of CVP and 

SWP water projects

CalLite 2007 Reclamation, DWR and state 

water contractors

Used for coordinated system-wide 

operations and water management 

decision projects

Upper 

Sacramento 

River Water 

Quality Model 

(USRWQM)

2001/2003 Reclamation, Service, NOAA, 

NMFS and CALFED Integrated 

Storage Investigation (ISI)

Used for planning and operations 

of reservoirs for water temperature 

management in anadromous fi sh 

spawning and rearing habitats

San Joaquin 

Basin 

Temperature 

Model

2005/2007 Consultants and Reclamation Used to simulate fl ow and water 

temperature relations correlating to 

reservoir operations 

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

Consultants under contract to the 

Service

Used in planning studies to evaluate 

effects of reservoir operations on 

anadromous fi sh spawning, incubation 

and rearing 

SALMOD 1996/2005 USGS and Reclamation consultants Used in planning studies to evaluate 

effects of reservoir operations 

on anadromous fi sh spawning, 

incubation and rearing habitats

Land Atmosphere 

Water Simulation 

(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 

including CVP/SWP operations
3406(g) 97

In FY 2008, results from the USRWQM water model 

were used as inputs to SALMOD to evaluate the 

effects of alternatives for the Shasta Enlargement and 

North of Delta Off-stream Storage EIS/R, feasibility 

investigations, and OCAP biological assessments. These 

models have been used to evaluate the benefi ts and 

impacts of alternate water management strategies for the 

Sacramento River. 

Reclamation staff completed initial model development 

and fi eld data collection studies for the RHEM in 2007. 

In 2008, a controlled fi eld study of cottonwood seedling 

growth was performed to develop parameters for the 

RHEM; additional development of a two-dimensional 

version of the RHEM is under way. 

The Ecologically Cogent Operations Suite of Integrated 

Models (ECOSIM) had some minor improvements in 

2008, including completing modifi cations to the water 

module code to dynamically simulate the Yuba River 

sub-system. More major improvements are planned for 

FY 2009. 

HydroGeoSphere (HGS) – Thermal/

Temperature Transport Module Development

The HGS model was modifi ed to link the model to 

CalSim and to incorporate a temperature module. 

The linkage of the HGS and CalSim includes four major 

tasks. These tasks include: 1) conduct literature review; 

2) modify code; 3) verify and validate the linkage and 

4) prepare historical and future meteorological data 

for input into the linked model. Most of the sub-tasks 

under Task 1 for literature review were completed in 

2008, with the exception of the linkage approach and 

fi nalization of the Task 1 report.

The major tasks for temperature module incorporation 

are: 1) apply fi eld data and information into the model; 

and 2) test and verify the module with San Joaquin 

Valley fi eld conditions. In 2008, with the assistance of 

the consultants (University of Waterloo), a temperature 

module was incorporated, verifi ed, and validated. 

Water Quality Modeling Tools – Water Quality 

and Temperature Models

The water quality modeling activities in 2008 included 

the application of the USRWQM and the San Joaquin 

Basin temperature model that provide simulations of 

water temperature for planning, operations, and river 

restoration projects of the Sacramento and San Joaquin 

Basin. The San Joaquin temperature model is used 

to evaluate fl ow and temperature relation for the San 

Joaquin River Restoration Program.
98 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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 produced, and provides the 

opportunity to protect and restore the retired land for 

wildlife habitat.

The San Joaquin Valley Drainage Program (SJVDP) 

recommended retiring 75,000 acres of drainage impaired 

farmland from irrigated agricultural production by 2040 

(SJVDP, 1990). The LRP 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 

 Land Retirement Program Sacramento

San Francisco

Los Angeles

FY 2008

Funding Obligation

$630,000 (Restoration Fund)

Accomplishments

• Retired 320 acres from agricultural production

• Restored 320 acres to upland habitat by planting 

three native seed mixes and installed artifi cial kit 

fox burrows at the Atwell Island Land Retirement 

Demonstration Proeject site

• Eliminated the production of 3,500 acre feet of 

poor quality agricultural drainage

• Produced over 1,000 pounds of native seed for 

site restoration at the San Joaquin Valley Native 

Plant Nursery

Restored Native Flora at the Atwell Island LRDP Site
3408(h) 99

Island, managed by BLM) to study the environmental 

impacts of land retirement and to evaluate cost-effective 

restoration strategies for retired lands (Figure 30). 

Measuring Success

Retiring and Restoring Lands

Of the targeted 15,000 acres, to date Interior has 

acquired approximately 9,300 acres and retired 

(removed from irrigated agriculture) approximately 

8,900 acres from agricultural production. In 2008, the 

program restored 320 acres of retired land to upland 

wildlife habitat (Table 20).

On average, the LRP has exceeded its land restoration 

performance goal of 400 acres per year. Since 1998, the 

LRP has restored approximately 5,300 acres. Complete 

restoration to upland habitats found in the San Joaquin 

Valley will take many years to achieve, but the program 

has developed cost effective restoration techniques and 

continues to adapt these 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 18,000 observations. Using the 

database, BLM developed plant and animal lists and a 

photo-illustrated fl ora for the Atwell Island Project Area.

In 2008, BLM planted 320 acres with three native seed 

mixes at the Atwell Island LRDP site. Artifi cial kit fox 

burrows were also installed on ecological restoration 

sites at the Atwell Island LRDP site.

At Tranquillity, the San Joaquin Valley Native Plant 

Nursery produced more than 1,000 pounds of native 

seed propagated from more than 100 plants species 

collected within a 50-mile radius of the site. 

Reducing Agricultural Drainage 

Implementating the LRDP has eliminated the production 

of approximately 3,500 acre feet of poor quality 

drain water annually, including in 2008. Five years 

of groundwater monitoring at the LRDP sites show 

a declining shallow water table in response to land 

retirement. The water table responses observed at the 

LRDP sites are representative of conditions present 

at a high percentage of lands that are targeted for 

retirement in the western San Joaquin Valley and the 

Tulare Lake Basin. The declining shallow water table 

observed beneath demonstration project lands indicates 

the success of land retirement as a drainage reduction 

strategy. 

The declining shallow water table is an important 

aspect of land retirement because the groundwater 

beneath the LRDP lands is generally of poor quality 

with high concentrations of salt and trace elements 

such as selenium. As long as the water table continues 

to decline as expected in response to land retirement, 

the 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 LRDP study. Selenium concentrations 

in biota have not changed signifi cantly over the study 

period and are below concentrations of concern to the 

U.S. Environmental Protection Agency (EPA) and the 

Service.

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 30. Land Retirement Program Sites
100 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2008 ANNUAL REPORT

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

(1992-2008)

Acres Acquired 

(Annual)

Acres Retired 

from Agriculture 

(Annual)

Acres Restored 

(Annual)

Year Atwell Island Tranquillity

Atwell Island and 

Tranquillity

Atwell Island and 

Tranquillity

1992 0 0 0 0

1993 0a 0 0 0

1994 0 0 0 0

1995 0 591 591 0

1996 0 0 0 0

1997 0 0 0 0

1998 0 995 994 1,220

1999 0 60 61 100

2000 2,645b 0 2,645 777

2001 1,414 444 686 702

2002 1,510 0 1,698 373

2003 616 0 250 261

2004 155 0 570 308

2005 625 0 850 349

2006 38 0 38 416

2007 213 0 213 475

2008 0 0 320 320

TOTAL 7,216 2,090 8,916 5,301

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.

102 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2008 ANNUAL REPORT

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/SacramentoSan Joaquin River Delta 

Capillary rise: Movement of water upwards from 

the water table (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 water table), 

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

Central Valley Habitat Joint Venture (CVHJV): 

The association of federal and state agencies 
APPENDIX A 103 

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 hatcheryborn

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 CVPIA provisions 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 Sacramento-San Joaquin 

Delta; pelagic organisms include, most notably, 

the delta smelt and longfi n smelt, federallylisted 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
104 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2008 ANNUAL REPORT

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: 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

106 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2008 ANNUAL REPORT

AF acre-feet

AFRP Anadromous Fish Restoration Program

AFSP Anadromous Fish Screen Program 

BA Biological Assessment

BLM Bureau of Land Management

BMP Best Management Practices

BO Biological Opinion

BWGWD Biggs West Gridley Water District

CAMP Comprehensive Assessment and Monitoring Program

CCWD Contra Costa Water District

CFS Cubic Feet per Second

CNDDB California Natural Diversity Database

CPAR CVPIA Program Activity Review

CVO Central Valley Operations Offi ce

CVP Central Valley Project

CVPIA (Act) Central Valley Project Improvement Act

DFG California Department of Fish and Game

DMC Delta Mendota Canal

DOI (Interior) Department of the Interior

DWR California Department of Water Resources

EA Environmental Assessment

EBMUD East Bay Municipal Utility District

ECOSIM Ecologically Cogent Operations Suite of Integrated Models

EIR Environmental Impact Report

EIS Environmental Impact Statement

EPA US Environmental Protection Agency

ERP Ecosystem Restoration Program

ESA Endangered Species Act

EWA Environmental Water Account

EWSOMP Ecosystems and Water Systems Operations Models Program

FERC Federal Energy Regulatory Commission

FMP Fisheries Management Plan

FWS (Service) US Fish and Wildlife Service

FY Fiscal Year

GCID Glenn-Colusa Irrigation District

GIS Geographic Information System

GPM Gallons per Minute

GPS Global Positioning System

GWD Grassland Water District

APPENDIX B: ACRONYMS
APPENDIX B 107 

HRP Habitat Restoration Program

ID Irrigation District

IEP Interagency Ecological Program

IFIM Instream Flow Incremental Methodology

ISI Integrated Storage Investigation

JPP Jones Pumping Plant

LAWS Land Atmosphere Water Simulation

LRDP Land Retirement Demonstration Project

LRP Land Retirement Program

LTP Long-term Plan

LTRC Long-Term Renewal Contracts

NEPA National Environmental Policy Act

NFH National Fish Hatchery

NMFS National Marine Fisheries Service

NOAA National Oceanic and Atmospheric Administration

NPS National Parks Service

NRCS Natural Resource Conservation Service

NWR National Wildlife Refuge

OCAP Operations Criteria and Plan

OMB Offi ce of Management and Budget

PART Program Assessment Rating Tool

PEIS Programmatic Environmental Impact Statement

PEIS/R Programmatic Environmental Impact Statement/Report

PG&E Pacifi c Gas & Electric

POD Pelagic Organism Decline

QA Quality Assurance

QC Quality Control

RBDD Red Bluff Diversion Dam

RBRPP Red Bluff Research Pumping Plant

RD Reclamation District

RHEM Riparian Habitat Establishment Model

ROD Record of Decision

ROI Return on Investment

RWSP Refuge Water Supply Program

SDFF South Delta Fish Facility Forum

SDIP South Delta Improvement Program

SDP Station Development Plan

SHIRA Spawning Habitat Integrated Rehabilitation Approach

SJRA San Joaquin River Agreement 

SJRGA San Joaquin River Group Authority

SJRRP San Joaquin River Restoration Program

SJVDP San Joaquin Valley Drainage Program

SNWR Sacramento National Wildlife Refuge

SRSC Sacramento River Settlement Contracts

SWP State Water Project

TAF Thousand acre-feet

TFCF Tracy Fish Collection Facility

TFFIP Tracy Fish Facility Improvement Program

TRRP Trinity River Restoration Program

UC University of California
108 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2008 ANNUAL REPORT

USCOE US Army Corp of Engineers

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

YOY Young-of-the-Year