U.S. Department of the Interior

Bureau of Reclamation

U.S. Fish and Wildlife Service

Central Valley Project 

Improvement Act

Public Law 102-575

ANNUAL REPORT

Fiscal Year 2009

TABLE OF CONTENTS i

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

II. INTRODUCTION ................................................................................................... 7

III. 2009 PROGRAM ACTIVITIES AND ACCOMPLISHMENTS .............................. 19

Section 3406 Activities:

(b)(1) Anadromous Fish Restoration Program .............................................................. 20 

(b)(1) “other” Habitat Restoration Program ............................................................................... 29

(b)(1) “other” & (b)(23) Trinity River Restoration Program........................................................................ 35

(b)(1)(B) Modifi ed CVP Operations .................................................................................... 39

(b)(2) Dedicated 800,000 acre-feet Project Yield ......................................................... 42

(b)(3) & (g) Water Acquisition Program – Instream Water ..................................................... 45

(b)(4) Tracy (Jones) Pumping Plant Program ................................................................ 47

(b)(5) Contra Costa Canal Pumping Plant ..................................................................... 51

(b)(9) & (b)(19) Flow Fluctuations and Reservoir Storage ............................................................ 53

(b)(10) Red Bluff Diversion Dam ..................................................................................... 55

(b)(11) Coleman National Fish Hatchery ........................................................................ 59

(b)(12) Clear Creek Restoration Program ....................................................................... 62

(b)(13) Spawning and Rearing Habitat Restoration Program.......................................... 66

(b)(15) Head of Old River Barrier .................................................................................... 70

(b)(16) Comprehensive Assessment and Monitoring Program ....................................... 73

(b)(20) Glenn-Colusa Irrigation District Program ............................................................ 81

(b)(21) Anadromous Fish Screen Program ..................................................................... 83 

(c)(1) San Joaquin River Restoration Program ............................................................. 87

(b)(3), (d)(1), (2) & (5) Introduction to the Refuge Water Supply Program .............................................. 90

(b)(3) & (d)(2) Water Acquisition Program - Refuge Water ......................................................... 95

(d)(5) Refuge Facilities Construction Program and San Joaquin Basin Action Plan ........97

 Lands Program

(d)(1), (2) & (5) Refuge Water Conveyance (Wheeling) Program ................................................ 99

(g) Ecosystem and Water Systems Operations Models ........................................ 101

Section 3408 Activities:

(h) Land Retirement Program ................................................................................. 105

Appendices:

Appendix A Glossary of Terms .............................................................................................. 109

Appendix B Acronyms ............................................................................................................113

Contents
ii CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2009 ANNUAL REPORT

List of Figures

Figure 1 Central Valley Project System (Map) .................................................................................... 9

Figure 2 CVPIA Provisions by Resource Area ..................................................................................11

Figure 3 Central Valley Refuges Receiving CVPIA Water Supplies (Map) ...................................... 12

Figure 4 Total CVPIA Obligations by Action Category and Fund Source (1993-2009) .................... 13

Figure 5 Habitat Restoration Program Project Locations (Map) ....................................................... 31

Figure 6 Trinity River Restoration Program (Map) ............................................................................ 36

Figure 7 Tracy (Jones) Pumping Plant (Location) ............................................................................. 48

Figure 8 Rock Slough Fish Screen (Proposed) (Location) ............................................................... 52

Figure 9 Red Bluff Diversion Dam (Location) ................................................................................... 56

Figure 10 Spawning Returns, Winter-Run Chinook, Sacramento River (1967-2008) (Graph) ........... 57 

Figure 11 Coleman National Fish Hatchery (Location) ...................................................................... 60 

Figure 12 Gravel Injection and Channel Restoration Sites, Clear Creek ........................................... 63 

Figure 13 Fall-Run Chinook Salmon Escapement, Clear Creek (2008) ............................................. 64 

Figure 14 Adult Spring-Run Chinook Salmon Population, Clear Creek (2001-2009) ........................ 64 

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

 Clear Creek (1998-2008) .................................................................................................... 64

Figure 16 Clear Creek Channel Restoration Project Phases ............................................................. 65

Figure 17 Recent Gravel Placement Sites in the Sacramento, American, and 

 Stanislaus Rivers ................................................................................................................ 67

Figure 18 Spawning Locations on the American River at the Sailor Bar Gravel Placement

 Area During FY 2009 ......................................................................................................... 69

Figure 19 Estimated Total Natural Chinook Production, Central Valley (1992-2008) .......................... 75

Figure 20 Estimated Abundance of 15-year-old White Sturgeon in San Pablo and Suisun .............. 76

 Bays, 1993-2005

Figure 21 Estimated Abundance of Adult Green Sturgeon in San Pablo and Suisun Bays,

 1993-2005 .......................................................................................................................... 76

Figure 22 Estimated Abundance of Adult Striped Bass in the Sacramento-San Joaquin

 River Delta and the Lower Portions of the Sacramento and San Joaquin Rivers,

 1992-2007. .......................................................................................................................... 77

Figure 23 Midwater Trawl Index for Young-of-the-year American Shad in the Sacramento-San

 Joaquin River Delta and San Pablo and Suisun Bays, 1992-2008 ................................... 77

Figure 24 Glenn-Colusa Irrigation District Pumping Plant ................................................................. 82

Figure 25 CVPIA Fish Screens Constructed (1992-2009) .................................................................. 86

Figure 26 Central Valley Refuges Receiving CVPIA Water Supplies ................................................. 91

Figure 27 Land Retirement Program Sites ....................................................................................... 106
TABLE OF CONTENTS iii

List of Tables

Table 1 FY 2009 Funding Obligations by CVPIA Provision ............................................................ 14

Table 2 AFRP Fish Production Estimates in All Central Valley Streams (1992-2008) .................... 28

Table 3 Chinook Salmon AFRP Production, in Battle, Butte and Clear Creeks, and

Mokelumne River (1992-2008) ...................................................................................................28

Table 4 Acres of Habitat Protected & Restored per Year (1996-2009) by the

 Habitat Restoration Program .............................................................................................. 30

Table 5 FY 2009 Projects Funded by the Habitat Restoration Program (HRP) .............................. 33

Table 6 Annual Target Escapement, Trinity River ........................................................................... 37

Table 7 Instream Flow Incremental Methodology (IFIM) Studies Active as of 2009 ....................... 41

Table 8 FY 2009 Use of (b)(2) Water by Location ........................................................................... 44

Table 9 Allocation and Use of (b)(2) Water (2001-2009) ................................................................. 44

Table 10 Annual (b)(3) Instream Water Acquisitions, toward 200,000 acre-feet target

 (1994-2009) ........................................................................................................................ 46

Table 11 Actions to Improve Tracy Fish Collection Facility, Completed to Date ............................... 50

Table 12 Coleman National Fish Hatchery (NFH) Facility Rehabilitation Phases (1991-2009) ........ 61

Table 13 Total Gravel (Tons) Placed by River (1997-2009) ............................................................... 68

Table 14 CAMP Recommended Monitoring Elements by Watershed, Implemented in 2009 .......... 78

Table 15 AFSP Projects and Cubic Feet per Second (cfs) Screened, Central Valley

 (1992-2009) ........................................................................................................................ 84

Table 16 Refuge Water Type and Mandated CVPIA Target .............................................................. 93

Table 17 Water Allocations by Refuge from 1989 Reports ............................................................... 93

Table 18 Cumulative Completed Construction Actions by Year (1997-2009) for the Refuge

 Facilities Construction Program and San Joaquin Basin Action Plan Lands Program ...... 98

Table 19 Ecosystem and Water Systems Operations Models Developed (1996-2009) ................. 103

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

 Island Sites (1992-2009) ................................................................................................... 107

EXECUTIVE SUMMARY 1

Since 1992, the Bureau of Reclamation (USBR or 

Reclamation) and the Fish and Wildlife Service (USFWS 

or 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 CVPIA Program continues 

to build upon the results from ongoing implementation 

studies and modeling, and adapts future actions to 

refl ect knowledge gained.

The total funding obligated for the Central Valley 

Project Improvement Act (CVPIA) Program 

activities for fi scal year (FY) 2009 (October 1, 2008 - 

September 30, 2009) was $96.7 million which included 

approximately: $59 million from the Restoration 

Fund, comprised of $56.1 million from the FY 2009 

appropriation and $2.9 million from prior year funds; 

$16.1 million from the Water and Related Resources 

Fund; $13.5 million from the American Recovery and 

Reinvestment Act (ARRA) Fund; $2.9 million from the 

Bay-Delta Fund; and $5.2 million from the State costshare funds.1

 These funds were used to achieve progress 

toward program goals in FY 2009.

PROGRESS TOWARD GOALS

The CVPIA Program developed a Draft Implementation 

Plan (IP) that proposes to provide focus and direction 

for the CVPIA Program for the coming 10 years (2010-

2019); it provides the foundation for planning, budgeting, 

performance management, and accountability processes. 

The IP was developed over a two year planning process 

1 This funding was an accounting adjustment that resulted in an 

obligation of $5.2 million under the State cost-share funds.

I. Executive Summary

that included both internal and external review. The 

internal review included participation by Reclamation 

and Service program managers, biologists, and 

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

program implementation. Two independent reviews, for 

the fi sheries program and refuge water supply program 

(RWSP), were conducted for the external review. The 

IP is currently under review by both the Service and 

Reclamation.

As stated above, the CVPIA Program conducted 

independent reviews for the fi sheries program and the 

refuge water supply program. The independent review 

panels provided programmatic recommendations to 

improve effectiveness and effi ciency of the programs. 

Certain independent review recommendations were 

incorporated as future strategies and implementation 

Black Necked Stilt - Merced National WIldife Refuge
2 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

activities in the IP. The agencies are optimistic about 

the ability to improve the fi sheries program and refuge 

water supply program by adopting many of the panel’s 

recommendations.

Over the past 17 years, the CVPIA Program has made 

signifi cant improvements to wildlife and fi sh habitat 

by restoring habitat and enhancing fi sh passage and 

survival. The enormity and complexity of the Central 

Valley ecosystem requires a comprehensive approach 

with participation at all levels. The CVPIA Program 

must also contend with recent events such as drought, 

poor ocean conditions, and pelagic organism decline. 

Despite these continued challenges, the CVPIA Program 

progresses toward meeting restoration goals, based on 

the ongoing partnerships with stakeholders and closely 

coordinated implementation of activities. The ongoing 

activities are comprised of operational and structural 

improvements and include monitoring and modeling 

efforts. This section highlights progress made to date 

for activities conducted within the main resource areas 

of fi sheries, refuge water supply and other sources. A 

full description of the CVPIA Program restoration 

progress and accomplishments is contained in the 

individual programs outlined in this report.

Central Valley Fisheries

This section focuses on the Anadromous Fish 

Restoration Program (AFRP) which serves as the 

overarching program to address the “fi sh-doubling 

goal.” A discussion on the San Joaquin River 

Restoration Program (SJRRP), and the Trinity River 

Restoration Program (TRRP) also follows:

Anadromous Fish Doubling Goal

The “fi sh-doubling” goal refers to the provisions in 

the CVPIA Section 3406 (b)(1) which requires the 

natural production of anadromous fi sh in Central Valley 

rivers and streams to be sustainable, on a long-term 

basis, at levels not less than twice the average levels 

attained during the period of 1967-1991. The Final 

Restoration Plan developed by AFRP in 2001, guides 

the implementation of the actions and evaluations which 

were developed to address the doubing goal. The AFRP 

doubling goal is also supported by the other CVPIA 

programs responsible for restoring habitat, modifying 

water operations, enhancing fi sh passages, monitoring 

progress and modeling water strategies.

For example, the Comprehensive Assessment and 

Monitoring Program (CAMP) assesses the progress 

toward the AFRP fi sh-doubling goals. CAMP’s 2009 

Annual Report contains anadromous fi sh monitoring 

data collected between 1992 and 2008 on 22 watersheds 

(USFWS, 2009). As of 2008, the average natural 

production for all races of Chinook salmon was 452,243, 

or approximately 46 percent of the doubling target. 

These numbers for Chinook salmon 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 (CDFG) Grand Tab2

. 

Following are trends for fi sh species in the Central 

Valley:

• Chinook winter-run production numbers have been 

trending upward since 1996, but showed a sharp 

decline in 2007 and 2008.

• Chinook spring-run numbers have generally 

improved since 1991, but declined precipitously in 

2008.

2

 The Grand Tab Report is a compilation of sources estimating the 

late-fall, winter, spring, and fall-run chinook salmon populations for 

streams surveyed.

White-faced lbis
EXECUTIVE SUMMARY 3

• Chinook fall-run production increased from the 

early 1990s to 2000, but has consistently declined 

each year since 2002.

• Chinook late fall-run production has increased 

from extremely low levels in the early 1990s, but 

declined precipitously in 2008.

• Steelhead numbers were trending upwards but 

declined in 2004 and have remained low to date.

• During the 1992-2005 timeframe, the estimated 

number of 15-year-old white sturgeon in San Pablo 

and Suisun Bays exceeded the AFRP production 

target in one of seven years when sampling was 

done.

• Green sturgeon numbers have trended upwards 

during the doubling period.

• Striped bass numbers have declined with 2007 

being the lowest estimate on record.

• Since 1967, the highest number of American shad 

occurred in 2003 (9,342); however, the numbers 

declined precipitously in 2008.

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. The greatest success has 

occurred in watersheds 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. 

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.

Trinity River Restoration Program (TRRP)

The Trinity River Restoration Program implements 

river restoration efforts and delivery of fl ows to improve 

anadromous fi sheries habitat. Historically, the Trinity 

River fl ows have been dammed and diverted to the 

Sacramento River providing water to the Central 

Valley for power generation and irrigation purposes. 

The dams and interrupted fl ows barred salmonids 

from upstream habitat and deteriorated downstream 

spawning and rearing habitat causing a severe drop in 

production. The goal of the restoration activities is to 

increase in-river spawner escapement by implementing 

natural and variable fl ow releases, re-constructing the 

river channel, augmenting gravel supply, and reducing 

fi ne sediment supply to the river through watershed 

restoration efforts. Also, since 2005, signifi cant 

progress has been made by completing 17 of the 47 

channel rehabilitation sites identifi ed in the Trinity River 

Mainstem Fishery Restoration Environmental Impact 

Report/Environmental Impact Statement (EIR/EIS) and 

its accompanying Record of Decision (ROD). All of 

the infrastructure improvements necessary to allow the 

program to regularly achieve annual fl ow release goals 

have been implemented.

San Joaquin River Restoration Program 

(SJRRP)

The San Joaquin River Restoration Program (SJRRP) 

is a comprehensive long-term effort to restore fl ows 

and a self-sustaining Chinook salmon fi shery to the 

San Joaquin River from Friant Dam to the confl uence 

of Merced River, while reducing or avoiding adverse 

water supply impacts. Much progress has been made to 

continue to lay the groundwork for the restoration efforts 

on the San Joaquin River including further development 

of environmental planning documents, implementation 

planning for interim fl ow measures, and continued 

data collection and monitoring. The draft Fisheries 

Management Plan (FMP) was recently developed and 

released for public review and sets the foundation for an 

adaptive management approach and identifi es program 

goals and objectives that are focused on meeting the 

requirements of the Settlement restoration goals3

. The 

FMP outlines an approach to adaptively manage the 

reintroduction of Chinook salmon and other fi shes to the 

San Joaquin River.

Refuge Water Supply

The Refuge Water Supply Program (RWSP) is 

comprised of three components: water acquisition, 

conveyance, and facilities construction. The RWSP’s 

goal is to ensure all CVPIA identifi ed refuges (wetland 

3 A stipulation of Settlement (Settlement) was reached on a lawsuit 

known as NRDC, et al., v. Kirk Rodgers, et al.
4 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

habitat areas) annually receive water of a specifi ed 

quantity, suitable fl ow rate, and suitable quality to 

support their wetland and aquatic environments. RWSP 

has an annual water delivery target of 555,515 acrefeet for full Level 4 water; comprised of the Level 2 

annual water delivery target of 396,244 acre-feet and 

Incremental Level 4 water supplies of 159,271 acre-feet.

CVPIA has created Full Level 4 conveyance capacity 

at 14 of the 19 identifi ed refuges served by the program. 

Conveyance capacity at the remaining fi ve refuges will 

be addressed through construction projects planned and 

prioritized for the next 10 years. During 2002 through 

2009, the Water Acquisition Program acquired between 

30,000 and 85,000 acre-feet each year of Incremental 

Level 4 water. Reclamation delivered approximately 

92 percent of Level 2 water on average between 2002 

and 2009, and delivered approximately 52 percent of 

Incremental Level 4 water on average betwen 2002 and 

2009.

The high cost of water continues to limit acquisition 

of Incremental Level 4 water. Purchasing permanent 

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

provides the most reliable source for refuge water, 

but these supplies have not been readily available on 

the market and those that are available have been cost 

prohibitive. 

Other Resources

The Habitat Restoration Program (HRP) has protected 

and restored approximately 105,000 acres since program 

inception. This acreage is almost 4 percent of the 2.7 

million acres restoration goal to restore habitat impacted 

by the Central Valley Project. The HRP’s priority 

actions include purchase of fee title or conservation 

easements on lands where threats are signifi cant; 

restoration of habitats resulting in improved conditions; 

and research to help facilitate species recovery.

The Land Retirement Program (LRP) purchases 

land, water and other property interests to protect 

and restore land for wildlife habitat. The LRP goals 

include: retirement of 15,000 acres of agricultural 

land by 2014; habitat restoration on 400 acres of retired 

lands annually; and the reduction of agricultural 

produced drainage water by 6,000 acre-feet annually. 

Program activities are implemented as part of the Land 

Retirement Demonstration Project (LRDP) and have 

resulted in the retirement of 9,006 acres. The program 

has restored more than 5,600 acres of total acreage 

retired, creating more sustainable uplands habitat. 

2009 ACCOMPLISHMENTS

This section summarizes the specifi c FY 2009 

accomplishments within the following resource areas: 

fi sheries, refuge water supply, and other resources.

Central Valley Fisheries

The AFRP restored fl oodplains on the Sacramento 

River National Wildlife Refuge (NWR); purchased and 

placed 6,400 tons of spawning gravel on the Mokelumne 

River; and completed a feasibility study, environmental 

compliance documents, and project designs to construct 

a bypass for out-migrating salmonids at two screened 

diversions in Antelope Creek.

The Modifi ed CVP Operations Program operated 

the system multiple times to provide benefi ts to 

anadromous fi sh on Clear Creek without impacting other 

CVP obligations or authorized purposes; completed 

monitoring for juvenile spring-run and fall-run Chinook 

salmon and steelhead rearing for the lower reach of 

Clear Creek; and completed modeling and a draft report 

for fall-run Chinook salmon and steelhead spawning on 

Clear Creek.

The Ecosystem and Water Systems Operations Models 

Program applied the CalSim II and CalLite models 

to evaluate provisions in the Delta smelt biological 

opinion4

; assisted the National Marine Fisheries Service 

(NMFS) by utilizing the CalSim II, ECOSIM-W, and 

CalLite models to develop feasible Reasonable and 

Prudent Alternatives (RPA) actions for the NMFS’ 

Operations Criteria Plan (OCAP) biological opinion; 

and applied the Upper Sacramento River Water Quality 

Model to support the Sacramento River Temperature 

Task Group in making and updating plans for the 

summer season reservoir operations, for the purposes 

of complying with NMFS’ biological opinion RPA 

covering endangered winter-run Chinook salmon and 

to aid the planning of operations and comply with State 

Water Resources Control Board Order 95-1.

4 Formal Endangered Species Act Consultation on the Proposed 

Coordinated Operations of the Central Valley Project (CVP) and State 

Water Project (SWP), dated December 15, 2008.
EXECUTIVE SUMMARY 5

The Dedicated 800,000 acre-feet Project-Yield program 

provides for the dedication and management of 800,000 

acre-feet annually for the purposes of implementing 

fi sh, wildlife and habitat restoration. Although, the 

Sacramento and San Joaquin River Basins were 

classifi ed as “dry” in water year 2009 (October 1st - 

September 30th), 600,000 acre-feet was available and 

managed for the purposes of restoration.

The Water Acquisition Program (WAP) acquired 38,500 

acre-feet of water (19 percent of the 200,000 acre-feet 

target) to improve instream fl ows and habitat restoration 

for anadromous fi sh. Acquiring instream fl ows supports 

the AFRP Final Restoration Plan goals to improve 

spawning and rearing habitat; and to increase migration 

fl ows for fall-, winter-, and spring-run Chinook salmon 

and steelhead.

The Tracy (Jones) Pumping Plant Program completed 

recessed holding tank stress tests for various species 

of delta fi sh entrained at the Jones Pumping Plant 

(JPP); completed phase 1 construction of a new onsite 

biological resources building; and commenced with 

planning and review for the Two Gates Fish Protection 

Demonstration Project.

The Contra Costa Canal Pumping Plant Program 

updated screen designs to bring them up to current 

construction code; completed environmental 

documentation and permits for the construction of the 

fi sh screen; started construction of Phase II of the Rock 

Slough Fish Screen; and conducted fi sh monitoring. 

Phase II construction includes improvements such 

as coffer dams and levee embankment construction, 

which follows earlier Phase I construction for road and 

approach improvements.

The (b)(9) Flow Fluctuation and Reservoir Storage 

Program used (b)(2) and (b)(3) 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 Red Bluff Diversion Dam (RBDD) Program 

proceeded on the design of the permanent pumping plant 

which will allow for water diversions of up to 2,500-

cubic feet per second (cfs); designed and constructed an 

interim pumping plant; and implemented operational 

changes to raise the gates a minimum of 18 inches 

to ensure protection of downstream migrating green 

sturgeon. Preliminary results for green sturgeon 

monitoring indicated spawning occurred from lateMarch to early July, and that the abundance of green 

sturgeon adults above RBDD was greater in 2009 than 

2008.

Coleman National Fish Hatchery (NFH) initiated and 

completed construction of the visitor kiosk and included 

an Americans with Disabilities Act (ADA) compliant 

visitor parking area and ramps. No future work is 

planned at this site and these activities are considered 

complete.

The Clear Creek Restoration Program successfully 

met water temperature fl ow objectives during critical 

seasons. Gravel was added to increase spawning habitat 

at Below Dog Gulch (1,000 tons), Above Peltier Valley 

Bridge (770 tons), Paige Bar (1,790 tons), Above NEED 

Camp (980 tons), and Below NEED Camp (1,230 tons). 

Results from monitoring indicated that the program 

has increased the fall-run Chinook escapement, and 

steelhead and spring-run Chinook populations.

The Spawning and Rearing Habitat Restoration Program 

purchased and placed approximately 9,900 tons of gravel 

in the Sacramento River and permitted for and placed 

10,500 tons of spawning gravel on the American River. 

The Program utilizes aerial photos, redd surveys, and 

boat gravel surveys for determining gravel augmentation 

locations.

The Head of Old River Barrier Program installed a 

seasonal, non-physical bubble curtain at the head of Old 

River to allow salmon smolts to stay in the San Joaquin 

River as they migrate out to the ocean. Research 

showed that the bubble curtain deterrance rate for 

Chinook salmon was 81.4%; however, the predation rate 

was also high, creating an offset.

The Glenn-Colusa Irrigation District (GCID) project 

and related testing and monitoring is complete. 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 2009, the program initiated the transfer 

of ownership of the structures to GCID and completed 

the operations and maintenance manual. The project 

and related testing and monitoring are 100% complete.

The Anadromous Fish Screen Program (AFSP) 

completed construction of the Phase I Meridian Farms 

Fish Screen Project to screen 30 cubic feet per second 

(cfs) at the New Grimes diversion (Sacramento River); 

continued implementation of a four-year screening 
and monitoring program on the Sacramento River in 

partnership with CALFED Ecosystem Restoration 

Program (ERP) and the Family Water Alliance; and 

continued to provide technical assistance for on-going 

AFSP projects including the Natomas Mutual (Sacramento 

River), Patterson (San Joaquin River), Reclamation 

District (RD) 2035 (Sacramento River), Meridian Farms 

(Phase II) (Sacramento River), and Yuba City (Feather 

River) fi sh screens.

The Trinity River Restoration Program released fl ows of 

454,500 acre-feet from the Lewiston Reservoir to provide 

adequate temperature and habitat conditions for fi sh and 

wildlife at different life stages. These released fl ows were 

within target fl ows of 369,000 to 815,000 acre-feet per 

year, and also within the dry year-target fl ows of 452,600 

acre-feet. The TRRP also completed construction of a 

one-mile channel rehabilitation site associated with the 

Sawmill Rehabilitation Project; placed approximately 

8,000 cubic yards of coarse sediment in the river; 

completed 10 priority watershed projects; and initiated 8 

new projects.

The San Joaquin River Restoration Program completed a 

draft of the Fisheries Management Plan and distributed it 

for public review; completed environmental compliance 

activities for the fi rst year of initial experimental fl ow 

releases from Friant Dam; and continued development of a 

plan to recirculate water back to the Friant Division longterm contractors.

The CAMP completed an annual report that synthesizes 

and analyzes anadromous fi sh monitoring data collected 

between 1992 and 2008 on 22 watersheds.

Refuge Water Supply

In 2009, the RWSP delivered 367,842 acre-feet of Level 2 

and 39,690 acre-feet of Incremental Level 4 water toward 

meeting the Full Level 4 water target of 555,515 acre-feet. 

The program also negotiated a fi fth amendment to extend 

the groundwater pumping reimbursement agreement with 

the CDFG to supplement Level 2 water at Gray Lodge 

Wildlife Area (WA) up to the full Level 2 allocation.

The Refuge Facilities Construction Program completed 

the draft Design Data Study of the Biggs West Gridley 

Water District (BWGWD) conveyance facilities for 

conveyance of refuge water supplies to Gray Lodge 

Wildlife Area (WA); and the San Joaquin Basin Action 

Plan Lands Program continued testing of the East Bear 

Creek Phase I Pumping Plant and Pipeline at the San Luis 

NWR.

Other Resources

The HRP protected an additional 5,165 acres of new 

habitat. To date, the program has protected approximately 

98,000 acres through fee titles or conservation easements, 

and restored approximately 7,400 acres.

The LRP restored 385 acres to upland habitat by planting 

native seed mixes at the Atwell Island Land Retirement 

Demonstration Project site; retired 90 acres from 

agricultural production; eliminated the production of over 

3,500 acre-feet of poor quality agricultural drainage water; 

and completed a draft report documenting fi ve years of 

physical and biological monitoring at the Atwell Island 

Demonstration Project.

For a complete description of the CVPIA Program 

restoration progress and accomplishments, the individual 

programs and activities are provided in this report.
INTRODUCTION 7

For the past 17 years, the CVPIA has guided the 

implementation of projects supporting the protection, 

restoration and enhancement of fi sh and wildlife 

associated with the Central Valley Project (CVP) 

(Figure 1). 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, approximately $1.1 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. 

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. 

This Annual Report summarizes the actions taken by 

Reclamation and the Service personnel, working with 

other federal agencies, tribes, the State of California 

(State), and numerous partners and stakeholders during 

FY 2009. 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 2009 accomplishments were 

completed with funds that were obligated in prior years.

II. Introduction

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $59 million

• Water & Related - $16.1 million

• State - $5.2 million

• Bay Delta - $2.9 million

• ARRA - $13.5 million

TOTAL - $96.7 million

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 Reclamation or 

the Service.

BACKGROUND

The Central Valley Project’s Role in 

California’s Water Resources

For 74 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 State 

Water Project (SWP). A portion of the water entering 

the delta is pumped south; the majority discharges to 

the San Francisco Bay and the 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 Endangered Species Act (ESA) 

and water quality mandates requires water releases from 
8 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

(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, 

and operational and management directives into the Act 

(Sections 3406 and 3408) that affect a wide variety of 

activities, including:

• Restoration of anadromous fi sh populations 

• Water supplies for State and federal refuges and 

wildlife habitat areas

• Retirement of drainage-impaired agricultural 

lands

• Mitigation for other CVP-impacted fi sh and 

wildlife

• Revisions to water contracts

• Modifi cation of water management and operations

• System-wide modeling to support decision-making

• Program monitoring to determine effectiveness

• Investigations and studies

Reclamation and the Service were joint lead federal 

agencies for the CVPIA Final Programmatic 

Environmental Impact Statement and its Record of 

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

broadly identifi ed the overall program and actions to 

achieve the purposes of CVPIA, including the fi sh and 

wildlife restoration provisions. Although some 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 

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 (Jones) 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 1992, in one of its last actions of the session, the 

102nd Congress 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;
INTRODUCTION 9

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 (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 

Figure 1. Central Valley Project System

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 

Sacramento

San Francisco

Los Angeles
10 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

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. Actions contained 

within the Final Restoration Plan were determined to 

be reasonable given numerous technical, legal, and 

implementation considerations; all AFRP actions are 

covered in the CVPIA PEIS/ROD.

Other CVPIA provisions that support the fi sh doubling 

goal include the fi sh screening activities conducted 

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

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

(20) Glenn-Colusa Irrigation District Program, and 

(b)(21) Anadromous Fish Screen Program (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 (g) 

Ecosystem and Water Systems Operations Model.

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.

The CVPIA also contains provisions for developing a 

restoration plan for the San Joaquin River and instituted 

a fee structure for Friant Division contractors for such 

activities. Planning and environmental studies are 

currently being completed under the authority and 

funding of the CVPIA. A Stipulation of Settlement 

(Settlement) was reached on a lawsuit known as 

NRDC, et al., v. Kirk Rodgers, et al. The Settling 

Parties reached agreement on the terms and conditions 

of the Settlement, which was subsequently approved 

by Federal Court on October 23, 2006. The “Settling 

Parties” include the Natural Resources Defense Council 

(NRDC), Friant Water Users Authority (FWUA), and 

the U.S. Departments of the Interior and Commerce. 

Implementation of the Settlement, including planning, 

environmental studies, and other activities necessary 

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 for a specifi c provision, 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:

• Fisheries Resource Area: Achieving the 

anadromous fi sh doubling goal; improving 

operational fl exibility; modeling and monitoring

• Refuges Resource Area: Providing adequate 

water to wildlife refuges 

• Other Resource Area: Mitigating terrestrial and 

other CVP-related impacts

Figure 2 identifi es the Resource Area for each active 

provision of the Act and shows which provisions are 

completed or inactive.

Fisheries Resource Area 

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, white 

sturgeon, and green sturgeon, which are believed to have 

been affected by CVP construction and operation. 
INTRODUCTION 11

to achieve the Settlement’s Restoration and Water 

Management goals are also authorized in the San 

Joaquin River Restoration Act (SJRRACT), included in 

the Omnibus Public Land Management Act of 2009. The 

SJRRACT, which authorizes and directs the Secretary 

to fully implement the Settlement, was signed by the 

President on March 30, 2009, and became Public Law 

111-11. The SJRRACT also established the San Joaquin 

River Restoration Fund (SJRR Fund).

Refuges Resource Area

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 

Fisheries Refuges Other

Central Valley Project

3406 (b)(1) Anadromous Fish Restoration Program

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

3406(b)(2) Dedicated Project Yield

3406(b)(3) Water Acquisition Program

3406 (b)(4) Tracy Pumping Plant Program

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

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

3406 (b)(8) Short Pulse Flows

3406 (b)(9) Flow Fluctuations

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) Comprehensive Assessment and 

Monitoring Program

3406 (b)(19) Reservoir Storage

3406 (b)(21) Anadromous Fish Screen Program

3406 (g) Ecosystem and Water System Operations 

Models

Trinity River Basin

3406 (b)(23) Trinity River Restoration Program

San Joaquin River Basin

3406 (c)(1) San Joaquin River Restoration Program

Refuge Water Supply

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

Water Acquisition Program

3406 (d)(1), (d)(2), and 

(d)(5) Wheeling and 

Conveyance

3406 (d)(5) Facilities 

Construction and San 

Joaquin Basin Action Plan 

Lands

Terrestrial Habitat and Species & 

Water Quality and Conservation

3406 (b)(1) “other” Habitat 

Restoration Program

3408 (h) Land Retirement Program

Completed & Inactive Programs

3406 (b)(6) Shasta Temperature 

Control Device

3(b)(14) Delta Cross Channel and 

Georgiana Slough

3406 (b)(17) ACID Diversion Dam

3406 (b)(18) Restore Striped Bass 

Fishery

3406 (b)(20) Glenn-Colusa Irrigation 

District Program

3406 (b)(22) Waterfowl Incentive 

Program

3406 (c)(2) Stanislaus River Basin 

Water Needs Program

3406 (d)(6) Central Valley Wetlands 

Supply

3406 (e) Supporting Investigations

3406 (f) Project Fisheries Impact 

Report

3406 (i) Water Conservation 

Program

3406 (j) Water Augmentation (Yield 

Study)

Figure 2. CVPIA Provisions by Resource Area

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 3).

Other Resource Area

The third focus of the CVPIA restoration initiatives 

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) Land Retirement Program (LRP), which 

purchases and retires land from agricultural production 

to improve water quality and provide for terrestrial 

habitat restoration.
12 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Fund, comprised of $56.1 million from the FY 2009 

appropriation and $2.9 million from prior year funds; 

$16.1 million from the Water and Related Resources 

Fund; $13.5 million from the American Recovery and 

Reinvestment Act (ARRA) Fund; $2.9 million from the 

Bay-Delta Fund; also included in the obligations was an 

accounting adjustment that resulted in an obligation of 

$5.2 million under the State cost-share funds.

Table 1 lists each active provision and the amount of 

funding obligated in FY 2009 for the fi sheries, refuges, 

and other resource areas.

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 2009, 

approximately $1.1 billion has been obligated to CVPIA 

since its implementation in 1993 (Figure 4). For FY 

2009, $96.7 million was obligated which included 

approximately: $59 million from the Restoration 

Figure 3. Central Valley Refuges Receiving CVPIA Water Supplies
INTRODUCTION 13

Completed and Inactive Programs

Several CVPIA provisions are now complete and/or 

otherwise not funded in the FY 2009 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 Channel and Georgiana 

Slough (Inactive)

• 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)

Contract Renewals

The Act directs Interior to “. . . upon request, renew any 

existing long-term repayment or water service contract 

for the delivery of water from the Central Valley 

Project . . .”

Since the passage of CVPIA, Reclamation has 

completed interim and long-term contract renewals 

Figure 4. Total CVPIA Obligations by Action Category and Fund Source (1993-2009)
14 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Table 1. FY 2009 Funding Obligations by CVPIA Provision

Provision

Water & 

Related 

Funds*

Restoration 

Funds* State*

Bay 

Delta* ARRA*

3405(a) Water Transfer Program 0 0 0 $418,000 0

3406(b)(1) Anadromous Fish Rest. 0 $6,349,800 0 0 0

3406(b)(1) “other” - Habitat Restoration 0 $1,449,000 0 0 0

3406(b)(1) “other” - Trinity River $3,788,000 $2,512,000 0 $794,000 $20,000

3406(b)(1) “other” - San Joaquin River 0 ($188,000) 0 0 0

3406(b)(1)(B) Modifi ed CVP Operations 0 $300,000 0 0 0

3406(b)(2) Dedicated 800,000 acre-feet 0 $663,000 0 0 0

3406(b)(3) Water Acquisition Instream 

VAMP 

Level 4

 0

 0

 0

 $6,001,000

 $6,149,000

 $6,154,000

 0

 0

 0

0

0

0

0

0

0

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

Two Gates

 $1,593,000

 0

 0

 0

 0

 0

0

$175,000

0

0

3406(b)(5) Contra Costa Canal $116,000 0 $1,000 0 $6,884,000

3406(b)(9) Flow Fluctuations 0 $4,000 0 0 0

3406(b)(10) Red Bluff Diversion Dam $4,173,000 0 0 0 $6,589,000

3406(b)(11) Coleman Fish Hatchery 0 0 0 0 0

3406(b)(12) Clear Creek Restoration $3,000 $745,000 <16,000> 0 0

3406(b)(13) Spawning and Rearing 0 $1,061,000 $9,000 0 0

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

3406(b)(16) Comp. Assessment and

 Monitoring

 0 $1,243,000 0 0 0

3406(b)(19) Reservoir Storage 0 0 0 0 0

3406(b)(20) Glenn-Colusa Irrigation $33,000 0 0 0 0

3406(b)(21) Anadromous Fish Screen $3,145,000 $3,920,000 0 $500,000 0

3406(b)(23) Trinity River Restoration $3,026,000 0 0 0 0

3406(c)(1) San Joaquin River 0 $13,820,000 0 $998,000 0

3406(d)(1) Refuge Water Supply Level 2 conveyance included in (d)(5)

3406(d)(2) Refuge Water Supply Level 4 acquisition included in (b)(3)

3406(d)(5) Refuge Fac. Const. Construction

Wheeling

 0

 0

 $3,925,000

 $8,351,000

 0

 0

$12,000

0

0

0

3406(d)(5) San Joaquin Basin Action 

 Plan Lands

 $208,000 $443,000 0 0 0

3406(g) Ecosystem and Water 

 Systems Operations 

 Models 

 0 $898,000 0 0 0

3408(h) Land Retirement Program $48,000 $460,000 0 0 0

3406(b)(6) Shasta TCD (State 

Cost-Share Accounting 

Adjustment)1

 <5,226,000> 5,226,000

TOTAL FUNDING OBLIGATED $16,133,000 $59,033,800 $5,220,000 $2,897,000 $13,493,000

* Rounded for presentation purposes

Amounts in ( ) = credit amount

1 Accounting adjustment; moving costs from Restoration Fund to State Cost-share, which resulted in an obligation.
INTRODUCTION 15

for the various CVP divisions and units. To date, 

Reclamation has executed 132 forty-year renewal 

contracts with Sacramento River Water Right Settlement 

contractors; 87 long-term renewal contracts with 

contractors from the Sacramento River Division, 

including the Trinity River, Shasta, Black Butte and 

Tehama-Colusa and Corning Canals units, DeltaMendota Canal Division, and Friant divisions. 26 longterm renewal contracts have either been negotiated or 

are in the process of being negotiated and are awaiting 

execution. 13 Sacramento River Water Right Settlement 

contractors elected not to renew and two contracts are 

pending renewal. 

Long-term renewal contracts for the seven Cross 

Valley contractors are currently being negotiated, as 

are contracts for the Sacramento Municipal Utility 

District (SMUD) and the City of Tracy. Reclamation 

and the nine San Luis Unit contractors have completed 

negotiations for long-term renewal contracts, and 

are awaiting execution pending completion of fi nal 

environmental documentation, including consultations 

with the Fish and Wildlife Service and the National 

Oceanic and Atmospheric Administration (NOAA).

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.

Reclamation has approved the transfer of CVP water in 

the following categories for the 2009 water year:

• 402,446 acre-feet of CVP agricultural water was 

approved for agricultural purposes

• 1,736 acre-feet of CVP agricultural water was 

approved for municipal and industrial purposes

• 10,650 acre-feet of CVP municipal and industrial 

water was approved for agricultural purposes

• 8,838 acre-feet of CVP municipal and industrial 

water was approved for municipal and industrial 

purposes

• 18,687 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) 

2009 (October 1 – September 30) which was classifi ed 

as a dry year. These conditions impacted water 

deliveries for agriculture and municipal and industrial 

users as well as affected the availability and cost of 

water to purchase on the open market for refuge water 

deliveries. Several recent developments have directly 

effected future implementation of CVPIA actions, 

including the Pelagic Organism Decline (POD), water 

project operations biological opinions (BO), the Offi ce 

of Management and Budget (OMB) performance 

management process, the outcome of independent 

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

for CVPIA implementation.

Pelagic Organism Decline

Abundance indices calculated by the California 

Department of Fish and Game (CDFG) through 2009 

show continued low abundance of 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. The 2009 indices 

for delta smelt and threadfi n shad were the lowest ever 

recorded. Delta water diverters reduced pumping in 

response to the decline. 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 have been issued by the 
16 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

supplies; implementation of fi sh and wildlife restoration 

actions and evaluations in the Delta, lower Sacramento 

River, Stanislaus River, and Antelope Creek; fi sheries 

monitoring; and construction of anadromous fi sh 

screens.

The 2008 Service BO and the 2009 NMFS BO have 

both been challenged in Federal District Court. The 

litigation on both BOs is ongoing.

Program Assessment Rating Tool 

The OMB Program Assessment Rating Tool (PART)

was developed to assess and improve the performance 

of federal programs. A PART review helps identify a 

program’s strengths and weaknesses to inform funding 

and management decisions aimed at making the 

program more effective. The PART therefore looks at 

all factors that affect and refl ect program performance 

including program purpose and design; performance 

measurement, evaluations and strategic planning; 

program management; and program results. Because 

the PART includes a consistent series of analytical 

questions, it allows programs to show improvements 

over time and allows comparisons between similar 

programs.

A PART was performed for CVPIA in 2006, and 

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

required several improvements actions, some of 

which were implemented in 2007 and 2008 and some 

which extended into FY 2009. In 2009, the Program 

completed two Independent Reviews, developed a 

Draft Implementation Plan, and continued to track 

performance toward the PART performance measures. 

In 2009, OMB began transitioning to a new system, 

the Performance Information Management System 

(PIMS) to replace PART. The Program will continue 

to coordinate with OMB as the new PIMS requirements 

are defi ned. 

Independent Reviews 

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 purpose 

of these independent reviews is to provide programmatic 

recommendations and guidance to the CVPIA Program 

Service and the NMFS that specifi cally address the need 

for additional fi sh protection due to exports.

Water Project Operations Biological 

Opinions 

The 2008 Biological Assessment on the Continued 

Long-term Operations of the CVP and the State Water 

Project (Operations BA) provides a detailed project 

description of the CVP system as a whole, including 

operations, modeling, and forecasting. The Operations 

BA 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. 

Based upon the BA, the Service and NMFS issued BO’s 

stating their conclusions about potential effects of CVP 

and SWP operations. 

On December 15, 2008, the Service issued its BO 

analyzing the effects of the CVP and SWP operations 

on the threatened delta smelt. The conclusion of the 

BO is that continued operations of the CVP and SWP, 

as proposed in the BA, are likely to jeopardize the 

continued existence of delta smelt. As a result, the 

Service provided a reasonable and prudent alternative 

(RPA) for CVP and SWP operations that the Service 

believes will avoid the likelihood of jeopardizing the 

continued existence of delta smelt. 

On June 4, 2009, NMFS issued its BO analyzing the 

effects of the CVP and SWP operations on threatened 

and endangered (T&E) salmonids and other listed 

species (e.g., green sturgeon). The conclusion of the 

BO is that continued operations of the CVP and SWP, 

as proposed in the BA, would jeopardize the continued 

existence of Sacramento River winter-run Chinook, 

Central Valley spring-run Chinook, Central Valley 

steelhead, Southern Distinct Population Segment of 

North American green sturgeon, and Southern Resident 

killer whales. As a result, NMFS provided a RPA for 

CVP and SWP operations that NMFS believes will 

avoid the likelihood of jeopardizing the continued 

existence of listed species. 

The Program will address the BO’s by committing 

substantial resources toward certain RPA requirements 

including: completion of the new pumping plant and 

fi sh screen at the Red Bluff Diversion Dam; completion 

of the Contra Costa Pumping Plant No. 1 fi sh screen; 

operational changes; dedication of instream water 
INTRODUCTION 17

to improve effectiveness and effi ciency and maximize 

restoration progress in a time of limited resources.

Reclamation and the Service sponsored two independent 

reviews: one to evaluate the anadromous fi sheries 

activities and one to evaluate the refuge water supply 

activities. These two elements represent a substantial 

portion of the annual Restoration Fund expenditures.

The purpose of the fi sheries independent review was 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 in 

December 2008 (FY 2009). The independent review 

panel provided valuable recommendations for improving 

the CVPIA fi sh restoration program, including 

recommendations to improve the program’s sciencebased framework, reorganize the program structure 

and management, improve program implementation 

by making full use of CVPIA authorities, and improve 

collaboration. 

In 2009, the refuges independent review was completed.

The purpose of the refuges independent review was 

to seek recommendations on how to implement the 

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 ve-member panel 

convened privately to review the program and develop 

draft recommendations; the panel deliberation sessions 

were conducted between March 2009 and May 2009. 

The fi nal report from the refuges independent review 

panel was submitted to Reclamation and the Service 

in November 2009. The report provided specifi c 

recommendations and made fi ndings on fi ve major 

elements of the RWSP: program management, water 

supply, water conveyance, program metrics, and refuge 

management. The panel recommendations included: 

transfer programmatic authority and Restoration Fund 

monies for acquiring all Incremental Level 4 water to an 

independent, third-party entity; prioritize the funding 

and completion of remaining external conveyance 

construction projects; realign and optimize management 

structure of the RWSP to optimize fl exibility and 

fungibility of Level 2 Water and any Incremental Level 

4 Water; and modify policies and practices that are 

inconsistent with the intent of the Act to improve CVP 

operations and deliver 100 percent of all Level 2 water to 

the refuge system. 

Reclamation and the Service considered the 

recommendations of both panels as they developed the 

Implementation Plan (see below) that will guide Program 

priorities and activities over the next 10 years. The 

Implementation Plan addresses the independent reviews 

by adopting certain recommendations and incorporating 

them as future strategies and implementation activities. 

The agencies are optimistic about the ability to improve 

the fi sheries and refuges program by adopting many of 

the panel’s recommendations. 

Implementation Plan 

The CVPIA Program developed an Implementation Plan 

(IP) that will provide focus and direction for the CVPIA 

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

the foundation for planning, budgeting, performance 

management, and accountability processes. The IP 

focuses on providing objectives and strategies for the 

following resource areas: Fisheries, Refuges, Other, and 

CVPIA Program Management.

The IP was developed over two years through internal 

and external processes. The internal process included 

participation by Reclamation and Service program 

managers, biologists, and engineers that are involved in 

the day-to-day work of Program implementation; these 

meetings culminated with the development of prioritized 

activities in each of the resource areas. As stated above, 

independent review panels also reviewed Program 

accomplishments and prepared recommendations for 

the fi sheries and refuges programs regarding priorities 

and effi ciencies to maximize progress towards the 

restoration goals. Certain independent review panel 

recommendations are incorporated into the IP as future 
18 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

strategies and activities. The IP is currently under 

review by both the Service and Reclamation.

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. In the case of this portion of 

CVPIA, currently funded through the Restoration Fund 

and focused on restoration efforts, return on investment 

is measured generally by increases in the natural 

production of anadromous fi sh; the delivery of water to 

wildlife refuges that is of suitable quality and quantity; 

the protection and restoration of sensitive species and 

habitats; the retirement and restoration of agricultural 

lands; the completion of structural improvements; 

and the implementation of operational changes to 

affect fl ows. The Program also measures completion 

of restoration activities pursuant to the Trinity River 

Restoration Plan, and additional specifi c goals exist 

for individual CVPIA Program activities, as discussed 

throughout this annual report.

The data generated from CVPIA modeling and 

monitoring activities support the identifi cation of 

these performance targets and also provide results 

and feedback on the effectiveness of actions. Planning 

and coordination between the various provisions will 

increase the effectiveness of resource allocation and 

decision-making. Close coordination between the 

programs is seen as critical to the success of CVPIA’s 

long-term goals.

The CVPIA Program is a complex, long-term effort 

to restore the Central Valley ecosystem that involves 

federal, State, local, and tribal entities, as well as public 

and private interests. Because of the scope and overall 

complexity, and large number of stakeholders involved 

in CVPIA, it is important that the Program clearly 

articulate specifi c, measureable goals for the restoration 

and a strategy for achieving the goals. The next steps 

will be to establish benchmarks for measuring progress 

in restoring the ecosystem. Reporting on annual goals 

will occur each year. Longer term or interim outcome 

oriented goals that will serve as a blueprint of how the 

restoration will occur, will be developed. This will 

enable all of the participating agencies to establish 

appropriate priorities and milestones for accomplishing 

the entire effort and improve their ability to accomplish 

the restoration in a timely and effi cient manner. This 

will also help ensure that the participating agencies do 

not duplicate or counter each other’s efforts. 

The IP was developed to guide decision-making in the 

planning and execution of the CVPIA Program over the 

next 10 years. The objectives and strategies contained 

in the IP are intended to maintain the momentum, 

guide the CVPIA Program through the uncertainties it 

faces, and provide stability for the future alignment of 

the CVPIA Program. The courses of action set forth 

in the strategies and activities in the IP, coupled with 

site-specifi c decision analysis that incorporate local and 

regional stakeholder considerations, will enable effective 

management of an integrated program. The Program 

is optimistic about the future and looks forward to 

carrying out the important mission enumerated in the 

Act.
2009 PROGRAM ACTIVITIES AND ACCOMPLISHMENTS 19

III. 2009 Program Activities and 

Accomplishments

This section summarizes FY 2009 program 

accomplishments, funding obligations from all funding 

sources, authorizing language from CVPIA, and 

background information for each active provision. 

Wherever possible, each program includes quantifi ed 

goals and targets to measure progress towards the Act’s 

implementation. The following programs are discussed 

in this section:

• Anadromous Fish Restoration Program

• Habitat Restoration Program

• Trinity River Restoration Program

• Modifi ed CVP Operations

• Dedicated 800,000 acre-feet Project Yield

• Water Acquisition Program - Instream Water

• Tracy (Jones) Pumping Plant Program

• Contra Costa Canal Pumping Plant

• Flow Fluctuations and Reservoir Storage

• Red Bluff Diversion Dam

• Coleman National Fish Hatchery

• Clear Creek Restoration Program

• Spawning and Rearing Habitat Restoration 

Program

• Head of Old River Barrier

• Comprehensive Assessment and Monitoring 

Program

• Glenn-Colusa Irrigation District Program

• Anadromous Fish Screen Program

• San Joaquin River Restoration Program

• Introduction to the Refuge Water Supply Program

• Water Acquisition Program - Refuge Water

• Refuge Facilities Construction Program and San 

Joaquin Basin Action Plan Lands Program

• Refuge Water Conveyance (Wheeling) Program

• Ecosystem and Water Systems Operations Models

• Land Retirement Program

Chinook salmon
20 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 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 

Sacramento

San Francisco

Los Angeles

Anadromous Fish Restoration 

Program 

Fisheries Resource Area (Central Valley)

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 

Anadromous Fish Restoration Program (AFRP) as 

the overarching program to address anadromous fish 

doubling in the Central Valley. The AFRP 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:

• 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

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $6,349,800

TOTAL - $6,349,800

Accomplishments

• 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 and purchased 

and placed 6,400 tons of spawning gravel on the 

Mokelumne River

• Continued to improve the opportunity for adult 

fi sh to reach their spawning habitats by providing 

funding to complete the environmental permits and 

construction bid package for the Antelope Creek 

Crossing Repair Project

• Conducted several activities to collect fi sh data 

to facilitate evaluation of restoration actions 

including: funding the monitoring at the Coleman 

National Fish Hatchery’s barrier weir fi sh ladder 

and providing funds to implement seven ongoing 

long term monitoring tasks on Clear Creek

man

der 

oing 

inc

Na

and

lon
3406(b)(1) 21

• 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 (Final Restoration Plan) in 

2001. As acknowledged in the CVPIA ROD, the Final 

Restoration Plan guides the implementation of the 

actions and evaluations which were developed to address 

the doubling goal. The 289 actions and evaluations 

in the Final Restoration Plan are categorized by six 

programmatic-level objectives:

• Improve habitat for all life stages of anadromous 

fish through provision of flows of suitable quality, 

quantity, and timing, and improved physical 

habitat 

• Improve survival rates by reducing or eliminating 

entrainment of juveniles at diversions 

• Improve the opportunity for adult fish to reach 

their spawning habitats in a timely manner 

• Collect fish population, health, and habitat data to 

facilitate restoration actions evaluation

• Integrate habitat restoration efforts with harvest 

and hatchery management 

• Involve partners in implementing and evaluating 

restoration actions 

The CVPIA Program is implementing these actions and 

evaluations to further efforts to meet the doubling goals 

for the natural production of anadromous fish.

MEASURING SUCCESS

Meeting Program Objectives

Key actions and evaluations undertaken or completed 

in 2009 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

Cottonwood Creek – Funds were provided this year to 

develop a sediment budget and assist in determining 

the cause of streambed instability. The study includes 

analyses of geomorphologic data from 1939 to present; 

quantifi es spatial and temporal characteristics of 

sediment supply, storage, and transport in the system; 

and identifi es the effects of sediment transport dynamics 

on perceived channel and watershed changes. The Nonnative Invasive Plant Management and Control Project 

was funded in FY 2009 to complete the environmental 

compliance documents and permitting to eradicate 

non-native noxious and invasive plants within the 

riparian corridor of Cottonwood Creek. These projects 

are a cooperative effort with the Cottonwood Creek 

Watershed Group and address Actions 1 and 5 in the 

Final Restoration Plan. 

Sacramento River – Phase II of the La Barranca Unit 

Restoration Project at the Sacramento River National 

Wildlife Refuge (NWR) was implemented during this 

reporting period. The 116 acre orchard was removed, 

roots and branches picked out, the soil was harrowed, 

and the site prepared for future restoration work. A 

restoration plan for this site was completed giving 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 outlined the 

implementation strategies for the site. The La Barranca 

Restoration Plan is available on the AFRP website at 

http://www.fws.gov/stockton/afrp/. This project was 

funded with FY 2008 funds and addresses Action 9 and 

Evaluations 1 and 5 in the Final Restoration Plan. 

Yuba River – The Hammon Bar Habitat Restoration 

Project Phase 2, of 4 phases, (Final Restoration Plan 

Evaluation 4) was funded in FY 2009 to complete a 

juvenile fi sh habitat assessment, land use analysis, 

permits, and designs. The pre-project assessment 

was completed this year for potential riparian habitat 

restoration targeting juvenile Chinook salmon and 

steelhead. This assessment involved geomorphic, 

hydrologic, hydraulic, and vegetation components, and 

included substantial public outreach. A topographic map 

for restoration planning and preliminary conceptual 

diagrams for restoration projects at Hammon Bar 

and locations upstream as far as Parks Bar were also 

developed during this reporting period. The permits 

and fi nal designs are still being developed but should be 

completed next year. This project is a cooperative effort 

between the USFWS, California Department of Fish and 

Game (CDFG), the South Yuba River Citizens League 

(SYRCL), Western Aggregates Inc., Yuba Outdoor 

Adventures, and the Yuba Preservation Foundation.
22 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Mokelumne River – The Mokelumne River Spawning 

Habitat Improvement Project (Final Restoration Plan 

Action 7) purchased and placed 6,400 tons of spawning 

gravel to improve natural production of Chinook salmon 

and steelhead at several spawning sites. This project 

enhanced an estimated 0.23 miles of river raising the 

streambed elevation, increasing the gradient and fl ow 

control features needed to provide gravel mobility and 

create additional downstream habitat in subsequent 

years. 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 UC Davis. This information will be 

available in the fi nal report after the project is completed 

in 2012. This project is a cooperative effort between the 

USFWS and the East Bay Municipal Utility District.

Cosumnes River – The Spawning Habitat Restoration 

Project (Final Restoration Plan Action 6 and Evaluation 

3) received additional FY 2009 funds to purchase and 

place more and higher quality spawning gravel in the 

restored channel area, as well as place additional gravel 

upstream for gravel recruitment. The site was monitored 

and characterized for spawning use, bed form and 

function during this reporting period. This information 

will be available in the fi nal report after the project 

is completed in 2010. AFRP is collaborating with 

Fisheries Foundation of California (FFC), OmochumneHartnell Water District, Robertson-Bryan, Inc., and 

CDFG and has leveraged $232,500 in cost share and 

in-kind services to date.

Stanislaus River – AFRP FY 2009 funds were provided 

for the implementation phase for both the Honolulu 

Bar and Lancaster Road fl oodplain and side-channel 

enhancement projects. Topographic, bathymetric, and 

vegetation surveys have been completed and preliminary 

conceptual plans have been developed for both projects. 

These projects are being designed to increase juvenile 

salmonid rearing habitat and decrease predation (Final 

Restoration Plan Action 2). The Stanislaus River 

Restoration Plan was completed during this reporting 

period and is available on the AFRP website at http://

www.fws.gov/stockton/afrp/. AFRP also participated 

in two outreach festivals, two river clean ups, various 

public meetings, and began the planning for a Stanislaus 

River Salmon Festival during this reporting period. 

These outreach activities have increased community 

and stakeholder support for the restoration projects 

in this watershed. AFRP is partnering with the U.S. 

Mokelumne River Spawning Habitat Improvement 

Project – Before (top) and After (bottom)

Army Corps of Engineers, USBR, Natural Resources 

Conservation Service (NRCS), CDFG, East Stanislaus 

Resource Conservation District, Tri-Dam, and FFC to 

host the Salmon Festival.

Tuolumne River – A Conceptual Plan to restore 120 

acres of riparian fl oodplain and implement instream 

gravel augmentation as well as improve fl oodplain 

function and connectivity to the river at Bobcat Flat 

was completed this year (Final Restoration Plan Action 

2). Both the survey work for the pre-project assessment 

and the permitting were initiated in FY 2009. AFRP 

is collaborating with Friends of the Tuolumne and the 

CDFG. 

Merced River – Outreach, education, permitting and 

planning for three different fl oodplain and channel 

restoration projects (Final Restoration Plan Action 3) 

were initiated in FY 2009. The Merced River Ranch 

Project fi nal designs were completed during this 

reporting period. A draft Environmental Assessment/

Initial Study Report has been completed. The fl ow 

parameters, topographic surveys, benthic macroinvertebrate sampling, and substrate quality assessments 
3406(b)(1) 23

were completed for all three fl oodplain and channel 

restoration projects. AFRP is collaborating with Santa 

Fe Aggregates, Inc., CDFG, CALFED Ecosystem 

Restoration Program (ERP), and the California 

Department of Water Resources (DWR).

Objective 2: Improve survival rates by reducing or 

eliminating entrainment of juveniles at diversions

Antelope Creek – The Juvenile Fish Passage 

Improvement Project at Edwards Diversion Dam (Final 

Restoration Plan Action 1) was initiated in FY 2008 

to have environmental compliance and construction 

plans developed. The juvenile fi sh passage improvement 

will prevent out-migrating salmonids from becoming 

entrained in the two diversion canals at Edwards 

Diversion Dam. Although the diversions are screened, 

no bypass system was installed during construction 

due to site complexity. The Tehama County Resource 

Conservation District (TCRCD) completed a feasibility 

study, the environmental compliance documents, and 

project designs during this reporting period. FY 2009 

funds have been obligated for implementation, and 

construction is expected to begin in the summer of 2010. 

This project is a cooperative effort between the USFWS, 

CDFG, NMFS, TCRCD, Los Molinos Mutual Water 

Company, and the Edwards Ranch.

Butte Creek – Over the past several years many projects, 

which benefi t salmonid survival and production, have 

been funded by AFRP to facilitate passage and reduce 

entrainment at facilities in the Butte Creek watershed. 

Two fi nal reports evaluating juvenile spring-run 

Chinook salmon entrainment were completed in 

FY 2009. The Lower Butte Creek Project, Phase III 

Consolidated Action Summary Report (July 2009 draft) 

is currently under review. 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. The reports show that implementing 

the potential 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. For more 

information on these activities and recently completed 

fi nal reports visit the AFRP website at http://www.fws.

gov/stockton/afrp/.

Objective 3: Improve the opportunity for adult fish 

to reach their spawning habitats in a timely manner 

Antelope Creek – A road crossing in the CDFG Tehama 

Wildlife Area is currently a barrier to spring- and fallrun Chinook salmon during dry years. In FY 2008, this 

project received USFWS National Fish Passage Program 

funds to develop the environmental compliance and 

construction designs for the Antelope Creek Crossing 

Repair Project in the Tehama Wildlife Area (Final 

Restoration Plan Action 1). In FY 2009, AFRP funds 

were added to this project to obtain formal permissions 

and permits, and complete a construction bid package. 

This project is a cooperative effort between the USFWS 

and CDFG.

Battle Creek – The Battle Creek Salmon and Steelhead 

Restoration Project (Final Restoration Plan Actions 2, 

6, and 7) has seen signifi cant progress in the past two 

years. Although no AFRP funds were used on the 

Restoration Project in FY 2009, the AFRP provided 

technical assistance and collaborated with partners 

to develop and implement restoration actions in this 

watershed. Phase 1A of the Restoration Project includes 

installing fi sh screens and ladders at the North Battle 

Creek Feeder and Eagle Canyon diversion dams and 

removing Wildcat diversion dam and appurtenant 

conveyance systems on the North Fork; installing 

Eagle Canyon Canal pipeline; and modifying Asbury 

dam on Baldwin Creek. USBR funded Phase 1A 

with $49.25 million. The National Environmental 

Policy Act (NEPA) ROD and construction bids were 

prepared during this reporting period. In April 2009, 

$26 million in funds from the American Recovery and 

Reinvestment Act (ARRA) were identifi ed and a Phase 

1B Implementation Agreement was drafted. For more 

information on the progress of these collaborative efforts 

go to http://www.usbr.gov/mp/battlecreek/index.html. 

Big Chico Creek – The permitting and environmental 

documentation for the Iron Canyon Fish Ladder Project 

(Final Restoration Plan Action 2) that was funded in 

FY 2007 will be completed in FY 2010. The California 

Environmental Quality Act (CEQA) Initial Study was 

completed in FY 2009 and progress is being made 

on the other permits. Construction funds are being 

sought by Chico State University Foundation, but so far 

have not been fully attained. Completion of the new 

passage facility at Iron Canyon will provide access to an 

estimated 8 miles of quality spring-run Chinook salmon 
24 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

habitat. This is a cooperative project with the USFWS, 

CDFG, and Chico State University.

Cottonwood Creek – The Anderson-Cottonwood 

Irrigation District (ACID) siphon is becoming 

exposed once again in Cottonwood Creek and poses 

a passage problem for adult salmonids. Funds were 

provided during this reporting period to complete the 

environmental documentation permits and design for 

the Cottonwood Creek ACID Siphon Project (Final 

Restoration Plan Action 2). This is a cooperative 

project with USFWS, CDFG, ACID, NMFS, and the 

landowners.

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 

(WSRCD) for the Millville Diversion Environmental 

Compliance Project (Final Restoration Plan Action 3) 

to complete all environmental compliance documents 

necessary to obtain permits to modify the diversion dam 

for fi sh passage. The conceptual design for a boulder 

weir fi shway was developed in FY 2009. This project 

will eventually open up 10 miles of historic habitat to 

fall-run Chinook salmon and Central Valley steelhead 

trout. The DWR Fish Passage Improvement Program 

is providing the initial engineering design. This is an 

interagency effort with DWR, CDFG, CALFED ERP, 

and the NRCS. 

Calaveras River – Final designs for the Budiselich 

Flashboard Dam boulder weir fi shway were completed 

this year. The joint NEPA/CEQA Programmatic 

Environmental Assessment/Initial Study was also 

completed during this reporting period. The Calaveras 

River Passage Improvement Project (Final Restoration 

Plan Action 3) will begin implementation to replace 

and/or retrofi t migration impediments to salmon and 

steelhead in the lower Calaveras River. This project will 

restore access to about 10 miles of habitat. This project 

is a cooperative effort between the USFWS, Stockton 

East Water District, FFC, the University of the Pacifi c, 

CDFG, and DWR. 

Cosumnes River – The Cosumnes River Passage 

Improvement Project (Final Restoration Plan Evaluation 

2) was funded in FY 2009 to improve fi sh passage at 

Rooney Dam. This project will eliminate this migration 

barrier by constructing a four-tiered boulder weir 

fi shway. The environmental documents and designs 

were completed this year and construction began in 

Fish passage barriers at the Budiselich Flashboard 

Dam in the Calaveras River (top) and Rooney Dam in 

the Cosumnes River (bottom)

the fall of 2009. AFRP is collaborating with FFC, 

Omochumne-Hartnell Water District, Robertson-Bryan, 

Inc., and CDFG. 

Objective 4: Collect fish population, health and 

habitat data to facilitate evaluation of restoration 

actions 

Battle Creek - FY 2009 funds were provided to continue 

an adult escapement survey of natural-origin steelhead 

and winter-, spring-, and late-fall Chinook salmon to 

monitor progress towards meeting the AFRP doubling 

goal production targets in Battle Creek. Monitoring 

occurred at the Coleman National Fish Hatchery’s 

barrier weir fi sh ladder between March 1 and 

August 1, 2009. This is the fi rst year for testing the 

motion-detection capabilities on a Digital Video 

Recorder and preliminary data suggest that motion–

detection is capturing nearly 100% of adult salmonid 

passage at the barrier weir fi sh ladder where viewing 

conditions are optimal. This new technology promises 

to provide signifi cant time and cost savings in the 

future. A rotary screw trap was also operated to 

measure downstream passage of natural-origin juvenile 
3406(b)(1) 25

salmonids. These studies assist with evaluating benefi ts 

resulting from habitat restoration actions and summary 

reports are available at http://www.fws.gov/redbluff/

cvpia.html.

Bear, Cottonwood, and Cow creeks – The video weir 

monitoring project for Bear, Cottonwood, and Cow 

Creeks was implemented from October to December 

2008. As an additional element in FY 2009, the Bear 

Creek site was operated for a longer time period 

(through April 2009) to determine the feasibility 

of determining adult steelhead escapement. The 

information is utilized to calculate natural production 

estimates and is used to guide AFRP restoration efforts 

and evaluate program performance. Annual summary 

reports are available on the AFRP website at http://

www.fws.gov/stockton/afrp/. This work was completed 

through a cooperative effort of the USFWS, CDFG, 

WSRCD, and the Cottonwood Creek Watershed Group. 

Clear Creek – AFRP FY 2009 funds were provided 

for the Clear Creek Anadromous Salmonid Monitoring 

Program (CCASMP) to continue to evaluate progress 

towards meeting the AFRP doubling goal production 

targets in this watershed. The CCASMP consists of 

seven ongoing, long-term monitoring tasks which 

include the operation of a segregation weir for spring 

and fall Chinook salmon; adult Chinook salmon (spring 

and late-fall) and steelhead escapement monitoring; 

juvenile salmonid production monitoring; fall Chinook 

spawning area mapping; and juvenile Chinook habitat 

use evaluation. Annual reports for these activities are 

available at http://www.fws.gov/redbluff/cvpia.html.

Mill Creek – A pilot study to assess the feasibility of 

counting adult Chinook salmon escapement in Mill 

Creek using a fi xed-location hydroacoustic split-beam 

array (DTx) and a Dual-frequency Identifi cation Sonar 

(DIDSON) was funded in FY 2007 and completed this 

year. The study concluded that the DIDSON was more 

effective and accurate in streams with high turbidity 

than either the DTx or the video weir. Results were 

comparable to those obtained by CDFG in 2008 through 

a Redd survey. The DIDSON may prove to be a cost 

effective alternative to traditional escapement surveys. 

The fi nal report for this project was submitted February 

2009 and is available on the AFRP website at http://

www.fws.gov/stockton/afrp.

Sacramento River – AFRP FY 2009 funds were 

provided to monitor juvenile green sturgeon and winter 

Chinook salmon escapement and juvenile production 

on the mainstem Sacramento River downstream of the 

Red Bluff Diversion Dam. These activities will evaluate 

progress towards meeting the AFRP doubling goal 

production targets for these species. Annual reports are 

available at http://baydelta.ca.gov/Php/Special_Reports/

red_bluff.php. 

Yuba River – Two VAKI Riverwatcher fi sh counting 

systems were operated as a demonstration project in 

2009 and used to count the number of fi sh passing 

upstream of the north and south fi sh ladders at 

the Daguerre Point Dam. AFRP purchased these 

monitoring systems in FY 2005 and the CDFG operates 

them with oversight by the South Yuba River Citizens 

League. Data were 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. A draft Monitoring and Evaluation Plan was 

also developed during this reporting period to evaluate 

instream fl ows as part of the Lower Yuba River Accord. 

Calaveras River – Data were 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 FFC and address the Final 

Restoration Plan Action 3 and Evaluation 2 for this 

watershed.

Stanislaus River – FY 2009 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. A study to 

determine the relative contribution rates of juvenile 

Chinook salmon that migrate as fry versus smolt outmigrants to adult escapement was initiated this year 

with USBR New Melones Revised Plan of Operations 

funding. The study uses state of the art microchemistry 

and microstructure techniques to assess juvenile 

migratory history from adult otoliths recovered in the 

river by CDFG. These studies assist with evaluating 
26 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

benefi ts resulting from habitat restoration actions; 

summary reports are available on the AFRP website at 

http://www.fws.gov/stockton/afrp.

Merced River – Rotary screw trapping to track juvenile 

salmonid outmigration was conducted in FY 2009. The 

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

habitat restoration actions. The project used FY 2008 

USFWS Fisheries Program funds. A summary report 

for this activity is available on the AFRP website at 

http://www.fws.gov/stockton/afrp.

Objective 5: Integrate habitat restoration efforts 

with harvest and hatchery management

Mokelumne River – A fi nal report was completed 

documenting the proportion of hatchery versus natural 

origin Chinook salmon for the 2004 escapement 

estimate. The study used otolith microstructure and 

microchemistry data to demonstrate that hatchery 

origin Chinook salmon are much more dominant than 

expected, with estimates of 97%. This study was 

funded in FY 2006 and the report is available on the 

AFRP website at http://www.fws.gov/stockton/afrp.

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 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. AFRP is currently collaborating with 

DWR and Pacifi c Gas & Electric (PG&E) through the 

Habitat Expansion Agreement Steering Committee to 

restore Central Valley spring-run Chinook salmon and 

steelhead. These efforts can potentially leverage $15 

million in additional funding for habitat restoration 

activities that can be used to recover these threatened 

species. 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 

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, sturgeon, striped bass, and 

American shad in relation to the doubling goals and 

the baseline period. The average natural production of 

Central Valley-wide Chinook salmon in the doubling 

period (1992-2008) is currently 452,243 and below 

the doubling goal target of 990,000 total anadromous 

fi sh. The natural production average of Central Valleywide Chinook salmon has been decreasing in the last 

few years as evidenced by the low adult escapement 

estimates in 2006, 2007, and 2008 resulting from poor 

ocean returns (Lindley et. al. 2009). Specifi cally, 

the average natural production of winter-run, springrun, fall-run, and late fall-run Chinook salmon in the 

doubling period (1992-2008) are 7,789; 15,446; 409,061; 

and 19,946, respectively. The average production for 

steelhead in the doubling period (1992-2008) is 1,127. 

The average natural production of white sturgeon and 

green sturgeon, 1992 through 2005, is 5,507 and 2,201, 

respectively. Striped bass average natural production 

from 1992 to 2007 is 885,670. American shad natural 

production in the doubling period (1992 to 2008) is 

2,680. These numbers are the most recent numbers that 

have been through the quality assurance/quality control 

(QA/QC) process from the CDFG Grand Tab. Updates 

and revisions are posted throughout the year on the 

AFRP website, and published in the Comprehensive 

Assessment and Monitoring Program annual report 

(USFWS, 2009).
3406(b)(1) 27

The Final Restoration Plan also provides doubling goals 

for specific rivers and creeks. Substantial gains to date 

are seen in watersheds where a signifi cant investment 

has been made in fl ow, passage, and habitat restoration 

(Battle, Butte, and Clear creeks). Average Chinook 

salmon production for the period of 1992-2008 has 

exceeded the doubling goal target on Battle, Butte, 

and Clear Creeks, and is just below the goal on the 

Mokelumne River, as seen in Table 3. 

In order to more accurately assess natural production, 

AFRP is demonstrating new escapement counting 

technologies, such as the Alaskan weir (Stanislaus 

River), Vaki-infra-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 (32S:34S) 

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.

Performance Measures 

The AFRP tracks progress toward several performance 

measures. The average natural production of Central 

Valley-wide Chinook salmon in the doubling period 

(1992-2008) is currently 452,243 and below the 2009 

target of 625,000 total Chinook salmon (reporting on 

PART). Also reporting on PART, since 1995, of the 

73 high and medium priority structural actions and 

evaluations in the Final Restoration Plan, 30 (41%) have 

been completed. 

Reporting on the CVPIA Program Activity Review 

(CPAR), of the 128 Final Restoration Plan actions 

with endpoints, 43 (34%) have been completed. The 

128 Restoration Plan actions include 53 structural 

actions and 75 non-structural actions. Of the 53 

structural actions with endpoints, 20 (38%) have been 

completed. A total of 23 (31%) of the 75 non-structural 

actions with endpoints have been completed. Actions 

requiring annual or in perpetuity projects such as gravel 

augmentation (replacing gravel lost behind dams) and 

fl ow augmentation are not considered to have endpoints. 

Status of these actions are also reported under other 

provisions of the CVPIA such as the (b)(2), (b)(3), and 

(b)(13) programs. 
28 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Table 2. AFRP Fish Production Estimates in All Central Valley Streams (1992-2008)

1

 Only streams and rivers with complete salmon production data sets (1992-2008) are shown.

2

 Annual doubling goals were derived from “Mills, T.J. and F. Fisher. 1994. Central Valley Anadromous Sport Fish Annual Runsize, 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.fws.gov/stockton/afrp/restplan_fi nal.cfm].”

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 2008.

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

production (1967-1991) from natural production (1992-2008), dividing the result by baseline natural production (1967-1991), and

multiplying by 100.

6

 Data is through 2005.

7 Production target for striped bass is expressed as the abundance of legal-sized striped bass estimated annually by the CDFG. Data is 

through 2007.

8 Production target for American shad is expressed as the juvenile index as derived from the CDFG fall midwater trawl in the Delta.

Anadromous 

Fish Species and 

Watershed1

AFRP Annual 

Doubling 

Goals2

Average 

Baselines

(1967-1991)3

Average Natural 

Production 

(1992-2008)4

Average % Natural 

Production Difference 

From Baseline5

All Chinook runs, all 

Central Valley streams

 990,000 497,240 452,243 -9

Fall-run, all Central 

Valley streams

 750,000 374,217 409,061 9

Winter-run, all Central 

Valley streams

 110,000 54,417 7,789 -86

Spring-run, all Central 

Valley streams

 68,000 34,425 15,446 -55

Late fall-run, all Central 

Valley streams

 68,000 34,182 19,946 -42

Steelhead, all Central 

Valley streams

 13,000 6,574 1,127 -83

Green sturgeon, all 

Central Valley streams

 1,966 983 2,2016 124

White sturgeon, all 

Central Valley streams

 11,000 5,571 5,5076 -1

Striped bass7 2,500,000 1,252,259 885,6707 -29

American shad8 4,300 2,129 2,680 26

Table 3. Chinook Salmon AFRP Production, in Battle, Butte and Clear Creeks, and Mokelumne River (1992-

2008)

Chinook Salmon 

Species and 

Watershed1

AFRP Annual 

Doubling 

Goals2

Average Baselines 

(1967-1991)3

Average Natural 

Production 

(1992-2008)4

Average % Natural 

Production Difference 

From Baseline5

Battle Creek, fall-run 10,000 5,012 19,801 295

Battle Creek, late fallrun 550 273 675 147

Butte Creek, fall-run 1,500 763 2,823 270

Butte Creek, spring-run 2,000 1,017 10,948 976

Clear Creek, fall-run 7,100 3,574 11,606 225

Mokelumne River, fallrun 9,300 4,679 8,564 83
3406(b)(1) “other” 29

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”, benefi ts federally listed Central Valley 

species and their habitats that were adversely impacted 

by construction and operation of the CVP and are 

not specifi cally addressed in other CVPIA sections. 

Habitat loss and fragmentation due to urbanization 

and agriculture conversion occurred on an estimated 

Sacramento

San Francisco

Los Angeles

Habitat Restoration Program 

Other Resource Area

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $1,449,000

Accomplishments

• Contributed funding towards the protection of 

5,165 acres (through acquisition)

• Funded eight projects that focused on high priority 

species and habitats impacted by the CVP. Of 

the eight projects funded by the HRP in FY 2009, 

four are research, two are acquisition, one is 

restoration, and one is outreach. Habitats that will 

benefi t include vernal pools; riparian; grasslands; 

oak woodlands; alkali scrub; and riverine dunes. 

Species that will benefi t include California redlegged frog; vernal pool invertebrates; vernal 

pool plants; San Joaquin kit fox; Tipton kangaroo 

rat; blunt-nosed leopard lizard; Contra Costa 

wallfl ower; Antioch Dunes evening primrose; and 

Lange’s metalmark butterfl y.

aroo

and 

leg

poo

rat

wa

Lan

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’ conservation and recovery, 

include purchase of fee title or conservation easements 

on lands where threats are signifi cant; targeted 

restoration of CVP-impacted habitats where actions 

will markedly improve conditions; research to facilitate 

species recovery; and, when funds are available, public 

outreach, education, planning, and land 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” that defi nes 

the program’s geographic focus area. The HRP also 

developed a “High Priority Species List” that defi nes 

species identifi ed in various recovery plans (both 

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

www.usbr.gov/mp/cvpcp).

HIGH PRIORITY SPECIES AND 

HABITATS

To date, the HRP has allocated about $25.5 million to 

fund approximately 97 projects supporting the recovery 

of federally listed threatened and endangered species 

such as:

• San Joaquin kit fox

• Giant kangaroo rat
30 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

• Blunt-nosed leopard lizard

• California red-legged frog

• Giant garter snake

• Bay checkerspot butterfl y

• Valley elderberry longhorn beetle

• Riparian brush rabbit

• Riparian woodrat

• Lange’s metalmark butterfl y

• Vernal pools species (plants and invertebrates)

• Gabbro soil plants

Figure 5 maps the HRP project locations from 1996-

2009.

Since 1996, HRP funds have been used to acquire 

(protect) more than 98,000 acres and restore more than 

7,300 acres, for a total of more than 105,000 acres; this 

Table 4. Acres of Habitat Protected & Restored per Year (1996-2009) by 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

2009 5,165 0 944 0

Subtotal 98,184 7,386 8,056 3,879

Total 105,570 11,935

Goal/Target 2.7 million

contributes towards one of the HRP’s performance 

goals. The 105,000 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 105,000 acres, almost 12,000 acres have been 

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 
3406(b)(1) “other” 31

Figure 5. Habitat Restoration Program Project Locations
32 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

protected and restored include vernal pool, riparian, 

alkali scrub, foothill chaparral, valley-foothill hardwood 

and grassland. 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 

(BLM) to help purchase Spivey Pond. The pond supports 

one of the few known populations of California redlegged frogs. In 2005, the HRP funded construction of a 

pond downstream of Spivey Pond, where occurrence of 

the species has recently been recorded. Additionally, in 

2009, funds were provided for surveys of the giant garter 

Snake Marsh pre-restoration. The invasion of yellow

water primrose in the marsh.

Snake Marsh post-restoration (approximately 1 year 

from initiation of construction). Removal of yellow water 

primrose in a 1-acre area created open water habitat to 

benefi t the federally threatened giant garter snake. 

snake, a federally threatened species, in the San Joaquin 

Valley. The discovery of 14 snakes in this area is the 

fi rst confi rmed population in the county in 15 years.

Since 1996, 71 surveys and studies and 13 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 2009, HRP funds 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 2009 projects.

Rickert Ranch property (Shasta County). In FY 2009, 

the HRP contributed funds towards acquisition of 

5,085 acres of multiple habitat types to benefi t several 

federally listed and other species.

Giant garter snake. In FY 2009, the HRP funded a 

study which resulted in a population of the federally 

threatened giant garter snake being discovered in San 

Joaquin County for the fi rst time in 15 years. Photo by 

Eric Hansen.
3406(b)(1) “other” 33

Table 5. FY 2009 Projects Funded by the Habitat Restoration Program (HRP) (continued on page 34)

Project Status Signifi cance

Shasta Land Trust (SLT) - Acquisition 

of conservation easement on the 5,085-

acre Rickert Ranch property in Shasta 

County. The easement will protect this 

working cattle ranch as well as its cultural 

and natural resources including riparian 

habitat, grasslands, vernal pools, vernal 

swales, and oak woodlands. HRP funded 

$415,000.

On-going - The conservation easement 

is under review by the land owners and 

funding agencies. The baseline conditions 

and monitoring reports are being 

developed. 

Supports species and habitat 

protection: Lands surrounding the 

easement property are threatened 

with development. Protecting the 

ranch will benefi t habitats for a host of 

potentially occurring species including 

valley elderberry longhorn beetle, 

vernal pool fairy shrimp, vernal pool 

tadpole shrimp, slender orcutt grass, 

Green’s popcorn fl ower, and CA redlegged frog.

American Land Conservancy 

(ALC) – Fee title acquisition of 80 acres 

of San Joaquin Valley upland habitat to 

enhance and improve conditions for listed 

wildlife species near Atwell Island in Kings 

County. HRP funded $110,000.

On-going - ALC has contacted the 

landowners of the 80-acre parcel to 

ascertain if there are willing sellers. 

When ALC receives a positive reply, it will 

initiate the process to get the property 

under option, complete an appraisal, and 

complete environmental assessments. If 

there are no fi ndings as a result of the 

environmental assessments, the project 

should close and transfer to BLM will be 

completed. 

Supports species and habitat 

protection: The primary goal of the 

acquisition is to permanently protect 

habitat for Tipton kangaroo rats, a 

federally endangered species; a 

secondary goal is to create a larger 

contiguous conserved habitat within 

BLM’s Atwell Island Project area 

through land acquisitions. Besides 

the Tipton kangaroo rat, other 

species such as the San Joaquin 

kit fox, blunt-nosed leopard lizard, 

tri-colored blackbird, mountain plover, 

and western spadefoot toad will also 

benefi t from the acquisition.

USFWS, Antioch Dunes NWR - Funding 

will contribute toward the continuation 

of captive propagation of the Lange’s 

metalmark butterfl y at the Moorpark 

College in the Exotic Animal Training & 

Management Program facility (Moorpark, 

CA). Additionally, it will continue the 

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 

$125,656

On-going - In August of 2009, eight 

butterfl ies were collected from the Sardis 

unit, and one from PG&E East parcel. 

Surveys for Lange’s metalmark butterfl y 

were conducted in Sept. 2009. A grazing 

study was implemented in spring of 2009. 

Supports species and habitat 

protection and restoration: The 

Lange’s metalmark butterfl y (federally 

endangered) is on the verge of 

extinction and is found only at the 

Antioch Dunes NWR; restoration of 

dunes habitat is enhancing native 

buckwheat host plant survivability 

and recovery of the wallfl ower and 

primrose, two federally endangered 

species.

Mr. Eric Hansen, Private Consultant and 

Researcher – The goals of the project are: 

Determine presence-absence of the giant 

garter snake (GGS) in the eastern Delta; 

establish control sites needed to evaluate 

effects of seasonal variability; assess 

current status of GGS and potential habitat; 

provide demographic and methodological 

foundation for future research; and 

formulate recommendations for water and 

habitat management for GGS in the San 

Joaquin County. HRP funded $122,648.

On-going - The fi eld portion of the 

study began in July 2009 and ended in 

September 2009. Various data were 

gathered including number of individuals, 

size of occupied areas, and reproductive 

status. Tissue samples were also collected 

for genetic analysis. The fi nal report is due 

in March 2010.

Supports species and habitat 

protection: Certain portions of 

San Joaquin County have not been 

surveyed for GGS, a federally 

threatened species, since 1994. The 

study resulted in the discovery of 

14 GGS, which means it is the fi rst 

confi rmed population in the county in 

15 years.
34 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Table 5. FY 2009 Projects Funded by the Habitat Restoration Program (HRP) (Continued)

Project Status Signifi cance

Vollmar Consulting - Study will determine 

current status of all known extant 

occurrences of Hartweg’s golden sunburst 

and San Joaquin adobe sunburst in the 

eastern San Joaquin Valley, as well as 

surveys for new potential habitat. HRP 

funded $53,620.

On-going - Vollmar Consulting has 

obtained initial verbal permission to 

conduct surveys on approximately 

500 acres of new potential habitat in 

southern Stanislaus County. They will 

begin cataloguing targeted survey sites 

in December 2009 and begin the formal 

process of obtaining landowner access 

beginning in January 2010. They will begin 

conducting fi eld surveys around early 

March 2010. 

Supports species and habitat 

protection: The Hartweg’s golden 

sunburst (federally endangered) 

and San Joaquin adobe sunburst 

(federally threatened), will be the 

subject of 5-year Reviews by the Fish 

and Wildlife Service in 2010. The 

last comprehensive surveys for these 

species were conducted in 1990 as 

part of status surveys to determine the 

need for federal listing. A total of 62 

known occurrences of the species will 

be visited with the project, as well as 

surveys of up to 1,000 acres of new 

potential habitat.

US Geological Survey (USGS) - Study 

will entail an evaluation of the genetic 

relationships among and within recovery 

units of the Alameda whipsnake in Alameda 

County. HRP funded $91,570.

On-going - Funds are being used to 

assess the genetic distinctiveness of 

the Alameda County whipsnake relative 

to other populations of the California 

whipsnake. All DNA sequencing and 

genotyping will be completed by the end 

of this December for the tissue samples 

in hand. USGS intends to fi ll in a few 

geographic sampling gaps by collecting 

more snakes in April 2010. 

Supports species and habitat 

protection: The degree of genetic 

divergence among the recovery 

units for the Alameda whipsnake, a 

federally endangered species, has 

never been determined. The results 

of the study will aid in determining 

whether the existing recovery units 

and corridors accurately refl ect the 

genetic structure of the species, and 

whether the current plan promotes 

recovery by protecting the full range of 

genetic variation that is present. 

USGS - Study will assess the probability 

of detecting populations of the giant garter 

snake in Butte County, at sites based on 

site conditions and survey method; quantify 

the relationship of habitat, microhabitat, 

and vegetative conditions with occurrence 

and abundance of the snake; and develop a 

predictive model and map that can identify 

where snake populations are likely to occur 

or identify sites appropriate for repatriation 

studies. HRP funded $60,000.

On-going - All ESA permits/consultation 

completed and Interagency Agreement 

between USBR and USGS has been 

consummated. USGS has arranged 

for access onto survey sites and has 

completed preliminary habitat modeling. 

Survey/trapping will begin in spring of 

2010.

Supports species and habitat 

protection: This project will provide 

quantitative guidelines for future 

surveys that seek to establish 

presence or absence of the giant 

garter snake in Butte County, and 

the occupancy/abundance model 

will help direct future research and 

conservation efforts for the species.

BLM, Pine Hill Preserve - The project will 

provide public outreach about gabbro soil 

rare plants and their habitats. The mission 

of the Pine Hill Preserve is to conserve 

in perpetuity the rare plant species and 

communities of the western El Dorado 

County gabbro soil formation. Five out 

of eight rare plant species protected at 

the Preserve are listed under the Federal 

Endangered Species Act. Currently, 

the Preserve provides protection and 

management for 4,122 acres of rare plant 

habitat. HRP funded $48,000.

On-going - As of October 2009, the plan 

is 80% fi nished. BLM staff are developing 

new brochures, signs, and other outreach 

and educational materials.

Supports species and habitat 

protection: The development of a 

plan to guide and implement public 

outreach and educational activities at 

the Preserve, and the implementation 

of recovery activities associated with 

public outreach, will help to promote 

protection, conservation, and recovery 

of rare plant species at the Preserve. 

Species that will benefi t include 

Stebbin’s morning glory, Pine Hill 

ceanothus, Pine Hill fl annelbush, El 

Dorado bedstraw, Layne’s butterweed, 

Red Hills soaproot, Bisbee Peak rushrose, and El Dorado mule-ears.
3406(b)(1) “other” and 3406(b)(23) 35

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 

Trinity River Restoration 

Program

Fisheries Resource Area (Trinity River Basin)

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 (Figure 6). The 

program uses 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 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $ 2,512,000

• Water and Related - $ 6,814,000

• Bay Delta - $ 794,000

• ARRA - $ 20,000

TOTAL - $10,140,000

Accomplishments

• Released fl ows of 454,500 acre-feet from 

the Lewiston Reservoir to provide adequate 

temperature and habitat conditions for fi sh and 

wildlife

• Completed construction of one channel 

rehabilitation site covering a project area of 

one mile in length associated with the Sawmill 

Rehabilitation Project 

• Placed approximately 8,000 cubic yards of coarse 

sediment

• Implemented new construction projects including 

road upgrades at the Grass Valley Creek and 

Indian Creek watershed; rehabilitation in the 

area burned by the 2008 Junction City Fire; and 

expansion and sediment removal in the Dark Gulch 

sediment retention basin

• Funded new projects for implementation in 2010 

including phase II road storm-proofi ng in the 

Democrat Gulch drainage and sediment reduction 

in the China Gulch and Dutch Creek drainages 

010

uction 

es

• Fu

inc

De

int

Sacramento

San Francisco

Los Angeles

Weaverville

Redding
36 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

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. 

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 makes management recommendations to the 

Trinity Management Council to adjust the program’s 

annual work plan 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. 

Escapement Increases – 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 

Figure 6. Trinity River Restoration Program

Lewiston Dam

Trinity Dam

Lewiston Reservoir

Trinity River Grass Valley Creek

Trinity River Restoration Area

North Folk Trinity River North Fork Trinity River

River Salmon and Steelhead Hatchery production goals 

developed by CDFG. The goals were subsequently 

adopted by the TRRP as escapement numbers. The 

in-river goals represent the 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 

acre-feet per year, with potential peak fl ows to 11,000 

cfs by 2008 and annually thereafter. The fl ow releases 

vary by water year type: 368,600 acre-feet (critically 

dry), 452,600 acre-feet (dry), 464,500 acre-feet (normal), 

701,000 acre-feet (wet), and 815,200 acre-feet (extremely 

wet). The variable fl ow releases are designed to provide 

adequate temperature and habitat conditions for fi sh and 

wildlife at different life stages.

Implementing construction projects – Measured by 

progress toward completion of 47 mechanical channel 

rehabilitation projects and all necessary infrastructure 

improvements. Since 2005, 17 of the 47 channel 

rehabilitation sites identifi ed in the ROD have been 

completed. Completion of the remaining 47 mechanical 

channel rehabilitation projects is targeted for FY 

2014. It is anticipated that maintenance and other site 

enhancements will be required for an additional three 

years to ensure functionality of these sites.

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. 
3406(b)(1) “other” and 3406(b)(23) 37

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

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. 

Since 2001, the CVPIA Restoration Fund has allocated 

approximately $12 million to the TRRP. The program 

has implemented 17 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 the TRRP 

include:

• Construction of 17 channel rehabilitation projects 

(Hocker Flat, four sites near Canyon Creek, three 

sites near Indian Creek, and nine sites in the 

Lewiston area).

• Addition of more than 30,400 cubic yards of 

coarse sediment for spawning and geomorphic 

purposes.

• 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 122 domestic water or sewer 

systems.

• Completion of a programmatic EIR/

Environmental Assessment (EA) that will 

streamline the environmental review process for 

coarse sediment augmentation activities and the 

remaining channel rehabilitation projects.

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 1.9 million acre-feet 

more water has been released to the river over the past 

nine years than would have occurred without the ROD.

MEASURING SUCCESS

Outcome-based Target – Escapement 

Increases 

To date, the annual escapement targets have not been 

met. Monitoring suggests an upward trend in coho 

salmon and steelhead run size over the last 13 years, 

but a continuing decline in fall-run Chinook returning 

adult spawners. The CDFG 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. The variable nature of these populations 
38 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

is demonstrated in 2008 run size estimates, which 

showed a smaller steelhead run than the past two years, 

but with a somewhat higher percentage of wild fi sh. 

Preliminary 2009 weir counts indicate a slight increase 

in steelhead though these are mostly hatchery fi sh.

Output-based Targets 

Increasing Minimum Flow Releases

Water Year 2009 was classifi ed as a dry water year in 

accordance with the ROD resulting in 454,500 acre-feet 

being released from the Lewiston Reservoir, which met 

the target fl ow release of between 369,000 and 815,000 

acre-feet per year and the dry year target of 452,600 

acre-feet.

Implementing Construction Projects

In FY 2009, the program completed construction of 

one channel rehabilitation site covering a project area 

of one mile in length associated with the Sawmill 

Rehabilitation Project. This project 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 this site in 2009 brings the total 

number of mechanical channel rehabilitation projects to 

17 (36% complete toward goal). The TRRP has received 

ARRA funds to expedite the completion of fi ve channel 

rehabilitation projects in 2010 and expects to complete 

the remaining 25 sites by 2014.

Coarse Sediment Management

In 2009, the program placed 5,700 cubic yards of 

gravel in the mainstem of the Trinity River as part 

of the Sawmill 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 April 

2009. In total, the program placed about 8,000 cubic 

yards of coarse sediment in the river during 2009, 

exceeding the annual target of 7,000 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 

64,400 cubic yards of coarse sediment has been added 

to the upper river since dam closure, with about 30,400 

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 

similar to that of pre-dam levels.

Watershed Restoration

In 2009, TRRP completed 10 priority watershed projects 

that were funded with 2008 funds and initiated eight 

new projects. The 2009 TRRP funding amount of 

$280,000 was leveraged with other funding sources 

to bring in an additional $365,000 to watershed 

restoration on Trinity River tributaries. New projects 

under construction in 2009 are road upgrades at the 

Grass Valley Creek and Indian Creek watershed; 

rehabilitation in the area burned by the 2008 Junction 

City Fire; and expansion and sediment removal in the 

Dark Gulch sediment retention basin. New projects 

funded in 2009 for implementation in 2010 are phase II 

road storm-proofi ng in the Democrat Gulch drainage 

and sediment reduction in the China Gulch and Dutch 

Creek drainages. These projects are expected to prevent 

up to 65,000 cubic yards of fi ne sediment from being 

delivered to the Trinity River. 

Sawmill Rehabilitation Project during winter base fl ow 

with large woody debris in side channel. Large woody 

debris serves as habitat for frys and juveniles and 

structure for geomorphic purposes.
3406(b)(1)(B) 39

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 

Sacramento

San Francisco

Los Angeles

Modifi ed CVP Operations

Fisheries Resource Area (Central Valley)

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 which 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. 

Reoperating the system under CVPIA Section (b)(1)(B) 

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. Interior modifi es base condition 

CVP operations using (b)(2) water, (b)(3) water, and by 

“reoperating” the system to provide instream benefi ts to 

anadromous fi sh. 

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 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $300,000

Accomplishments

• Reoperated the system multiple times to provide 

benefi ts to anadromous fi sh on Clear Creek

• Completed response-to-comments document for 

stakeholder review of draft report for spring- and 

fall-run Chinook salmon and steelhead spawning 

on the Yuba River and sensitivity analysis for 

above report

• Completed monitoring for juvenile spring-run and 

fall-run Chinook salmon and steelhead rearing for 

the lower reach of Clear Creek

• Completed modeling and draft report for fall-run 

Chinook salmon and steelhead spawning on 

Clear Creek

• Completed monitoring for fi sheries investigation 

task “Clear Creek Biovalidation – how well does 

IFIM compare to fi eld observations”

• Completed fi sheries investigation task “Reexamine Clear Creek data on adult Spring 

Chinook – is the increase in Weighted Useable 

Area due to an increase in quality or is it an 

increase in area?”

ble

• Co

exa

Ch

Are

inc
40 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Instream Flow Incremental Methodology (IFIM) is a 

habitat-based model developed by the Service to assess 

instream fl ow needs for aquatic resources, including 

anadromous fi sh. The program goal is to provide 

up to nine specifi ed instream fl ow studies. 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, South Cow and 

Butte Creeks. 

The Service uses the IFIM 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 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 2009 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 

American River IFIM study (2003) which demonstrated 

that the amount of spawning habitat for fall-run Chinook 

salmon and steelhead increased considerably with fl ows 

increasing up to 2,000 cfs . In 2009, the data from this 

IFIM study were used to justify operational changes in 

the allocation of (b)(2) water in the American River and 

fl ows were maintained in the 800 to 950 cfs range from 

October through February to provide as much spawning 

habitat as possible.

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 

Collecting IFIM Field Data in South Cow Creek
3406(b)(1)(B) 41

South Cow creeks to the priority list of rivers to be 

modeled over the next fi ve years. The scope of the 

IFIM program was broadened in FY 2009 to include 

fi sheries investigations, with the goal of providing 

scientifi c information to other CVPIA programs to use 

in assessing fi sheries restoration actions.

Since 1995, 12 IFIM studies have been completed 

meeting the program goal to provide up to nine IFIM 

studies under the (b)(1)(B) authority.

MEASURING SUCCESS

In FY 2009, 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. 

Table 7 illustrates progress on the studies that were 

active in 2009. (Dates indicate completion of an activity.)

Table 7. Instream Flow Incremental Methodology (IFIM) Studies Active as of 2009

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 2010 FY 2010

Redd dewatering and juvenile 

Chinook and steelhead stranding

FY 2007 FY 2008 FY 2010 FY 2010

Spring- and fall-run Chinook 

salmon and steelhead spawning

FY 2004 FY 2006 FY2006 FY 2010

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 FY 2010 FY 2010

Juvenile spring-run Chinook 

salmon and steelhead upper 

reach rearing

FY 2007 FY 2010 FY 2010 FY 2010

Juvenile spring-run and fall-run 

Chinook salmon and steelhead 

lower reach rearing

FY 2009 FY 2010 FY 2010 FY 2010

South 

Cow 

Creek

Fall-run Chinook salmon fry and 

juvenile rearing

FY 2010 FY 2010 N/A FY 2010

Fisheries 

Investigation

Clear Creek Biovalidation – how 

well does IFIM compare to fi eld 

observations 

FY 2009 FY 2010 N/A FY 2010

Re-examine Clear Creek data 

on adult Spring Chinook – is the 

increase in Weighted Useable 

Area due to an increase in 

quality or is it an increase in 

area?

N/A FY 2009 N/A FY 2009

As shown in Table 7, the major accomplishments for 

2009 include the following:

Yuba River – Completion of response-to-comments 

document for stakeholder review of draft report for 

spring- and fall-run Chinook salmon and steelhead 

spawning and sensitivity analysis for above report.

Clear Creek – Completion of monitoring for juvenile 

spring-run and fall-run Chinook salmon and steelhead 

lower reach rearing and completion of modeling and 

draft report for fall-run Chinook salmon and steelhead 

lower reach spawning. 

Fisheries Investigations – Completion of monitoring 

for fi sheries investigation task “Clear Creek 

Biovalidation – how well does IFIM compare to fi eld 

observations” and completion of fi sheries investigation 

task “Re-examine Clear Creek data on adult Spring 

Chinook – is the increase in Weighted Useable Area due 

to an increase in quality or is it an increase in area?”
42 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 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...”

Sacramento

San Francisco

Los Angeles

Dedicated 800,000 acre-feet 

Project Yield

Fisheries Resource Area (Central Valley)

WATER MANAGEMENT 

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. 

Generally, (b)(2) fi sh actions fall into the following 

categories:

• Instream fl ow augmentations on CVP-controlled 

streams to protect salmon and steelhead 

and contribute toward meeting AFRP Final 

Restoration Plan fl ow objectives.

• Increased releases from Goodwin Reservoir to 

help meet the Water Quality Control Plan (WQCP) 

requirements for San Joaquin River fl ows at 

Vernalis for fi sh and wildlife standards.

• Increased releases from Keswick and/or Nimbus 

reservoirs to help meet the WQCP fi sh and wildlife 

standards.

• Export reductions at the CVP Tracy (Jones) pumps 

to protect at-risk fi sh species (notably salmon, 

steelhead, and delta smelt) and to help meet the 

WQCP Delta standards.

In the past, the management of (b)(2) water was 

coordinated with the management of CALFED’s 

Environmental Water Account (EWA), since the use of 

both (b)(2) and EWA often contributed concurrently to 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $663,000

Accomplishments

• Due to low CVP storage and dry hydrology the 

(b)(2) shortage provision limited fi sh actions to 

600,000 acre-feet (for the second consecutive 

year). This water was managed for fi sh, wildlife, 

and habitat restoration purposes

• Augmented low base fl ows on Clear Creek, the 

American River, and the Stanislaus River

• Assisted in meeting WQCP requirements with 

water from the American River

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

(3) water for juvenile salmonid outmigration on 

the Stanislaus River

• Curtailed exports to assist in meeting WQCP 

Delta requirements, to comply with FWS and 

NOAA Biological Opinions, and to meet the 

VAMP export target during the April 17 to 

May 17 period

• Cu

De

NO

VA

Ma
3406(b)(2) 43

the CVPIA’s goal of doubling the natural production 

of anadromous fish and protection of other aquatic 

resources, including endangered fi sh species. However, 

in 2009 there was very little EWA water to manage. 

In the 2009 water year, both the Sacramento and 

San Joaquin River Basins were classifi ed as “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) water was ultimately limited 

to 600,000 acre feet during the 2009 water year. In 

addition, two new Biological Opinions (BOs) on the 

Long Term Operations of the Central Valley Project and 

State Water Project were issued during the 2009 water 

year (USFWS BO in December 2008 for the protection 

of the federally-listed delta smelt, and the NOAA BO 

in June 2009 for the protection of listed salmonids and 

sturgeon). Both BOs affected the use of (b)(2) water (see 

Table 8). 

Throughout the 2009 water year, Interior managed (b)(2) 

water consistent with recent court rulings, including:

1. The Ninth Circuit Court’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), and

2. The U.S. District Court for the Eastern District 

of California’s memorandum opinion in San 

Luis & Delta Mendota Water Authority v. 

Department of the Interior (SLDMWA), 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

 Interior 

continued to manage (b)(2) water in accordance 

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

Interior’s December 17, 2003 (b)(2) Guidance 

Memo.

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.

MONITORING AND EVALUATION

The (b)(2) program funds specifi c monitoring and 

evaluation projects to assess the effectiveness of the use 

of the (b)(2) water.

In addition, other projects throughout the Central Valley 

provide real-time fi sh monitoring data which helps 

inform decisions on when and where (b)(2) fi sh 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 Reclamation’s, Mid-Pacifi c Region, Central 

Valley Operations Offi ce home page at www.usbr.gov/

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 four notable exceptions: 

In wetter precipitation years (2005 and 2006) a portion 

of the dedicated water was banked pursuant to CVPIA 

Section 3408(d) for use in the subsequent year. In water 

year 2008 (critically dry) and 2009 (dry), only 600,000 

acre-feet of (b)(2) was available for fi sh actions (Table 9).

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.
44 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Table 9. Allocation and Use of (b)(2) Water (2001-2009)

Allocation and Use of (b)(2) Water by Year (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

2009 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.

Table 8. FY 2009 Use of (b)(2) Water by Location

River Action Timeframe Results

American Augmented low base 

fl ows

October 2008 – 

February 2009

Contributed towards AFRP Final Restoration 

Plan fl ow objectives and improved conditions 

for fall-run Chinook and steelhead during 

spawning, incubation, and rearing.

Assisted in meeting 

WQCP Delta 

requirements

Intermittent, spring 

water year 2009

Assisted in meeting WQCP delta outfl ow.

Clear Creek Augmented low base 

fl ows throughout water 

year 2009

Intermittent, 

November 2008 – 

September 2009

Contributed to AFRP Final Restoration 

Plan fl ow objectives and improved instream 

conditions for fall-run Chinook, spring-run 

Chinook, and steelhead during spawning, 

incubation, rearing, and downstream migration.

Stanislaus Augmented low base 

fl ows

Intermittent, fall and 

winter water year 

2009

Contributed towards AFRP Final Restoration 

Plan fl ow objectives and improved instream 

conditions for fall-run Chinook and steelhead 

during spawning and rearing periods.

(b)(2) water used in 

conjunction with acquired 

(b)(3) water to provide 

pulse fl ow in spring 2009 

for juvenile salmon and 

steelhead outmigration 

(during April 17 to May 17 

period)

April – May 2009 Improved survival of salmon and steelhead 

smolts emigrating down the Stanislaus and 

San Joaquin Rivers, and improved habitat 

conditions in the central and southern delta for 

listed aquatic species.

CVP Jones 

Pumping Plant

Export curtailments to 

assist in meeting WQCP 

Delta requirements

Intermittent, winter 

and spring water 

year 2009

Protected estuarine habitat for anadromous 

fi shes and other estuarine dependent species.

Export curtailments 

related to Delta Cross 

Channel gate closure

November – 

December 2008

Benefi tted winter-run and spring-run Chinook 

outmigrants and other species.

Export curtailments to 

help meet Biological 

Opinion requirements for 

delta smelt

Intermittent, winter 

and spring water 

year 2009

Provided increased protection for delta smelt 

(ESA threatened) and minimized entrainment 

at the CVP pumps.

Export curtailment to 

meet export target during 

the April 17 to May 17 

period

April – May 2009 Benefi tted San Joaquin Basin fall-run Chinook 

and steelhead outmigration, contributed to 

AFRP Final Restoration Plan fl ow objectives, 

and contributed to protection for listed delta 

smelt.
3406(b)(3) and 3406(g) 45

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) acquires water 

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

yield ((b)(2) water) for fisheries. The target for instream 

acquisitions is 200,000 acre-feet per year, for use 

on the San Joaquin and Sacramento Rivers and their 

tributaries, as described in the CVPIA PEIS/ROD. The 

WAP also acquires water for CVPIA-designated refuges 

Sacramento

San Francisco

Los Angeles

Water Acquisition Program – 

Instream Water 

Fisheries Resource Area (Central Valley)

and wildlife management areas. WAP activities for 

refuge water acquisitions are discussed in Section 3406 

(b)(3) and (d)(2), Water Acquisition Program-Refuge 

Water. 

The WAP is designed to acquire instream fl ows to meet 

two primary objectives in support of the AFRP Final 

Restoration Plan: 

• Improve spawning and rearing habitat 

• Increase migration flows for fall-, winter- and 

spring-run Chinook salmon and steelhead

MANAGING FLOWS PURSUANT 

TO SAN JOAQUIN RIVER 

AGREEMENT AND VERNALIS 

ADAPTIVE MANAGEMENT PLAN

In support of these objectives, 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 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - Instream Water - $ 6,001,000

• Restoration Fund - VAMP - $ 6,149,000

TOTAL - $12,150,000

Accomplishments

• Acquired 38,500 acre-feet for San Joaquin River 

Agreement/Vernalis Adaptive Management Plan

iver 

Plan

• Acq

Ag
46 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

requirements. Fall flows assist adult salmon migrating 

into the tributaries prior to spawning. 

The WAP, in cooperation with the Central Valley 

Operations Offi ce (CVO), and the San Joaquin River 

Group Authority’s (SJRGA) member agencies, acquires 

and 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. In FY 2009, the 

program acquired 38,500 acre-feet for SJRA/VAMP.

Table 10 shows the volume of water purchased for the 

years 1994 through 2009.

Reclamation has not been able to acquire the full 

200,000 acre-feet of target flows due to a lack of 

willing sellers and 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 oneyear transfers with local water agencies that have 

transferable water to sell. However, in this reporting 

year, water was not acquired for instream purposes in 

the Sacramento Valley due to lack of available water 

supplies for permanent acquisition, that would benefi t 

anadromous fi sh.

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

Acquisitions, toward 200,000 acre-feet target 

(1994-2009)

Year

Annual Water 

Acquisitions 

(acre-feet)

Percentage of 

200,000 AcreFeet 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%)

2009 38,500 (19%)
3406(b)(4) 47

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) (Figure 7). 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, costeffective fi sh collection, holding, transport and release 

technology and operational procedures that will improve 

fi sh protection in the south delta at the entrance to the 

JPP. The data and information generated will help 

evaluate present-day operations and effi ciencies for 

TFCF, as well as assisting 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 located at the USBR Denver 

Technical Service Center. Research planning and 

execution is enhanced through coordination, review 

Clifton Court

Forebay

Tracy Fish Collection Facility

Suisun

Bay

San

Francisco

Bay

Tracy (Jones) Pumping Plant 

Program 

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Water and Related - $1,593,000

• Bay Delta - Two Gates - $ 175,000

TOTAL - $1,768,000

Accomplishments

• Continued study efforts to determine Tracy Fish 

Collection Facility present-day fi sh salvage 

effi ciencies for various species of delta fi sh 

entrained at the JPP

• Completed assessment 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 at the 

TFCF

• Completed recessed holding tank stress tests for 

various species of delta fi sh entrained at the JPP

• Collected water quality data at the entrance to the 

DMC intake canal

• Distributed Tracy Research Volume Series and 

Technical Bulletins

• Updated the Tracy Research Program website

• Completed phase 1 of construction of a new 

onsite biological resources building

• Commenced with planning and review for the 

Two Gates Fish Protection Demonstration 

Project, including

- Establishment of joint State-Federal teams 

to expedite the review and processing of the 

Demonstration Project

- Completion of CALFED Science Program 

Independent Review Panel evaluation of the 

Demonstration Project

- Establishment of a Demonstration Project web 

site and enhanced public interaction

web

D

- E

s
48 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

and assistance from others including CDFG, DWR, the 

Service, NMFS, universities, private consultants, and 

the San Luis Delta Mendota Water Authority.

Due primarily to budgetary constraints, Reclamation 

and DWR management agreed in 2005 not to proceed 

with construction of new full-scale testing/fi sh screen 

facilities in the south delta. Instead the agencies opted 

to develop and implement improvement actions at 

the existing TFCF and Skinner fi sh salvage facilities 

(including improved technology and operational 

procedures) to reduce fi sh losses and improve fi sh 

salvage success while achieving CVPIA goals as well 

as federal ESA biological opinion objectives. This new 

strategy 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. 

IMPLEMENTING THE SOUTH 

DELTA FISH FACILITY FORUM 

STRATEGY

Since the TFFIP was implemented, physical and 

operational changes to the TFCF have shown some 

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. 

Reclamation estimates that it will take approximately 

another four to six years to fully assess the existing 

TFCF and implement all remaining physical and 

operational improvements presently identifi ed at TFCF. 

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 the JPP intake by a few feet 

and increased primary channel velocities which 

reduces salvage effi ciency.

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. This resulted in a higher level of 

fi sh stress and mortality and caused 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.

Since 1992, Reclamation has identifi ed 23 “actions” 

related to improving fi sh protection at the existing 

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 specifi c fi sh loss reduction targets, although 

recent 2009 NOAA Fisheries BO RPAs have stipulated 

that Reclamation shall improve the whole facility 

effi ciency for the salvage of Chinook salmon, Central 

Valley steelhead, and southern Distinct Population 

Segment of green sturgeon so that overall survival is 

greater than 75 percent for each species. The program’s 

primary “goal” is to implement and complete the 23 

identifi ed actions, which should result in increased 

survivability of all delta fi sh species entering the DMC 

intake at the TFCF. 

Tracy (Jones)

Pumping Plant

Delta-Mendota Canal

Figure 7. Tracy (Jones) Pumping Plant
3406(b)(4) 49

MEASURING SUCCESS

Program Actions

To date, the program has completed 14 of 23 actions 

(Table 11), or 61 percent of the program’s present goal. 

Actions in 2009 included continued study efforts to 

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

for different species of fi sh; completion 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; completion 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 continued 

construction of a new onsite research building; phase 

1 of construction is complete (phase 2 remains to be 

completed).

Another signifi cant component was added to the 

program in FY 2009 with initiation of the Two 

Gates Fish Protection Demonstration Project. 

The Demonstration Project was developed by the 

Metropolitan Water District of Southern California 

and the San Luis & Delta Mendota Water Authority 

(SLDMWA) to test alternative ways of protecting delta 

smelt. The 5-year experiment is designed to modify 

fl ows in the Sacramento-San Joaquin Delta to reduce 

entrainment of smelt and other sensitive aquatic species 

in CVP and SWP export pumps. There was progress 

made in 2009 towards construction and installation 

of the Two Gates Demonstration Project with the 

completion of initial planning and project review. FY 

2009 accomplishments included the establishment of 

joint State-Federal teams to expedite the review and 

processing of the Demonstration Project, completion 

of the CALFED Science Program Independent Review 

Panel evaluation of the Demonstration Project, and 

establishment of a Demonstration Project web site 

and enhanced public interaction. Additionally, there 

was ongoing development of Draft Environmental 

Assessment, Finding of No Signifi cant Impact (FONSI), 

Biological Assessment and Biological Opinions.

Program Research

The program has published 42 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 2009, the 

program completed distribution of Tracy Research 

Volume Series No. 42 and Tracy Technical Bulletins 

2008-1, -2 and -3, as well as updating and redistributing 

Volume No. 13 (“Guidance to Authors”). The program 

also published a PhD Dissertation related to fi sh holding 

stress on Chinook salmon.

The program facilitated the ongoing development of the 

Tracy Research technical website and enhanced data 

accessibility. The information contained on the website 

is used by many of the scientists and engineers studying 

the Sacramento-San Joaquin Delta region for fi shery and 

water quality affects and concerns. 

In 2010, 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
50 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Table 11. Actions to Improve Tracy Fish Collection Facility, Completed to Date

Actions Start Date

Completion 

Date

1 Implemented periodic predator removals 1992 1992 (“ongoing”)

2 Upgraded instrumentation at the TFCF 1992 1993

3 Replaced high pressure utility pump with low pressure utility pump 1995 1996

4 Epoxy coated recessed collection tanks 1997 1997

5 Constructed aquaculture facility onsite 1997 2005

6 Constructed extraction device for Chinese mitten crabs/debris removal 1998 1999

7 Installed air system in recessed collection tanks 1999 1999

8 Developed onsite laboratory for fi sh taxonomic work 1999 1999

9 Added air system to fi sh haul trucks 2000 2000

10 Upgraded fi sh count area to accommodate DNA sampling & fi sh ID 2000 2000

11 Updated fi sh identifi cation key for training of operators 2000 2000

12 Replaced worn (“leaky”) bypass transition boxes 2003 2004

13 Replaced fi sh transfer bucket with new/improved fi sh transfer bucket 2006 2008

14 Replaced fi sh haul trucks with new/improved fi sh haul trucks 2006 2008

15 Constructed new biological resources building 2006 2010*

16 Replaced existing trash rack cleaner with new/improved trash rack 

cleaner

2006 2010*

17 Replaced primary louvers/cleaners with new primary louvers/cleaning 

system

2006 2013*

18 Replaced secondary louver/cleaners with new secondary louvers/

cleaning system

2006 2011*

19 Developed land onsite to improve ability to conduct research and operate 

the facility

2006 2012*

20 Construct new secondary screening and transfer system 2010 2016*

21 Construct new aquaculture facility onsite 2012 2013*

22 Automate velocity control pumps for the fi sh bypass system 2013 2014*

23 Construct third fi sh release site 2014 2015*

* Estimated Completion Date
3406(b)(5) 51

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.”

The Contra Costa Canal is an essential feature 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. 

Contra Costa

Canal Pump

Suisun

Bay

San

Francisco

Bay

Contra Costa Canal Pumping 

Plant 

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Water and Related - $ 116,000

• State - $ 1,000

• ARRA - $6,884,000

TOTAL - $7,001,000

Accomplishments

• Updated screen designs to bring up to current 

construction code

• Completed environmental documentation and 

permits for the construction of the fi sh screen

• Conducted fi sh monitoring at Rock Slough 

headworks and Pumping Plant No. 1

• Started construction of Phase II of the Rock 

Slough Fish Screen

Co

hea

•Sta

Slo

Contra Costa Pumping Plant No. 1 is located at the head 

of the Contra Costa Canal. 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 (Figure 8). 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 

Pumping Plant No.1 and one or more new intake 

structures 

• Work with CCWD to modify operations (change 

the pumping schedule) to take less water when fi sh 

are nearby

• 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

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 programs, including the 

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

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

species in addition to the Contra Costa Canal Pumping 

Plant Program (b)(5).
52 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

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; the Teams reviewed 

preliminary designs and recommended 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 for 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 identifi ed potential fi sh 

screen alternatives. 

Prior to 2009, a decision by Reclamation and USFWS to 

screen Rock Slough had been delayed several times due 

to funding and appropriate land acquisition. In 2009, the 

program received American Recovery and Reinvestment 

Act (ARRA) funding to build a new fi sh screen. The 

project will eliminate the annual incidental take of 

ESA listed species due to project pumping effects as 

described in previous NMFS (2009) and USFWS (Los 

Vaqueros 2009) BOs. The project is consistent with the 

NMFS Operations Criteria and Plan (OCAP) BO issued 

June 4, 2009.

In 2009, the program used ARRA funding to update the 

fi sh screen design to bring it up to current construction 

code and completed environmental documentation and 

permits for the project.

The program started construction of Phase II of the 

Rock Slough Fish Screen in September 2009. These 

improvements include in-water work such as coffer 

dams and levee embankment construction; these 

improvements are required to immediately meet inwater work restrictions. Phase III, the construction 

1 The team is made up of representatives from CDFG, 

DWR, Service, Reclamation, NOAA Fisheries, and the Contra 

Costa Water District (CCWD)

Figure 8. Rock Slough Fish Screen (Proposed)

Equipment staging for the commencement of Phase II 

of the Rock Slough Fish Screen

Rock Slough Fish Screen, North Coffer Dam

of the fi sh screen and appurtenances is scheduled for 

completion in November 2011.

Fish monitoring continued through 2009 according to 

the monitoring plan. 
3406(b)(9) and 3406(b)(19) 53

CVPIA Section 3406(b)(9) 

“(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...”

And CVPIA Section 3406(b)(19)

“(19) Reevaluate existing operational criteria in 

order to maintain minimum carryover storage at 

Sacramento and Trinity River reservoirs to protect 

Sacramento

San Francisco

Los Angeles

Flow Fluctuations and Reservoir 

Storage

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $4,000

TOTAL - $4,000

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 American River fl ows from October 

2008 through March 2009 with (b)(2) water to 

minimize redd dewatering for fall-run Chinook and 

steelhead

• Augmenting Stanislaus River fl ows with (b)(3) water 

October through mid-December 2008 and used (b)

(2) water in early February to minimize a potential 

fl ow fl uctuation

Developed the Interim Emergency Response Plan in 

October 2008; the plan was implemented in WY 2009 

to increase protection of three listed anadromous 

salmonid species. The plan covers the American and 

Sacramento Rivers.

s

n and

to incre

salmon

Sacram

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 

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

(b)(2). Specifi c performance goals were not established 

for this program. Rather, this program’s activities are 

directed by CVPIA provisions that allow for operational 

changes that will enhance habitat for anadromous fi sh.

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 
54 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

timed fl ows and fl ows of adequate quality to support 

fi sheries restoration as well as meet other project 

purposes. 

Reclamation and the Service convened weekly 

interagency (b)(2) team meetings in water year 2009 to 

determine how to minimize damaging fl ow fl uctuations 

to the extent possible on CVP-controlled streams (Clear 

Creek, Sacramento River, American River, and the 

Stanislaus River).

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 (WY) 2009 

(October 2008 through September 2009), 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. The Service uses this report as guidance for 

determining when to initiate surveys. Due to extremely 

low storage levels and dry hydrology in water year 

2009, fl ows on the Sacramento River were relatively low 

and stable in the fall and winter of 2008/2009. From 

mid-November 2008 through March 2009 large fl ow 

fl uctuations did not occur (coincident with the greater 

part of salmon and steelhead spawning and rearing 

periods)

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

2000 fl ow fl uctuation study was published by the 

CDFG 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 water year 

2009, American River fl ows were augmented using 

(b)(2) water from October 2008 through early March 

2009. Large fl ow fl uctuations during this period did not 

occur. The American River Operations Work Group 

continued to meet monthly to discuss both the American 

River operations and to discuss the work to determine 

threshold fl ows and ramping rates required to protect 

lower American River fi shery resources. 

The Interim Emergency Response Plan for the American 

and Sacramento Rivers, developed in October 2008, was 

implemented on the ground in the spring and summer of 

2009. On three separate occasions (May, August, and 

September) crews monitored potential isolation areas on 

the American River. No rescue efforts were necessary, 

but valuable insights on fl ow fl uctuations at specifi c sites 

were obtained, such as identifying potential stranding 

sites. 

Stanislaus River: In water year 2009, Stanislaus River 

fl ows were augmented using (b)(3) water from October 

through early December 2008. A small volume of (b)(2) 

water was used in early February to augment fl ows and 

avoid a potential fl ow reduction. 

Other Activities: Reclamation coordinated with the 

CDFG, the Service, and NMFS to develop the Interim 

Emergency Response Plan for the American and 

Stanislaus Rivers in October 2008. The monitoring and 

rescue provisions in the plan were implemented in WY 

2009 to increase protection of three listed anadromous 

salmonid species, winter-run Chinook salmon, springrun Chinook salmon, and Central Valley steelhead, 

in the American and upper Sacramento Rivers during 

periods when the operation of Reclamation’s facilities 

could have resulted in the stranding or isolation of such 

listed species. In WY 2009, several monitoring surveys 

took place on the American River but fi sh rescue efforts 

were not needed. 

The American River from Guy West Bridge
3406(b)(10) 55

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 (Figure 9). The dam has 11 gates, 

which when partially closed, divert water to the TehamaColusa and Corning canals to provide water for farmers, 

the Sacramento National Wildlife Refuges (SNWR), 

Red Bluff

Diversion Dam

Sacram

e nto Ri ver

Trinity Shasta Lake

Lake

Redding

Black

Butte

Reservoir

Te hama- C o

ul sa Canal

Corning

Canal

Stony

Creek

Red Bluff Diversion Dam 

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Water and Related - $ 4,173,000

• ARRA - $ 6,589,000

TOTAL - $10,762,000

Accomplishments

• Achieved unimpeded passage for approximately 

80 percent of adult spring-run Chinook and 

virtually all adult green sturgeon based on the 

current operation of the facility (two-month 

closure of the gates)

• Changed operations to raise the gates a 

minimum of 18 inches to ensure protection of 

downstream migrating green sturgeon

• Proceeded on the design of the permanent 

pumping plant

• Designed and constructed an interim pumping 

plant 

• Conducted several monitoring efforts including 

sampling of green sturgeon eggs, larvae, 

and juveniles and surveillance and velocity 

measurements of the interim pump screens

• Completed the fi nal report for the 2007 study on 

Chinook salmon genetics assessment

on 

and

me

• Co

Ch

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. 

Until 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 

to allow passage of winter-run chinook; the spawning 

distribution shifted, with less spawning below the 

RBDD and more spawning in colder water above the 

dam. However, the improved passage still blocked adult 

green sturgeon (ESA-listed), white sturgeon, and many 

adult winter- and spring-run Chinook (both ESAlisted); this continued to cause spawning in downstream 

waters too warm for successful egg incubation. In 

addition, losses of out-migrating juvenile salmon were 

measured at up to 50 percent, and increased feeding and 

ambush settings created a dysfunctional predator-prey 

relationship between the out-migrating salmonids and 

the native Sacramento pikeminnow. 

A 1993 BO required that the gates remain out of the 

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

September 15 through May 15) to allow for expanded 

passage of winter-run Chinook. 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 (see fi gure 10). Declines 

in 2007 and 2008 were primarily caused by unusually 

poor ocean environmental conditions and not the result 
56 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

of any changes at RBDD. Both the fall- and winter-run 

spawning distributions changed signifi cantly after the 

raised gates period with fi sh spawning further upriver.

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 an 

unusually large number of green sturgeon “holding” in 

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

the 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 

alternatives of a new pumping plant, gravity diversions, 

fi sh ladders and gates’ open/close timing to improve 

fi sh passage. Delays in selecting an alternative resulted 

from the process of listing of the green sturgeon as a 

threatened and endangered species. Following listing, 

the EIS/EIR was recirculated in 2006 to include 

discussion of the Operations Criteria and Plan (OCAP) 

BO requirements, and to make it clear the assessment 

of the potential impacts to the green sturgeon was 

unchanged. Reclamation’s stated preference was a twoRed Bluff

Diversion Dam

Corning Canal

Lake Red Bluff

Sacramento River

Tehama-Colusa Cana

Figure 9. Red Bluff Diversion Dam

month gate closure and construction of a new screened 

pumping plant. However, it was recognized that 

operations of a new pumping plant would be determined 

as part of the OCAP ESA consultation. 

The purpose of the RBDD Program 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 has 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 was met several years ago by installation of a 

siphon on the Glenn-Colusa Irrigation District (GCID) 

Canal at Stony Creek to allow year-round deliveries. Use 

of the RBDD for this purpose was therefore abandoned, 

although the planned changes at Red Bluff will provide a 

back-up to conveyance via GCID’s facilities.

MEASURING SUCCESS

Fish Passage

Based on the current operation of the facility (twomonth closure of the gates), approximately 80 percent 

of the adult spring-run Chinook and virtually all adult 

green sturgeon achieve unimpeded upstream passage. 

No further green sturgeon fatalities have been observed 

since the 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). 

In 2009, the gates began to be raised a minimum of 18 

inches to ensure protection of downstream migrating 

green sturgeon.
3406(b)(10) 57

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

2007

Figure 10. Spawning Returns, Winter-Run Chinook, Sacramento River (1967-2008)

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 assumed construction of a 2,500 cfs 

facility, forgoing any reliance on the existing pumping 

plant.

In 2009, the program received American Recovery 

and Reinvestment Act (ARRA) funding to build a new 

pumping plant. The completion of the new pumping 

plant will assist the program in meeting output and 

outcome targets and therefore minimize passage 

problems for anadromous fi sh. In FY 2009, plans 

proceeded on the design of the permanent pumping 

plant; construction of the facility is scheduled to start 

early in FY 2010 with the ARRA funding, even though 

full funding has not yet been secured. Contrary to 

the anticipated continued use of the dam for the midsummer months, the pumping plant is now expected to 

be used year round in light of the OCAP consultation.

In December 2008, NMFS required an additional two 

months of gates opening during the construction of the 

pumping plant, necessitating the design and construction 

of an interim pumping plant by May 2009. The 

interim pumping plant was built on schedule, but has 

encountered mechanical problems with the pumps, along 

with the observation that a few of the fi sh screens did not 

meet fi sh screening engineering criteria. However, the 

interim pumping plant still successfully delivered water 

when needed.

Monitoring

Green Sturgeon Egg and Larval Monitoring 

Sampling of green sturgeon spawning habitat using 

artifi cial substrate mats to acquire eggs continued for 

the second of three seasons. In 2009, green sturgeon 

eggs were sampled from four sites. Eggs were sampled 

above, at, and below RBDD. Preliminary results 

indicate that green sturgeon spawning occurred from 

late-March to early July. 

Green sturgeon larval sampling, for migrating young 

of the year, occurred in 2009 using a benthic D-net. 

Preliminary data suggests that the abundance of green 

sturgeon adults above RBDD was greater in 2009 than 

2008 as evidenced by greater total capture of green 
58 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

sturgeon larvae using the D-net. Additionally, larvae 

and juveniles were sampled from the RBDD rotary traps 

in 2009. 

Video Evaluation and Velocity Monitoring at 

the Interim Pump Screens

The program used underwater video cameras to test the 

suitability of available technology for monitoring and 

to conduct surveillance of the interim pump screens. 

Specifi cally, the surveillance was to document whether 

fi sh are being impacted by the pumps (i.e., impingement, 

impaired swimming/avoidance ability, impact with 

the screen, etc). The results from 2009 are still under 

analysis. This project is expected to continue in FY 

2010.

The program also conducted velocity measurements 

at the interim pump fi sh screens to determine whether 

the pumps or screens are operating within specifi ed 

parameters. A draft preliminary report of the 2009 

fi ndings is currently under review. This monitoring is 

expected to continue during FY 2010.

Chinook Salmon Genetics Assessments at 

the Red Bluff Diversion Dam 

The program has been collaborating with an on-going 

study of Chinook salmon genetics at the RBDD since 

2007. Chinook salmon tissue samples are collected at 

the fi sh trapping facility of the RBDD. In 2009, the fi nal 

report for calendar year 2007 study was completed.

Conceptual Rendering of the New Fish Screen and 

Pumping Facilities (courtesy of CH2M Hill)
3406(b)(11) 59

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 

(Figure 11).

In order to continue to mitigate the effects of these 

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

as follows:

Coleman

Fish Hatchery

Shasta Dam

Keswick Dam

Trinity

Lake Shasta

Lake

Sacra me nto R vi er

Anderson

Ba t tle C

Coleman National Fish 

r

Hatchery

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• None

Accomplishments

• Completed construction of a visitor kiosk at the 

Coleman NFH

• Co he

Co

• Rehabilitate and expand the Coleman NFH by 

implementing the Station Development Plan for 

Coleman NFH on Battle Creek

• Modify the fi sh trap at Keswick Dam to ensure 

effi cient operation at all project fl ow release levels

• Modify the basin below the Keswick Dam 

spillway to prevent the trapping of fi sh 

The program has an output-based performance 

goal to complete the infrastructure improvements 

to enhance conditions for anadromous fi sh and 

maintain hatchery production targets as identifi ed 

in the 1987 Coleman National Fish Hatchery Station 

Development Plan (SDP) and subsequently modifi ed 

over the last 22 years by management requirements.

Specifi c modifi cations to the SDP include noncompletion 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 
60 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

• Coleman NFH: 12 million fall-run Chinook 

salmon smolts, 1 million late-fall-run Chinook 

salmon smolts and 600,000 steelhead smolts

MEASURING SUCCESS

The 1987 SDP outlined a nine-phase strategy to 

rehabilitate the hatchery and implementation was 

authorized through the 1992 passage of CVPIA 

legislation. As shown in Table 12, 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), which 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 (Phases 6-8). The two phases 

that remain to be implemented are expected to be 

completed by 2010 (Phases 2 and 9).

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. 

Coleman Fish

Battle Creek

Hatchery

Figure 11. Coleman National Fish Hatchery

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 have been 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. 

Domestic Water System and Visitor 

Facility Improvements

In 2005 and 2006, the CVPIA implemented a program 

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

tens of thousands of visiting public. 

In 2006, the program began design of a visitor kiosk and 

informational panels at the Coleman NFH; design was 

completed in FY 2008. Construction of the visitor kiosk 

was initiated and completed in FY 2009 and included 

an Americans with Disabilities Act (ADA) compliant 

visitor parking area and ramps. Construction cost 

overruns precluded the ability to purchase information 

panels.

Visitor Kiosk at Coleman National Fish Hatchery
3406(b)(11) 61

Table 12. Coleman National Fish Hatchery (NFH) Facility Rehabilitation Phases (1991-2009)

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
62 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

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...”

The construction of McCormick-Saeltzer Dam in 1903; 

construction of Whiskeytown Dam in the 1960s; and 

aggregate and gold mining in Clear Creek, caused 

widespread degradation of creek habitat. This led to 

precipitous drops in Chinook salmon and steelhead 

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,

• Provide 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

2. Fish passage: Obtain unimpeded fi sh passage 

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 25,000 tons of gravel annually,

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 

Sacramento

San Francisco

Los Angeles

Clear Creek Restoration 

Program

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Water and Related - $ 3,000

• Restoration Fund - $ 745,000

• State - (16,000)

• TOTAL - $ 732,000

Amounts in ( ) = credit amount

Credit amounts are due to de-obligations 

being larger than current year obligations

Accomplishments

• Flows were increased to 200 cfs from midSeptember through mid-June and to an average 

of 135 cfs during the summer 

• Flows to achieve temperature control were met 

99 percent of the time

• Gravel was added at Below Dog Gulch (1,000 

tons), Above Peltier Valley Bridge (770 tons), 

Paige Bar (1,790 tons), Above NEED Camp (980 

tons), and Below NEED Camp (1,230 tons)

• Fall Chinook escapement was 7,677 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 120 in 2009

• Adult steelhead populations increased as 

indicated by redd counts, from approximately 38 

in 2001 to 409 in 2009

• Began permitting and design work for the Clear 

Creek Long-Term Spawning Gravel Supply 

Project that could supply 23 years worth of gravel 

for Clear Creek

ear

ravel 

Be

Cre

Pro

for 
3406(b)(12) 63

MEASURING SUCCESS

Progress against the remaining program goals is 

summarized in the following sections.

Instream Flow

An average of approximately 80,000 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 an average of 135 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 

2009. 

Lastly, the program has met the instream habitat goal of 

90 percent weighted useable area for fi sh use for the last 

seven years including in FY 2009. This goal is met with 

(b)(2) water.

Gravel Placement

Since 1995, an estimated 116,000 tons of gravel have 

been injected at specifi c locations on the creek, resulting 

in a steady increase in spawning habitat (Figure 12). 

This added gravel has recharged spawning gravel within 

approximately three miles of the creek. In 2009, gravel 

was added at Below Dog Gulch (1,000 tons), Above 

Peltier Valley Bridge (770 tons), Paige Bar (1,790 tons), 

Above NEED Camp (980 tons), and Below NEED 

Camp (1,230 tons) for a total of 5,770 tons (23% of the 

program’s annual goal).

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

maintain fi sh habitat. In FY 2009, permitting and design 

work began for the Clear Creek Long-Term Spawning 

Gravel Supply Project that could supply 23 years worth 

of gravel for Clear Creek at a fraction of the current cost 

by using remnant mine tailings adjacent to the creek.

A 10-year programmatic environmental assessment for 

restoration on Clear Creek was fi nalized in 2009. This 

will provide NEPA coverage for the next ten years.

4. Channel restoration: Restore two stream miles 

by 2010 (from approximately river mile 2.5 to 

4.5),

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 

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.

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

Figure 12. Gravel Injection and Channel 

Restoration Sites, Clear Creek
64 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

1967-1991 2007 2008

8000

7000

6000

5000

4000

3000

2000

1000

0

Figure 13. Fall–Run Chinook Salmon Escapement, 

Clear Creek (2008)

2001 2002 2003 2004 2005 2006 2007 2008 2009

200

180

160

140

120

100

80

60

40

20

0

AUGUST SNORKEL COUNT

Figure 14. Adult Spring-Run Chinook Salmon 

Population, Clear Creek (2001-2009)

1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

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 (1998-2008) 

Channel Restoration

The two-mile stream channel is 80 percent restored 

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

Phase 3B fl oodplain revegetation is expected to begin 

in FY 2010. Spawning surveys in 2008 showed that 

Phase 3B increased the total amount of spawning habitat 

by 15 percent. Phase 3C is not complete. An inventory 

of future channel restoration needs was initiated but 

canceled due to the shortfall in Restoration Funds in 

2008; the inventory will be scheduled in 2011. 

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 2008 (FY 2009), fall Chinook 

escapement was 7,677 compared to the average baseline 

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

in Figure 13. This 2008 escapement is remarkable 

compared to escapements in the rest of the Central 

Valley watersheds which were much lower due to the 

coast-wide collapse of Chinook salmon fi shery. In 2008, 

all other Central Valley fall-run Chinook escapements 

decreased and as a whole were only 20% of the 1992 to 

2007 average. Similarly, adult steelhead populations 

also continued to increase on Clear Creek, as indicated 

by redd counts, increasing from approximately 38 in 

2001 to 409 in 2009. Figure 14 depicts the increase of 

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

120 in 2009. All of the cohorts of spring Chinook have 

increased since restoration began. 

Despite the increases in adult populations, juvenile 

fall-run Chinook production has decreased since 

1996 from 7.4 to 3.4 million fi sh, and the number of 

juvenile fall-run Chinook produced per adult female 

has decreased from about 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 CALFED Environmental 

Water 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.
3406(b)(12) 65

Figure 16. Clear Creek Channel Restoration Project Phases

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.

Implementation of the NEED Camp Spawning Gravel 

Injection, Summer 2009
66 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

CVPIA Section 3406(b)(13) 

“Develop and implement a continuing program...

to restore and replenish spawning gravel...and 

rearing habitat... on the American, Stanislaus 

Spawning and Rearing Habitat 

Restoration Program Sacramento

San Francisco

Fisheries Resource Area (Central Valley) Los Angeles

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 

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 CDFG 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $1,061,000

• State - $ 9,000

TOTAL - $1,070,000

Accomplishments

Sacramento River

• Purchased and injected 9,900 tons of gravel

• Monitoring showed that winter-run Chinook 

preferentially use injected gravel sites for 

spawning

American River

• Redd density for Chinook and steelhead 

combined on the 2009 placed gravel was about 

0.022 redds per square meter, near the program 

goal of 0.03 redds per square meter

• Egg retention in FY 2009 was ten percent, 

meeting the program goal

• Permitted for and placed 10,500 tons of 

spawning gravel at Sailor Bar

• Acquired aerial photography documenting 

Chinook spawning throughout the river

• Completed testing and permitting for a long 

term local gravel source from historic mining 

operations along the river

• Produced spawning gravel from dredger tailings 

at Mississippi Bar

• Mapped spawning distribution and monitored 

juvenile fi sh use at placement site

• Assessed intragravel conditions and invertebrate 

colonization

rate 

• Ma

juve

• Ass

colo
3406(b)(13) 67

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 in 

some years. 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

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.

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

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: 

1

 Egg retention refers to female salmon that die before 

spawning. It is determined by cutting dead salmon open and 

examining the proportion of total eggs remaining (retained)

Sacramento

San Francisco

Eureka

South Lake Tahoe

San Jose

Monterey

Fresno

Coalinga

Solvang

1

Sacramento R iver Stanislaus River

A merican River

Clear

Creek

New Melones

Reservoir

Folsom

Lake

Shasta

Lake

Whiskeytown

Lake

Pacific Ocean

Keswick Dam

Red Bluff Diversion Dam

Nimbus Dam

Goodwin Dam

Shasta 

Lake

Sacramento

River

Keswick 

Dam 

Gravel Sites

Gravel Sites

Gravel Sites

San

Joaquin

River Stanislaus

River

Suisun

Bay Goodwin Dam

Gravel Sites

80

80

5

280

5

Figure 17. Recent Gravel Placement Sites in the 

Sacramento, American, and Stanislaus Rivers

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 

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, winter-run Chinook salmon 

spawning increased from an average percentage of 

one percent of the Chinook population spawning in the 

gravel placement reach prior to CVPIA to an average 

of 33 percent spawning in the area that gravel was 

added since CVPIA was enacted (1993-2008). 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. Monitoring showed that winter-run Chinook 

preferentially use injected gravel sites for spawning.
68 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

In 2009 approximately 9,900 tons of gravel (99% 

of annual target) were purchased and placed in the 

Sacramento River. Refer to Table 13 for total gravel 

placed by river, from 1997 to 2009. 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. Monitoring work in 

progress on the Sacramento River includes: conducting 

substrate mapping of the river bottom, mapping channel 

cross sections to examine channel evolution, preparing 

a gravel budget for the river using a sediment transport 

model, and analyzing past aerial spawning survey data 

in relation to project locations.

Stanislaus River 

No activities were conducted in the Stanislaus River in 

2009. Meetings with local residents near the permitted 

placement reach at Knights Ferry resulted in the 

decision to focus on different project locations on the 

Stanislaus River in future years. 

American River

Studies in the American River identifi ed existing 

areas of overly high-density spawning by salmonids, 

indicating spawning habitat area limitations. The 

program used this data in FY 2009 to prioritize 

gravel placement to improve these conditions. 

Accomplishments in 2009 on the American River 

included the permitting, processing, and placement 

of 10,500 tons of spawning gravel (150 percent of 

annual target) at Sailor Bar. The monitoring included 

measurements of spawning habitat quality, fi sh 

use, invertebrate colonization and acquisition of 

aerial photography documenting Chinook spawning 

throughout the river. Redd density in 2009 for Chinook 

and steelhead combined on the placed gravel was about 

0.022 redds per square meter (149 redds in 6,800 square 

meters of placed gravel), near the goal of 0.03 redds 

per square meter (Figure 18). More than half of the 

observed in-river steelhead spawning in 2009 occurred 

on this project. Chinook egg retention in FY 2009 

was 10 percent, meeting the goal, although Chinook 

escapement of 2,742 in-river spawners was the lowest 

ever recorded. 

In 2009, with the assistance of the Water Forum, the 

program processed gravel from historic gold mining 

operations piled along the river at Mississipi Bar. To 

process the gravel, City of Sacramento workers sorted 

and washed it. Local gravel availability is low so 

utilizing on-site gravel sources reduced the cost of 

projects. 

The program developed a draft planning framework for 

the American River to focus activities and to accomplish 

tasks in as effi cient, effective and scientifi cally 

defensible way as possible. The scope of the planning 

framework covers spawning and rearing habitats. The 

framework includes a vision statement, management 

goals, design standards, and testable hypotheses. The 

program intends to develop planning framework 

documents for all three of the CVP (b)(13) streams in the 

future. 

Table 13. Total Gravel (Tons) Placed by River (1997-2009)

River

Total Gravel Placed 

Since 1997 (Tons)

Gravel Placed in 

2009 (Tons)

Annual Target 

(Tons)

Percent of Annual 

Target for 2009

Sacramento 180,700 9,900 10,000 99%

Stanislaus 14,100 0 3,000 0%

American 23,500 10,500 7,000 150%

Placing spawning gravel in the American River at Sailor 

Bar.

Processing (sorting and washing) dredger tailings along 

the American River to produce spawning gravel.
3406(b)(13) 69

American River at Sailor Bar 2009 gravel placement area showing pre-project (top photo) and post-project (bottom 

photo) conditions. Pre-project conditions consisted of cobbles too large for spawning and little juvenile rearing habitats. 

Spawning sized gravel was added to a riffl e to create suitable spawning habitat and rock piles were added for fi sh cover 

and to enhance invertebrate production.

Figure 18. Spawning Locations on the American River at the Sailor Bar Gravel Placement Area During FY 

2009
70 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Fisheries Resource Area (Central Valley)

Head of Old River Barrier 

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) was a 

joint federal and State program that covered 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 

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

River to keep young salmon in the San Joaquin River as 

they migrate to the ocean in the spring. In addition, a 

fi sh ladder at the head of Old River would 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 would 

protect water levels and water quality in the south delta 

channels. Water levels are protected by keeping the gates 

open when the tide is coming in (fl ood) and closing the 

gates to trap some of the tide at a specifi c elevation. 

Water quality would be improved during periods of poor 

San Joaquin River water quality by the circulation of 

water caused by the gate operations. 

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 BOs on 

the operations of the CVP and SWP by the Service and 

NMFS was required prior to construction. These BOs 

cover the gate operations only; a separate BO for the 

construction effects is also required. The Service issued 

a BO in December 2008 on operations of the CVP and 

SWP that includes gate operations. NMFS subsequently 

issued a BO on operations of the CVP and SWP in June 

2009. The NMFS BO precluded the construction of the 

barriers until more is known about critical habitat and 

species effects. A rock barrier would reduce the San 

Joaquin River fl ows into the south delta where that fl ow 

is needed to sustain delta smelt habitat.

In the absence of a permanent operable gate, the Head 

of Old River Barrier was closed this year with a nonFY 2009

CVPIA Funding Obligations 

by Funding Source

None

Accomplishments

• Installed and monitored a seasonal, non-physical 

bubble curtain at the head of Old River

•Ins sical

bub
3406(b)(15) 71

physical “bubble curtain” from April 15 to May 15 to 

allow salmon smolts to stay in the San Joaquin River 

as they migrate out to the ocean. The bubble curtain is 

comprised of three components: sound, bubble curtain, 

and hi-intensity light-emitting diode (LED) strobe lights. 

A statistically signifi cant proportion of Chinook salmon 

were deterred by the bubble curtain; the deterrence rate 

was 81.4%. However, the predation rate was so high that 

the protection effi ciency was not statistically different 

between barrier off and barrier on. The data suggest that 

much of the gains accomplished by the bubble curtain’s 

determent of smolts are offset by the predators in the 

adjacent scour hole.

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. A 

seasonal, temporary bubble curtain was installed at the 

head of Old River in 2009. Until the permanent gates 

are constructed, temporary barriers of some sort 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.

Reclamation worked in coordination with Fish Guidance 

Systems (Southampton, England), Jacobs Engineering 

(Southampton, England), EIMCO Water Technologies 

(Salt Lake City, UT), Hydroacoustic Technology Inc. 

(Seattle, WA), the San Joaquin River Group Authority 

(Davis, CA) and the California Department of Water 

Resources (Sacramento, CA) to design, implement, 

and monitor the non-physical barrier. Funding for the 

installation of the bubble curtain and monitoring was 

provided by CALFED. 

The monitoring of the Old River Barrier was conducted 

by Reclamation with the cooperation of the Vernalis 

Adaptive Management Program (VAMP) team. The 

VAMP team used acoustic telemetry to assess survival 

rate in several routes through the Sacramento-San 

Joaquin Rivers Delta.

The primary release point for the 2009 VAMP 

experiments was Durham Ferry, several miles upstream 

of the San Joaquin River-Old River Divergence. The 

Chinook smolts with acoustic transmitters that were 

released there and survived to the Divergence were 

detected by an array of hydrophones deployed in the 

vicinity of the Divergence. These detections provided 

measures of Deterrence Effi ciency and Protection 

Effi ciency as the Chinook smolts pass through the area 

of the Old River Barrier.

In addition to acoustic telemetry, a Dual-frequency 

Identifi cation Sonar (DIDSON) camera was deployed 

immediately upstream of the barrier. The DIDSON 

recorded images throughout the period after each 

VAMP release. These DIDSON recordings were used 

primarily to observe the behavior of fi shes in the vicinity 

of the barrier.

A report was written by Reclamation Technical Service 

Center to document the results of the monitoring. The 

report is titled “Effectiveness of a Non-Physical Fish 

Barrier at the Divergence of the Old and San Joaquin 

Rivers (CA)”. 
72 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

First third of the bubble line installed and functioning at 

the Old River Barrier

Sound projectors, strobe lights and bubble line 

constructed in modules on shore
3406(b)(16) 73

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-, late 

fall-, winter-, and spring-run), steelhead, striped bass, 

American shad, white sturgeon, and green sturgeon. 

Sacramento

San Francisco

Los Angeles

Comprehensive Assessment 

and Monitoring Program

Fisheries Resource Area (Central Valley)

CAMP primarily relies on other entities (e.g., CDFG) 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. 

It 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. 

In FY 2009, 71 of these activities were conducted, 

generally by entities outside of the program, such as the 

state and water districts (Table 14). In 2004, the CAMP 

issued a contract to evaluate statistical procedures for 

assessing progress toward the fi sh doubling goals and 

determining sustainability of production increases. The 

report, which was developed by Ken Newman (USFWS) 

and Dave Hankin (Humboldt State University), cited 

a need for better Chinook salmon 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.

MEASURING SUCCESS

The CAMP performance measure is to develop an 

annual report. Toward that end, the CAMP has 

produced seven annual reports since program inception. 

These documents were fi nalized in 1998, 1999, 2001, 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $1,243,000

TOTAL - $1,243,000

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 goals

• Continued work with the Pacifi c States Marine 

Fisheries Commission to develop statistical 

and structural design recommendations for 

a comprehensive database to document and 

understand changes in the abundance of juvenile 

Chinook salmon

• 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

ns 

• Up

sa

as

pe
74 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

2002, 2007, 2008, and 2009. Each report monitors the 

production of anadromous fi sh and assesses progress 

toward the AFRP fi sh production targets during 

different periods.

The 2009 annual report synthesizes and analyzes 

anadromous fi sh monitoring data collected between 

1992 and 2008 on 22 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 2008; striped bass 

through 2007; and green and white sturgeon through 

2005. Figure 19 provides a graph depicting the natural 

production of four runs of Chinook salmon from 22 

watersheds in the Central Valley; fi gures 20 and 21 show 

estimated abundance of white and green sturgeon in 

San Pablo and Suisun Bays; fi gure 22 shows estimated 

abundance of adult striped bass in the Sacramento - San 

Joaquin River Delta and the downstream portions of 

the Sacramento and San Joaquin Rivers; and fi gure 23 

provides a graph depicting the midwater trawl index for 

young-of-the-year 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 2008 are 

contained in the 2009 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 2009 annual report concludes that the 

majority of the AFRP production targets have not been 

met on a regular basis, which suggests a substantial 

increase in restoration efforts will be required to 

promote measurable increases in the production of 

the above-mentioned fi sh taxa and thereby achieve the 

AFRP production targets. 

Concerns about low Chinook salmon numbers prompted 

a closure of the ocean harvest of Central Valley Chinook 

salmon in 2008 and 2009. The inland harvest of fallrun Chinook salmon in the Central Valley was also 

dramatically curtailed in those same years to improve 

the probability that the number of salmon will increase 

in the future. 

In addition to the aforementioned annual report, the 

CAMP had several other accomplishments in FY 

2009. These include: (1) working with partners to 

review, revise, and improve protocols for collecting, 

analyzing, and storing Chinook salmon data from the 

Yuba River; these data are necessary to assess trends in 

the production of Chinook salmon and thereby infer the 

effects of restoration activities; (2) providing funding to 

mark juvenile Chinook salmon at the Coleman National 

Fish Hatchery and Nimbus Fish Hatchery with the goal 

of developing more accurate estimates of the natural 

production of adult Chinook salmon; (3) developing 

databases that characterize rotary screw trap operations, 

stream discharge measurements, and water temperature 

data; these databases will be used to identify data gaps 

and facilitate CVPIA staff’s access to data that are 

currently being collected; (4) funding contracts that 

analyze existing Chinook salmon data with the goal of 

assessing the effects of restoration activities; and (5) 

updating and maintaining the CAMP website which acts 

as a portal for disseminating information pertaining to 

the CAMP and anadromous fi sh monitoring activities in 

the Central Valley. 

In FY 2009, 66 of the 82 CAMP-recommended 

monitoring elements were completed (Table 13). Two 

were completed with the assistance of CVPIA funds 

or staff. These included: (1) operation of a rotary 

screw trap in the Stanislaus River that was funded with 

CAMP and AFRP funds, and (2) operation of a rotary 

screw trap in the Merced River that was facilitated with 

AFRP staff assistance. 64 monitoring elements were 

conducted by other entities, e.g., CDFG.

Program Planning & Evaluation

In FY 2009, the CAMP developed a proposal to develop 

a Comprehensive Fisheries Assessment and Monitoring 

Program (CFAMP). As proposed, the CFAMP would 

engage in activities that have a programmatic focus 

substantially greater than what historically has been 

undertaken by the CAMP. The CFAMP would also act 

to integrate CVPIA-funded data collection activities 

at a scale that does not currently exist. The proposal 

will be reviewed by CVPIA managers and staff, and if 

deemed to be desirable, the CAMP would lead an effort 

to develop a CFAMP Implementation Plan. That plan 

would describe the relative roles and responsibilities of 

different CVPIA programs pertaining to anadromous 

fi sh; establish mechanisms for collecting more 

robust, integrated data sets; and identify strategies for 

developing management recommendations that improve 

the effi cacy of future restoration actions.
3406(b)(16) 75

The CAMP program was expanded in FY 2009 to 

include a new data manager position on its permanent 

staff. This individual’s role will focus on: (1) assessing 

current data being collected by all CVPIA programs; 

(2) conducting management and program manager 

meetings to determine data needs for decision making; 

(3) coordinating data management activities with other 

federal and State agencies and other organizations; 

(4) conducting data management training; and (5) 

developing short-term and long-term data management 

plans.

Figure 19. Estimated Total Natural Chinook Production, Central Valley (1992-2008)

USFWS staff collecting juvenile salmon data using 

rotary screw traps below the Red Bluff Diversion Dam 
76 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Figure 21. Estimated Abundance of Adult Green Sturgeon in San Pablo and Suisun Bays, 1993-2005

Figure 20. Estimated Abundance of 15-year-old White Sturgeon in San Pablo and Suisun Bays, 1993-2005
3406(b)(16) 77

Figure 22. Estimated Abundance of Adult Striped Bass in the Sacramento-San Joaquin River Delta and the 

Lower Portions of the Sacramento and San Joaquin Rivers, 1992-2007. Note: 2004, 2005, and 2007 estimates 

are provisional and only include male fi sh.

Figure 23. Midwater Trawl Index for Young-of-the-year American Shad in the Sacramento-San Joaquin River 

Delta and San Pablo and Suisun Bays, 1992-2008.
78 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Table 14. CAMP Recommended Monitoring Elements by Watershed, Implemented in 2009

CAMP 

Element Monitoring Method Watershed Species Lead Agency

FY 2009 

Element 

Status

 4 Angler survey American River Fall-run Chinook salmon CDFG Completed

 1 Carcass survey American River Fall-run Chinook salmon CDFG Completed

 2 Hatchery count American River Fall-run Chinook salmon CDFG Completed

 3 Hatchery marking American River Fall-run Chinook salmon USFWS Completed

76 Rotary screw trap American River Fall-run Chinook salmon CDFG Not completed

65 Rotary screw trap Battle Creek Fall-run Chinook salmon USFWS Completed

34 Carcass survey Battle Creek Late fall-run Chinook salmon USFWS/CDFG Not completed

 6 Hatchery count Battle Creek Fall-run Chinook salmon USFWS Completed

35 Hatchery count Battle Creek Late fall-run Chinook salmon USFWS Completed

51 Hatchery count Battle Creek Steelhead USFWS Completed

7 Hatchery marking Battle Creek Fall-run Chinook salmon USFWS Completed

36 Hatchery marking Battle Creek Late fall-run Chinook salmon USFWS Completed

52 Hatchery marking Battle Creek Steelhead USFWS Completed

 5 Video camera Battle Creek Fall-run Chinook salmon CDFG/USFWS Completed

70 Rotary screw trap Big Chico Creek Fall-run Chinook salmon CDFG Not completed

71 Rotary screw trap Big Chico Creek Spring-run Chinook salmon CDFG Not completed

 8 Carcass survey Butte Creek Fall-run Chinook salmon CDFG Completed

72 Rotary screw trap Butte Creek Fall-run Chinook salmon CDFG Not completed

73 Rotary screw trap Butte Creek Spring-run Chinook salmon CDFG Not completed

45 Snorkel survey Butte Creek Spring-run Chinook salmon CDFG Completed

 9 Carcass survey Clear Creek Fall-run Chinook salmon CDFG Completed

64 Rotary screw trap Clear Creek Fall-run Chinook salmon USFWS Completed

10 Carcass survey Deer Creek Fall-run Chinook salmon CDFG Completed

68 Rotary screw trap Deer Creek Fall-run Chinook salmon CDFG Completed

69 Rotary screw trap Deer Creek Spring-run Chinook salmon CDFG Completed

46 Snorkel survey Deer Creek Spring-run Chinook salmon CDFG Completed

14 Angler survey Feather River Fall-run Chinook salmon CDFG Completed

11 Carcass survey Feather River Fall-run Chinook salmon DWR Completed

12 Hatchery count Feather River Fall-run Chinook salmon CDFG Completed

13 Hatchery marking Feather River Fall-run Chinook salmon CDFG Completed

82 Hatchery marking Feather River Spring-run Chinook salmon CDFG Completed

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

81 Angler survey Merced River Fall-run Chinook salmon CDFG Not completed

15 Carcass survey Merced River Fall-run Chinook salmon CDFG Completed

16 Hatchery count Merced River Fall-run Chinook salmon CDFG Completed

17 Hatchery marking Merced River Fall-run Chinook salmon CDFG Completed

80 Rotary screw trap Merced River Fall-run Chinook salmon USFWS Completed with 

CVPIA funds

18 Carcass survey Mill Creek Fall-run Chinook salmon CDFG Completed

47 Redd survey Mill Creek Spring-run Chinook salmon CDFG Completed

66 Rotary screw trap Mill Creek Fall-run Chinook salmon CDFG Completed

67 Rotary screw trap Mill Creek Spring-run Chinook salmon CDFG Completed

22 Angler survey Mokelumne River Fall-run Chinook salmon CDFG Completed

20 Hatchery count Mokelumne River Fall-run Chinook salmon CDFG Completed

21 Hatchery marking Mokelumne River Fall-run Chinook salmon CDFG Completed
3406(b)(16) 79

CAMP 

Element Monitoring Method Watershed Species Lead Agency

FY 2009 

Element 

Status

19 Ladder count Mokelumne River Fall-run Chinook salmon East Bay Municipal 

Utility District

Completed

77 Rotary screw trap Mokelumne River Fall-run Chinook salmon East Bay Municipal 

Utility District

Completed

23 Ocean harvest Pacifi c Ocean Fall-run Chinook salmon CDFG Not completed

39 Ocean harvest Pacifi c Ocean Late fall-run Chinook salmon CDFG Not completed

44 Ocean harvest Pacifi c Ocean Winter-run Chinook salmon CDFG Not completed

50 Ocean harvest Pacifi c Ocean Spring-run Chinook salmon CDFG Not completed

54 Mark-recapture Sacramento-San 

Joaquin River Delta

Striped bass CDFG Completed

56 Mark-recapture Sacramento-San 

Joaquin River Delta

White sturgeon CDFG Completed

57 Mark-recapture Sacramento-San 

Joaquin River Delta

Green sturgeon CDFG Completed

55 Midwater trawl survey Sacramento-San 

Joaquin River Delta

American shad CDFG Completed

26 Aerial redd count Sacramento River Fall-run Chinook salmon CDFG Completed

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

42 Aerial redd count Sacramento River Winter-run Chinook salmon CDFG Completed

27 Angler survey Sacramento River Fall-run Chinook salmon CDFG Completed

38 Angler survey Sacramento River Late fall-run Chinook salmon CDFG Completed

49 Angler survey Sacramento River Spring-run Chinook salmon CDFG Completed

53 Angler survey Sacramento River Steelhead CDFG Completed

25 Carcass survey Sacramento River Fall-run Chinook salmon CDFG Completed

41 Carcass survey Sacramento River Winter-run Chinook salmon CDFG Completed

40 Hatchery marking Sacramento River Winter-run Chinook salmon USFWS Completed

61 Rotary screw trap Sacramento River/

Glenn-Colusa 

Irrigation Diversion

Winter-run Chinook salmon CDFG Not completed

62 Rotary screw trap Sacramento River/

Glenn-Colusa 

Irrigation Diversion

Fall-run Chinook salmon CDFG Not completed

63 Rotary screw trap Sacramento River/

Glenn-Colusa 

Irrigation Diversion

Spring-run Chinook salmon CDFG Not completed

24 Ladder count Sacramento River-Red 

Bluff Diversion Dam

Fall-run Chinook salmon USFWS Completed

43 Ladder count Sacramento River-Red 

Bluff Diversion Dam

Winter-run Chinook salmon USFWS Completed

48 Ladder count Sacramento River-Red 

Bluff Diversion Dam

Spring-run Chinook salmon USFWS Completed

58 Rotary screw trap Sacramento River-Red 

Bluff Diversion Dam

Winter-run Chinook salmon USFWS Completed

59 Rotary screw trap Sacramento River-Red 

Bluff Diversion Dam

Fall-run Chinook salmon USFWS Completed

60 Rotary screw trap Sacramento River-Red 

Bluff Diversion Dam

Spring-run Chinook salmon USFWS Completed

28 Angler survey San Joaquin River Fall-run Chinook salmon CDFG Not completed

30 Angler survey Stanislaus River Fall-run Chinook salmon CDFG Not completed

29 Carcass survey Stanislaus River Fall-run Chinook salmon CDFG Completed

78 Rotary screw trap Stanislaus River Fall-run Chinook salmon USFWS Completed with 

CVPIA funds

Table 14. CAMP Recommended Monitoring Elements by Watershed (continued)
80 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

CAMP 

Element Monitoring Method Watershed Species Lead Agency

FY 2009 

Element 

Status

31 Carcass survey Tuolumne River Fall-run Chinook salmon CDFG Completed

79 Rotary screw trap Tuolumne River - 

Grayson Ranch

Fall-run Chinook salmon Turlock Irrigation 

District

Completed

33 Angler survey Yuba River Fall-run Chinook salmon CDFG Completed

32 Carcass survey Yuba River Fall-run Chinook salmon CDFG Completed

75 Rotary screw trap Yuba River Fall-run Chinook salmon CDFG Completed

Table 14. CAMP Recommended Monitoring Elements by Watershed (continued)
3406(b)(20) 81

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 

(Figure 24). 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 

Lake

Oroville

Black

Butte

Lake

GCID-Hamilton 

City Pump Plant

Sacra m ento

Rive r

Glenn C- olusa Canal

Glenn-Colusa Irrigation 

District Program 

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Water and Related - $33,000

TOTAL - $33,000

Accomplishments

• Completed the operations and maintenance 

manual

• Initiated the transfer of ownership of the 

structures to GCID

• Co

m

• In

str

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.

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 

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 has provided 10 years of maintenance 
82 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

GCID Hamilton City

Pumping Plant

Glenn-Colusa Canal

Oxbow Outlet Channel

Sacramento River

Figure 24. Glenn-Colusa Irrigation District 

Pumping Plant

and monitoring on the adjacent site to ensure survival 

of all species. The Service has accepted the mitigation 

areas and incorporated them into an existing refuge. 

2009 Accomplishments

The principal efforts in 2009 were to complete the 

operations and maintenance manual; initiate the transfer 

of ownership of the structures to GCID; and close out 

the cost sharing assistance agreements and associated 

activities. 

The project and related testing and monitoring are 100 

percent complete. The completed facility screens up to 

105,000 acre-feet of fi rm annual water supply to 20,000 

acres of Sacramento National Wildlife Refuge lands.

Glenn-Colusa Irrigation District Fish Screen
3406(b)(21) 83

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 

Sacramento

San Francisco

Los Angeles

Anadromous Fish Screen 

Program

Fisheries Resource Area (Central Valley)

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $3,920,000

• Water and Related - $3,145,000

• Bay Delta - $ 500,000

TOTAL - $7,565,000

Accomplishments

• Completed construction of the Phase I Meridian 

Farms Fish Screen Project to screen 30 cfs at the 

New Grimes diversion (Sacramento River)

• Continued implementation of a four-year 

screening and monitoring program on the 

Sacramento River in partnership with CALFED 

ERP and the Family Water Alliance. Activities 

included monitoring at three diversion sites and 

selection of an additional fi ve sites to monitor in 

2010

• Continued to provide technical assistance for 

on-going AFSP projects including the Natomas 

Mutual (Sacramento River), Patterson (San 

Joaquin River), RD 2035 (Sacramento River), 

Meridian Farms (Phase II) (Sacramento River), 

and Yuba City (Feather River) fi sh screens

mas

r),

er),

on

M

Jo

Me

an

screens and relocation of diversions, to protect juvenile 

Chinook salmon, steelhead trout, green sturgeon, 

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 the natural production of anadromous fi sh in 

Central Valley streams.

To date, the AFSP has assisted the state in screening 

25 diversions ranging from 17 cfs to 960 cfs for a 

cumulative total of approximately 4,600 cfs (Table 15).

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

• Approximately 2,500 in the Sacramento-San 

Joaquin Delta 

• Approximately 360 in the Suisun Marsh basin

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 (ERP). The AFSP 
84 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Table 15. AFSP Projects and Cubic Feet per Second (cfs) Screened, Central Valley (1992-2009)

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 Water 

Treatment Plant 

(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

2009 Meridian Farms Phase I (New 

Grimes)

Sacramento River 30 1

TOTAL 4,597 25

* See Figure 25

also provides technical support to a diverter during 

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

screen project. 

MEASURING SUCCESS

In 2009, construction was completed on the Phase I 

Meridian Farms (New Grimes) Fish Screen Project. 

This project constructed a new 30 cfs screened pumping 

plant with fi sh screen located north of the unscreened 

Grimes diversion. This fi sh screen project protects outmigrating spring-, fall-, and winter-run 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 

Meridian Farms Water Company. 

In 2009, 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 195 cfs 

diversion on the San Joaquin River
3406(b)(21) 85

Meridian Farms New Grimes Diversion Fish Screen Project (Sacramento River). This is a stainless steel wedgewire 

cylindrical fi sh screen with internal and external cleaning brushes. A track allows the screen to be pulled up for 

inspections and during non-irrigation periods.

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

the Sacramento River

• Meridian Farms Phase II: Project to consolidate 

two diversions totaling 135 cfs into a one screened 

diversion on the Sacramento River

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

74 cfs municipal diversion on the Feather River

In 2009, the AFSP continued implementation of a 

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 2009 included monitoring at three diversion sites and 

selection of an additional fi ve sites to monitor in 2010. 

The AFSP issued the following fi nal reports: “Literature 

Search and Data Analysis of Fish Loss at Unscreened 

Diversions in California’s Central Valley”, “Evaluation 

of Unscreened Diversions 2007-2008”, and “Surveys 

of Water Diversions in the Sacramento River – 2008”. 

This information will improve understanding of which 

specifi c diversions are the most important to screen by 

allowing correlation of site-specifi c characteristics to 

fi sh entrainment data from past and future monitoring 

efforts. The AFSP participated in and supported 

CALFED ERP Fish Screen Forum workshops to 

enhance agency coordination on fi sh screen projects and 

share technical information pertaining to fi sh screening. 
86 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Figure 25. CVPIA Fish Screens Constructed (1992-2009)

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

2009 Projects 

Glenn & Provident ID

Legend

Meridian Farms (New Grimes) - Phase I
3406(c)(1) 87

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 

Fisheries Resource Area (San Joaquin River 

Basin)

San Joaquin River 

Restoration Program 

Friant Dam

Suisan

Bay

San

Francisco

Bay

Monterey

Bay Mendota Pool

S a n Joa quin Riv er

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $13,820,000

• Bay Delta - $ 998,000

TOTAL - $14,818,000

Accomplishments

• Continued work on a Program-level 

environmental document that analyzes the 

impacts of the implementation of the SJRRP

• Completed a draft of the Fisheries Management 

Plan and distributed for public review

• Completed environmental compliance activities 

for the fi rst year of initial experimental fl ow 

releases from Friant Dam, termed Interim Flows

• Continued preparation of specifi c operational 

guidelines for releasing Restoration Flows and 

the framework for the Recovered Water Account

• Continued development of a plan to recirculate 

water back to the Friant Division long-term 

contractors

ount

ate 

th

• Co

wa

co

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 SJRRP include 

Reclamation, the Service, NMFS, DWR, and CDFG. 

The San Joaquin River Restoration Settlement Act, 

included in the Omnibus Public Land Management Act 

of 2009, was signed by the President on March 30, 2009, 

and became Public Law 111-11. The San Joaquin River 

Restoration Settlement Act authorizes and directs the 

Secretary to fully implement the San Joaquin River 

Restoration Settlement of NRDC1

, et al. v. Kirk Rodgers, 

et al. (Settlement). 

MEASURING SUCCESS

In FY 2009, signifi cant progress was made towards 

supporting the development of the Program 

Environmental Impact Statement/Report (PEIS/R) 

and implementing specifi c actions in the Settlement, 

consistent with CVPIA Section 3406(c)(1) and the San 

1 The Natural Resources Defense Council
88 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Joaquin River Restoration Settlement Act. Specifi c 

accomplishments in FY 2009 include:

Program-wide Activities

• Continued work on a Program-level environmental 

document that analyzes the impacts of the 

implementation of the Settlement.

• Provided public access to SJRRP activities 

through the web, quarterly updates mailed to a 

broad distribution list, public meetings, public 

technical feedback meetings, and briefi ngs at local 

forums.

• Initiated expanded outreach activities for 

landowners adjacent to the river by providing 

notifi cations and fi eld advisories for fi eld 

activities, holding monthly landowner meetings, 

and executing a fi nancial assistance agreement 

with a local agency to provide for a landowner 

coordinator. Continued to negotiate the terms for 

Temporary Entry Permits with landowners and 

the San Joaquin River Resources Management 

Coalition to allow for access to private property 

to collect needed data for environmental 

documentation and facility designs.

• Provided 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.

Restoration Activities

• Developed and released for public review a draft 

Fisheries Management Plan (FMP). The FMP 

incorporates Strategic Habitat Conservation 

Planning concepts and lays out a structured 

approach to adaptively manage the reintroduction 

of Chinook salmon and other fi shes to the San 

Joaquin River. The FMP also incorporates many 

of the recommendations from the Independent 

Review of the CVPIA Fisheries Program including 

the following: public feedback in the development 

process; a life-cycle oriented conceptual model 

framework; quantitative modeling tools; and a 

peer review process. The public draft FMP was 

released in June 2009.

• Completion of a draft 2010 Interim Flow Fisheries 

Implementation Plan detailing specifi c monitoring 

procedures and recommendations to gather the 

appropriate fi sheries and physical habitat needs.

• Completion of a draft Fish Reintroduction 

schedule that identifi es the necessary steps 

required for the U.S. Fish and Wildlife ESA 10(A)

(1)(a) permit application and the subsequent 

National Marine Fisheries Service Experimental 

Population Designation (ESA 10(j)) rule making.

• Completed the planning, environmental 

compliance, and permitting activities for the fi rst 

year of initial experimental fl ow releases from 

Friant Dam, termed Interim Flows, that began on 

October 1, 2009.

• Initiated planning, environmental compliance, and 

design efforts for two of the high priority, Phase 1 

channel improvements identifi ed in the Settlement:

- Reach 4B, Eastside Bypass, and Mariposa 

Bypass Low Flow Channel and Structural 

Improvements Project, and

- Mendota Pool Bypass and Reach 2B Channel 

Improvements Project

• Continued the collection of data regarding cultural 

resources, topography, geology, and other data 

required to complete site-specifi c environmental 

reviews and engineering designs on public lands 

and private property where access has been 

obtained. 

• Began drilling activities for groundwater 

monitoring wells on public rights-of-way and 

private property where access has been granted to 

monitor Interim Flows.

• Began blunt-nosed leopard lizard surveys in the 

Eastside and Mariposa bypasses.

Water Management Activities

• Continued progress on the development of specifi c 

operational guidelines for releasing Restoration 

Interim Flow Releases
3406(c)(1) 89

Flows and the framework for a Recovered Water 

Account.

• Continued progress on development of a plan to 

recirculate water back to the Friant Division longterm contractors.

• Initiated the preparation of Guidelines for 

Financial Assistance to Local Projects.

• Initiated the Friant-Kern and Madera Canals 

Expansion Feasibility Study.

• Initiated the Friant-Kern Canal Reverse Flow 

Pumpback Feasibility Study.
90 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

CVPIA Section 3406(b)(3)

“3406 (b)(3) Develop and implement a program 

in coordination and in conformance with the plan 

required under paragraph (1) of this subsection 

for the acquisition of a water supply to supplement 

the quantity of water dedicated to fi sh and wildlife 

purposes under paragraph (2) of this subsection 

and to fulfi ll the Secretary’s obligations under 

paragraph 3406(d)(2) of this title....”

CVPIA Section 3406(d)(1)

“3406 (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 twothirds 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...”

CVPIA Section 3406(d)(2)

“3406 (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...”

CVPIA Section 3406(d)(5)

“3406 (d)(5) The Secretary is authorized and 

directed to construct or to acquire from nonFederal 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 SacramentoSan Joaquin Delta Estuary...”

The Refuge Water Supply Program (RWSP) is 

comprised of three components : 

Water Acquisition

• 3406 (b)(3) Water Acquisition Program (WAP) 

- acquisition of Incremental Level 4 quantities 

specifi ed in 3406 (d)(2)

Conveyance

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

– delivery of Level 2 water and Incremental Level 

4 water

Facilities Construction

• 3406 (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

Sacramento

San Francisco

Los Angeles

Introduction to the Refuge 

Water Supply Program 

Refuges Resource Area
3406(b)(3) and (d)(1),(2), and (5) Introduction 91

• San Joaquin Basin Action Plan Lands 

(SJBAPL) – specifi c facilities construction 

to support delivery of water to the lands 

specifi ed in the San Joaquin Basin Action Plan/ 

Kesterson Mitigation Action Plan, December 

1989 report

The RWSP’s goal is to ensure that all CVPIA identifi ed 

wetland habitat areas, hereinafter referred to as refuges, 

annually receive water of specifi ed quantity, suitable 

fl ow rate, and suitable quality to support their wetland 

and aquatic environments. A total of 19 refuges are 

served by the program (shown in Figure 26). The 

RWSP’s water accounting of acquisitions and deliveries 

is done in accordance with Reclamation’s Mid-Pacifi c 

Region’s water service contract year (CY). The CY 

begins March 1 and ends on the last day of February in 

the following year. The RWSP components (acquisition, 

conveyance, and construction) work together to 

implement the CVPIA provisions. 

The RWSP’s three water types are defi ned as Level 

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

water, as shown in Table 16. 

Figure 26. Central Valley Refuges Receiving CVPIA Water Supplies
92 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Long-Term Supply Contracts Provide 

Stability for Refuge Operators

To ensure reliability for refuge managers, Reclamation 

entered into long-term water supply contracts with 

the three refuge managing agencies: CDFG, 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 

through May, Reclamation’s Central Valley Operations 

Offi ce announces the water supply allocation available 

to the CVP contractors and CVPIA refuges (Level 2 

water) for the current CY. Level 2 water is water from 

CVP yield. Concurrently, the Interagency Refuge 

Water Management Team (IRWMT) establishes 

the initial annual Level 2 and Incremental Level 4 

water delivery schedules for each refuge by March 

1. The IRWMT is comprised of representatives from 

Reclamation, the Service, CDFG, GWD, and the 

Central Valley Joint Venture. The creation of this team 

was established through a provision in the long-term 

water supply contracts. 

Use of Groundwater for Refuge Water 

Supplies

The RWSP strives to expand its current diversifi cation 

of sources of water to meet the needs of the refuges in 

the absence of surface water supplies, which is subject 

to variable hydrologic conditions, and 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 it usually 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 

to provide a portion of their Level 2 supplies, and 

Level 2 is the amount of water required for minimum 

wetlands and wildlife habitat management, based 

on historic average annual deliveries before 1989. 

Reclamation is required to annually provide full Level 

2 water supplies. Most Level 2 water is provided from 

the yield of CVP water. A portion of Level 2 water is 

provided from non-CVP diverse 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 water supplies; it equals 

159,271 acre-feet. Each year, Reclamation strives 

to provide as much Incremental Level 4 water as 

possible. The CVPIA specifi es that Reclamation must 

acquire this Incremental Level 4 water supply through 

voluntary measures such as water conservation, 

conjunctive use, purchase, lease, donation, or similar 

activities.

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 

Action Plan December 1989” published by Interior 

and incorporated into CVPIA by reference. These 

reports collated all existing information on existing and 

required water use, power needs, surface water delivery 

systems, groundwater availability, recreation, wildlife 

resources, and habitat management objectives for all 

of the refuges. Based on this information, alternative 

plans were formulated to provide dependable water 

supplies for each refuge, utilizing several water delivery 

“options,” including Level 2 and Level 4.

Table 17 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 

managing 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 remain the same.
3406(b)(3) and (d)(1),(2), and (5) Introduction 93

Table 17. 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 16. Refuge Water Type and Mandated CVPIA 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.
94 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

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 has funded a three year project to examine 

the utility of integrating groundwater as part of the 

Incremental Level 4 water supplies provided to those 

refuges served by the GWD.

In FY 2009, Reclamation initiated rehabilitation 

of existing groundwater wells and the design and 

construction of new groundwater pumping wells at 

Gray Lodge and Volta Wildlife Areas, Pixley National 

Wildlife Refuge, and Grassland Resource Conservation 

District under the ARRA. Once completed, these 

groundwater pumping wells will provide groundwater 

to these refuges. These ARRA funded groundwater 

pumping wells are expected to be operational by late 

fall 2010.

Improving Quality of Water Supplies 

In late FY 2007, Reclamation entered into an agreement 

with GWD to implement a water quality monitoring 

program on lands within the Grasslands Ecological 

Area. GWD will be monitoring water quality on the 

Grassland Resource Conservation District, and refuge 

lands managed by CDFG and the Service. Equipment 

installation and initial data collection began in 2009. 

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 a 

requirement of the 2005 CALFED legislation to reduce 

water quality impacts of refuge discharges that receive 

federal water and discharge into the San Joaquin River. 

The plan is expected to be fi nalized in FY 2010 and its 

conclusions will be put into practice in future years. 

The RWSP has already initiated an activity included 

in the draft BMP plan. This activity implements a 

water quality monitoring program to track fl ows and 

discharges from CVPIA refuges to the San Joaquin 

River.

Refuge Independent Review

In FY 2009, the RWSP participated in the Refuge 

Independent Review process. The RWSP developed 

presentations, provided supportive documentation, 

performed research, drafted responses to panel inquiries, 

and coordinated response efforts between RWSP staff 

and public meeting participants. This activity was a 

result of the Offi ce of Management and Budget (OMB)’s 

Program Assessment and Rating Tool (PART) process. 
3406(b)(3) and (d)(2) 95

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. Unfortunately, this target was not and has 

not been achieved for the following key reasons: 1) 

insuffi cient funding; 2) variable hydrology (currently, 

California is experiencing a prolonged drought that 

may be entering its fourth year); 3) lack of water; 4) 

lack of willing sellers; and 5) variable water market 

conditions that are infl uenced by hydrology, water 

availability, crop market prices, as well as other 

factors. The uncertainties inherent in these reasons in 

any given year, makes the acquisition of Incremental 

Level 4, which has a limited budget, unpredictable and 

very challenging. 

During FY 2002 through FY 2009, the Water 

Acquisition Program (WAP) acquired between 30,000 

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

Refuges Resource Area

Sacramento

San Francisco

Los Angeles

Water Acquisition Program - 

Refuge Water

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $6,154,000

TOTAL - $6,154,000

Accomplishments

• Acquired 31,663 acre-feet of water for 

Incremental Level 4 deliveries during FY 2009 

• Modifi ed agreement with GWD to continue to 

implement a water quality monitoring program on 

lands within the Grassland ecological area

09

o

m on

In

• Mo

im

lan

Pintail Ducks, Sacramento National Wildlife Refuge

4 water for CVPIA refuges. These acquisitions relied 

primarily on transfers from the San Joaquin River 

Exchange Contractors, one-year transfers from other 

CVP contractors and groundwater purchases. The 

average of this volume represents approximately 40 

percent of the mandated Incremental Level 4 water 

quantity (159,271 acre-feet). 
96 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

MEASURING SUCCESS

FY 2009 was a dry year (third year of a drought), 

resulting in very few willing sellers and much higher 

water prices. Consequently, the WAP was able to 

purchase only 31,663 acre-feet of water for Incremental 

Level 4 purposes. Of this amount, approximately 

21,737 acre-feet were obtained from the Exchange 

Contractors, 4,727 acre-feet from Stevenson Water 

District, and 5,199 acre-feet from a groundwater 

project operated by the GWD. 

In FY 2009, Reclamation modifi ed its agreement 

with GWD to continue to implement a water quality 

monitoring program on lands within the Grassland 

ecological area. GWD will be monitoring water 

quality on GWD, CDFG refuge lands and USFWS 

lands. The data generated will be used to manage 

wetlands more effi ciently and monitor the quality of 

water leaving the refuges.
3406 (d)(5) 97

CVPIA Section 3406(d)(5)

As of FY 2009, 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 Lands Program identifi ed 17 

construction projects (with a total of 46 major structures 

Refuges Resource Area

Sacramento

San Francisco

Los Angeles

Refuge Facilities Construction 

Program and San Joaquin Basin 

Action Plan Lands Program 

or 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 or actions identifi ed in the 

environmental documents and related design and 

specifi cation documents. Table 18 lists all major 

structures or actions completed, with 1997 being the fi rst 

year for completion.

MEASURING SUCCESS

Refuge Facilities Construction Program – 

2009 Accomplishments

Reclamation completed 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. Also, Reclamation 

completed a composite HEC-RAS model that was a 

combination of alternatives for the conveyance facilities 

of the BWGWD. The composite alternative further 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $4,368,000

• Bay Delta - $ 12,000

• Water and Related - $ 208,000

TOTAL - $4,588,000

Accomplishments

• Completed draft Design Data Study for 

conveyance facilities of the BWGWD for 

conveyance of Refuge water supplies to Gray 

Lodge WA, covering canal water level study, fl ow 

measurement study, seepage study, proposed 

system improvements, and cost estimates 

• Developed a HEC-RAS1

 model to provide 

preliminary design for the composite (selected) 

alternative to convey Level 4 water supplies 

through the BWGWD system

• Issued a one year extension for continued 

monitoring of canal water levels and fl ows. This 

data was used to refi ne the HEC-RAS model as 

fi nal design commenced in late 2009

• Continued testing of the East Bear Creek Phase I 

Pumping Plant and Pipeline, San Luis NWR, Los 

Banos, CA. Revised operating procedures were 

implemented and tested

1

 HEC-RAS is a computer program that modelts the 

hydraulics of water fl ow through natural rivers and 

other channels.
98 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

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%)

2009 31 actions (67%)

Table 18. Cumulative Completed Construction 

Actions by Year (1997-2009) for the Refuge 

Facilities Construction Program and San Joaquin 

Basin Action Plan Lands Program

refi ned the extent of conveyance system improvements 

needed to satisfy the delivery of Full Level 4 water 

supplies to the Gray Lodge WA. 

The program developed an internal draft acquisition 

plan for BWGWD to contract fi nal design services. 

Reclamation continued to evaluate design-build options 

and construction sequencing plans. 

Reclamation extended the intensive monitoring of 

the BWGWD canal system to collect information on 

operations and canal response to changes in the water 

supply.

San Joaquin Basin Action Plan - 2009 

Accomplishments

Work in FY 2009 consisted of the fi nal construction 

inspections and in-depth testing of the Phase I, East 

Bear Creek Pumping Plant and Pipeline at the San Luis 

NWR in Los Banos, California. Final training exercises 

to familiarize USFWS staff with the operation of the 

pumping plant and related facilities are expected to 

occur in the fi rst quarter of FY 2010 and the project will 

be substantially complete the second quarter of FY 2010.

East Bear Creek Unit, Storage and Regulating 

Reservoir
3406 (d)(1), (d)(2) and (d)(5) 99

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

Reclamation delivered approximately 92 percent of 

Level 2 water on average, between 2002 and 20091. 

1 Accounting for Refuge water deliveries is in accordance 

with Reclamation’s refuge Contract Water Year, which begins 

March 1 and ends on the last day of February in the following 

year.

Refuges Resource Area

Sacramento

San Francisco

Los Angeles

Refuge Water Conveyance 

(Wheeling) Program 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $8,351,000

TOTAL - $8,351,000

Accomplishments

• Delivered approximately 367,842 acre-feet 

of Level 2 water to the refuges in FY 2009; 

approximately 56,991 acre-feet was delivered 

from diverse sources such as groundwater and 

water rights water 

• Delivered approximately 39,690 acre-feet of 

Incremental Level 4 water to the refuges in FY 

2009

• Negotiated a fi fth amendment to extend the 

groundwater pumping reimbursement agreement 

with CDFG. Groundwater combined with limited 

surface water deliveries provides Full Level 2 

water supplies at Gray Lodge Wildlife Area

• 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

• Completed fi nal design on Gray Lodge/Pixley 

Well Construction Project

• Participated in the Refuge Independent Review 

process 

y

iew 

Co

We

• Pa

pro

This includes water from diverse sources other than 

CVP yield. Reclamation also delivered approximately 

52 percent of Incremental Level 4 water on average 

during this same time period. These percentages are 

based on the water allocations from the refuge Water 

Supply Contracts.

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 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.
100 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

MEASURING SUCCESS

In FY 2009, approximately 367,842 acre-feet of Level 

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

56,991 acre-feet were from diverse sources other 

than Project water, such as water rights water and 

groundwater. And approximately 39,690 acre-feet 

of Incremental Level 4 water (after accounting for 

conveyance losses of 1,349 acre-feet) was delivered to 

the refuges. 

In FY 2009, Reclamation negotiated an amendment 

to the Gray Lodge WA groundwater pumping 

reimbursement agreement with CDFG and extended 

the term through the end of Contract Water Year 2009. 

Groundwater is combined with limited surface water 

deliveries to provide full Level 2 water supplies at Gray 

Lodge WA. 

Snow Geese, Sacramento National Wildlife Refuge

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 covers FY 2001-2007, and efforts 

are coordinated with the Service, CDFG, and DWR. 

The resulting task order will culminate with an invoice 

to CDFG for their cost share portion. 

Reclamation and the Service continued management 

of a conservation easement of 113 acres of giant garter 

snake habitat on a privately-owned site in Glenn 

County. Providing this habitat satisfi es the mitigation 

requirements made necessary by CVPIA refuge 

conveyance construction activities in the Sacramento 

Valley. The site was restored from agricultural use to 

wildlife habitat in 2002 and is maintained annually 

from May 1 through September 30 in order to meet the 

critical habitat needs of the giant garter snake during its 

active season.

Final design was completed for the Gray Lodge and 

Pixley Well Construction Project. This project will 

result in additional groundwater for use as a portion of 

Level 2 water supplies at the Gray Lodge WA and Pixley 

National Wildlife Refuge.
3406(g) 101

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 

Fisheries Resource Area (Central Valley)

Sacramento

San Francisco

Los Angeles

Ecosystem and Water Systems 

Operations Models

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $898,000

TOTAL - $898,000

Accomplishments

• Applied CalSim II and CalLite models to evaluate 

provisions in the Delta smelt biological opinion 

• Assisted NOAA in utilizing CalSim II, ECOSIM-W 

and CalLite models to develop feasible 

Reasonable and Prudent Alternatives for the 

biological opinion

• Applied the Upper Sacramento River Water 

Quality Model to support the Sacramento River 

Temperature Task Group in making and updating 

plans for the summer season reservoir operations

• Expanded the water quality modeling capabilities 

on the existing San Joaquin Basin temperature 

model to include features of modeling water 

quality parameters (EC concentration and salt 

loading)

• Engaged consultants services to assist the 

Service in updating and enhancing the existing 

salmon population model, inSALMO, for future 

fi shery management modeling needs

• Developed a short-term modeling plan to evaluate 

modeling tools and future modeling goals

• Continued the development of surface and 

subsurface watershed and operations model 

linkage – HGS and CalSim

l

mo

• Co

su

lin

and systems in the Sacramento, San Joaquin, and 

Trinity River watersheds. The primary purpose of 

this effort shall be to support the Secretary’s efforts 

in fulfi lling the requirements of this title through 

improved scientifi c understanding concerning, but 

not limited to, the following:

(1) a comprehensive water budget of surface and 

groundwater supplies, considering all sources of 

infl ow and outfl ow available over extended periods;

(2) related water quality conditions and 

improvement alternatives, including improved 

temperature prediction capabilities as they relate to 

storage;

(3) surface-ground and stream-wetland 

interactions;

(4) measures needed to restore anadromous 

fi sheries to optimum and sustainable levels in 

accordance with the restored carrying capacities 

of Central Valley rivers, streams, and riparian 

habitats;

(5) development and use of base fl ows and channel 

maintenance fl ows to protect and restore natural 

channel and riparian habitat values;

(6) implementation of operational regimes at State 

and Federal facilities to increase springtime fl ow 

releases, retain additional fl oodwaters, and assist 

in restoring both upriver and downriver riparian 

habitats;
102 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

(7) measures designed to reach sustainable harvest 

levels of resident and anadromous fi sh, including 

development and use of systems of tradeable harvest 

rights;

(8) opportunities to protect and restore wetland and 

upland habitats throughout the Central Valley;

(9) measures to enhance the fi rm yield of existing 

Central Valley Project facilities, including 

improved management and operations, conjunctive 

use opportunities, development of offstream storage, 

levee setbacks, and riparian restoration.”

The goal of the Ecosystem and Water Systems 

Operations Models Program (EWSOMP) is to develop 

the measures specifi ed in the Act that are broadly 

available and readily accessible and to develop 

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.

Since 1998, EWSOMP has provided a high level of 

support for the development of the integrated CVP/SWP 

water operation model, CalSim II. The primary benefi t 

of CalSim II has been for planning investigations, 

including the 2008 Operations Criteria and Plan 

(OCAP). CalSim II has been used in many 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, was 

jointly developed by Reclamation and DWR in FY 

2007. The key objectives in developing the CalSim 

III model includes: 1) increasing spatial resolution of 

surface water and conveyance systems so water demand, 

water supply and water use patterns can be developed in 

association with local water agencies, with results used 

for local planning studies; and 2) calibrating the water 

use effi ciency factors using historical diversion data. To 

respond to the periodic need for less detailed and more 

rapid analyses, a water management screening tool 

(CalLite) was also developed in FY 2007. The CalLite 

model is available to the public through DWR’s website. 

As with any model, improvements continue to be made. 

In addition to CalSim II, CalSim III, and CalLite 

model development, the program has supported the 

development and application of other types of river 

management and ecological models. These include 

water quality, groundwater, fi sh population, and 

riparian habitat models used by Reclamation; Service; 

federal and State water contractors; and public interest 

organizations for modeling support of operations and 

planning. This program also supports Reclamation 

and Service staff participating in modeling forums, 

professional organizations, conferences and training 

courses and provides support for model application to 

State and local partners.

MEASURING SUCCESS

EWSOMP continues to perform data collection 

activities to support modeling and improve the scientifi c 

understanding of ecosystems in the Sacramento, San 

Joaquin and Trinity watersheds. To date, the program 

has completed eight types of models of the nine 

identifi ed in the Act 

The models that have been completed are the Upper 

Sacramento River Water Quality Model (USRWQM), 

the Riparian Habitat Establishment Model (RHEM), 

CalSim II, and Land Atmosphere Water Simulation 

(LAWS). Models that are currently being updated to 

enhance modeling capabilities include Ecologically 

Cogent Operations Suite of Integrated Models 

(ECOSIM), Individual-Based Salmon Life-Cycle 

Framework (inSALMO) fi sh population model, 

HydroGeoSphere (HGS), and SALMOD. CalSim III, 

San Joaquin Basin Temperature Model, and CalLite 

model modifi cations have not been completed (Table 19).

In FY 2009, Reclamation and the Service jointly 

developed a short-term modeling plan for evaluating the 

modeling tools and future modeling goals. This shortterm plan will set the stage for developing the long-term 

modeling needs for this program. 

Of the models listed in Table 19, the following are 

currently under development or undergoing signifi cant 

modifi cations: 
3406(g) 103

Table 19. Ecosystem and Water Systems Operations Models Developed (1996-2009)

Model Description

Act 

Model 

Type

Initiation/ 

Operational 

Date

Agencies Involved in 

Development

CalSim II Used for coordinated system-wide 

planning and operations of CVP 

and SWP water projects

1, 9 & 6 1998/2002 Reclamation, DWR, Service, 

federal/State water contractors, 

Sacramento Valley Settlement 

Contractors

CalSim III Used for coordinated system-wide 

planning and operations of CVP 

and SWP water projects

1, 9 & 6 2007 Reclamation, DWR, Service, 

federal/State water contractors, 

Sacramento Valley Settlement 

contractors and San Joaquin 

Valley Exchange Contractors

CalLite Used for coordinated systemwide operations and water 

management decision projects

1, 9 & 6 2007 Reclamation, DWR and State 

water contractors

Upper Sacramento 

River Water Quality 

Model (USRWQM)

Used to aid Sacramento River 

Temperature Task Group in 

making and updating plans for 

the summer season reservoir 

operations

2 2001/2003 Reclamation, Service, NOAA, 

NMFS, CALFED Integrated 

Storage Investigation (ISI)

Upper San Joaquin 

Basin Temperature 

Model

Used to evaluate basin-wide 

water temperature and reservoir 

operation relations

2 2007 CDFG and Reclamation

Riparian Habitat 

Establishment Model 

(RHEM)

Used for planning and operations 

of reservoirs for the recruitment and 

survival of riparian vegetation. The 

program no longer supports this 

modeling activity. Currently, the 

North of Delta Offstream Storage 

Investigation (NODOS) project 

supports this modeling activity

5 2007 Reclamation, CALFED ISI

InSalmo Used in planning studies to 

evaluate effects of reservoir 

operations on anadromous fi sh 

spawning, incubation and rearing

4 & 8 1996/2005 Developed by the Service. In 

FY 2009 Reclamation initiated 

a contract to enhance the 

model

SALMOD Used in planning studies to 

evaluate effects of reservoir 

operations on anadromous fi sh 

spawning, incubation and rearing 

habitats

4 & 8 1996/2005 Developed by USGS and 

refi ned by USGS and 

Reclamation contractors; used 

by Reclamation, Service and 

CALFED ISI

Land Atmosphere Water 

Simulation (LAWS)

Used to develop hydrologic 

budgets and water demands for 

CalSim model. The program 

no longer supports this model. 

Currently, the modeling activity is 

supported by NODOS Project

6 & 9 2002/2006 Reclamation

HydroGeoSphere (HGS) Used for planning of surface and 

subsurface hydrologic interactions 

related to water supply, water 

quality and ecosystem restoration

1 & 3 2003/2005 Reclamation

Ecologically Cogent 

Operations Suite of 

Integrated Models 

(ECOSIM)

Used for analyses of changes to 

the macroscopic water resources 

for CVP/SWP operations

1, 9 & 6 1998/1998 Service
104 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

Water Operations Tools – CalSim II/III 

Model

The major accomplishments for the CalSim II model in 

FY 2009 included Service modelers applying CalSim II 

and CalLite models to evaluate provisions in the Delta 

smelt biological opinion. At the request of NOAA, 

Service modelers also applied CalSim II, ECOSIM-W 

and CalLite models to develop feasible Reasonable and 

Prudent Alternatives (RPA) for the biological opinion. 

CalSim III achieved signifi cant improvement for 

evaluating hydrology and groundwater in the 

Sacramento Basin. In FY 2009, Reclamation and DWR 

modelers continued the improvements and applications 

of the Graphic Users Interface (GUI) for CalSim III. 

Water Management Tool – CalLite Model

In FY 2009, Reclamation and DWR continued testing 

the CalLite model and incorporated the climate change 

impacts and sea level rise capabilities. The base model 

was released in the summer of 2009. This tool provides 

more rapid and interactive policy evaluation for water 

conditions and water management actions in the Central 

Valley. The major accomplishment in FY 2009 was 

CalLite’s extensive use in evaluating part of the 2008 

USFWS OCAP biological opinion and its extensive use 

in screening alternatives for the Bay-Delta Conservation 

Plan (BDCP). 

Ecosystem Modeling Tools Development

A major accomplishment in FY 2009 for ECOSIM was 

its extensive use in modeling the 2009 NOAA OCAP 

biological opinion. 

Fish Population Modeling Tool

The Service, in coordination with Reclamation, initiated 

a contract in FY 2009 to signifi cantly enhance the 

inSALMO fi sh population model. The purpose of 

improving this model is to prepare inSALMO for real 

world management in the Central Valley by adjusting 

and adding the focus to: 1) seasonal fl ow/temperature 

relation to the operations decision, 2) better usage on 

environmental water, and 3) planning and evaluation of 

restoration activities. 

Surface and Subsurface Integrated 

Modeling

The linkage of HydroGeoSphere 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. In FY 2009, the literature review of existing 

linkage approaches of optimization and groundwater 

modeling was completed. A brain-storming session was 

undertaken to initiate evaluation of the linkage between 

optimization and fully-coupled numerical models. Due 

to the complexity of the system, the temperature module 

(based on fi eld data from the San Joaquin Basin) will be 

continuously tested in FY 2010. 

Water Quality Modeling Tools – Water 

Quality and Temperature Models

The major water quality modeling activities in FY 2009 

included: 1) the application of the Upper Sacramento 

River Water Quality Model to support the Sacramento 

River Temperature Task Group in making and updating 

plans for the summer season reservoir operations; and 2) 

enhancement of the water quality electrical conductivity 

(EC) concentration and salt loading modeling capability 

of the existing San Joaquin Basin temperature model. 

The San Joaquin water quality improvement tasks 

continued in FY 2009 and will be completed in early FY 

2010. 
3408(h) 105

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 

Other Resource Area

Sacramento

San Francisco

Los Angeles

 Land Retirement Program 

FY 2009

CVPIA Funding Obligations 

by Funding Source

• Restoration Fund - $460,000

• Water and Related - $ 48,000

TOTAL - $508,000

Accomplishments

• Retired 90 acres from agricultural production

• Restored 385 acres to upland habitat by planting 

native seed mixes at the Atwell Island Land 

Retirement Demonstration Project site

• Eliminated the production of over 3,500 acre-feet 

of poor quality agricultural drainage water 

• Distributed native seed for the restoration of 

San Joaquin Valley conservation lands from the 

decommissioned San Joaquin Valley Native Plant 

Nursery 

• Performed appraisals on seven parcels of land 

(280 acres) for acquisition at the Atwell Island 

Land Retirement Demonstration Project site

• Completed a draft report documenting fi ve years 

of physical and biological monitoring at the Atwell 

Island Demonstration Project

years 

Atwell

La

• Co

of

Isl

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 

Island, managed by BLM) to study the environmental 

impacts of land retirement and to evaluate cost-effective 

restoration strategies for retired lands (Figure 27). 

As stated above, the original program goal was to 

acquire and retire 15,000 acres for the LRDP. This 

included 8,000 acres in the Tulare Basin (Atwell 

Island Site) and 7,000 acres in the San Joaquin 

Basin (Tranquillity Site). Westlands Water District 

subsequently retired approximately 100,000 acres in 

the San Joaquin Basin which superseded the CVPIA 

land retirement program goals for acquisition in the San 

Joaquin basin. The program does not plan to pursue any 
106 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

further land acquisition at the Tranquillity site, but does 

plan to complete the 8,000 acre goal in the Tulare Basin 

(Atwell Island Site). When the LRDP acquisition is 

complete, the program will have acquired 8,000 acres at 

the Atwell Island site and 2,090 acres at the Tranquillity 

site for a total of 10,090 acres. To complete the program 

goal of acquiring 8,000 acres at the Atwell Island site, 

the program needs to acquire an additional 700 acres at 

Atwell Island. 

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) over 9,000 acres 

from agricultural production. In 2009, the program 

retired 90 acres and restored 385 acres of retired land to 

upland wildlife habitat (Table 20).

In 2009, appraisals were requested for 200 acres of 

land at the Atwell Island site; offers on these parcels 

are pending. Willing sellers were also identifi ed for 

an additional 280 acres and the program performed 

appraisals on these seven parcels of land for acquisition 

at the Atwell Island LRDProject site. This will 

contribute to the 700 acres remaining to be acquired at 

this site to meet the program goal.

On average, the LRP has exceeded its land restoration 

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

LRP has restored approximately 5,600 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.

Successful habitat restoration techniques have been 

developed at the Atwell Island project site. In 2009, 400 

acres were planted with seeds of local desert adapted 

native plants. A good response of annual fl ora was 

observed at the restoration sites in the spring of 2009. 

Approximately 2,400 linear feet of canal bank was 

also planted with perennial native grasses, shrubs, and 

trees. Contracts were awarded for collection of seed 

from native plants in the project vicinity and to grow-out 

several species that are rare in the wild. Also in 2009, 

the program distributed native seed for the restoration 

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 27. Land Retirement Program Sites

of San Joaquin Valley conservation lands from the 

decommissioned San Joaquin Valley Native Plant 

Nursery. 

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.

Reducing Agricultural Drainage 

Implementing the LRDP has eliminated the production 

of approximately 3,500 acre feet of poor quality 

drain water annually, including in 2009. 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 
3408(h) 107

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

(1992-2009)

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

2009 0 0 90 385

TOTAL 7,216 2,090 9,006 5,686

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 Atwell Island Water District was paid for by CVP Conservation Program.
108 CENTRAL VALLEY PROJECT IMPROVEMENT ACT – FISCAL YEAR 2009 ANNUAL REPORT

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.

In 2009, a draft report documenting fi ve years of 

physical and biological monitoring at the Atwell Island 

Demonstration Project was completed. 
APPENDIX A 109

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
110 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2009 ANNUAL REPORT

Central Valley Habitat Joint Venture (CVHJV): 

The association of federal and state agencies 

and private parties established for the purpose 

of developing and implementing the North 

American Waterfowl Management Plan as it 

pertains to the Central Valley of California

Constant Fractional Marking Program (CFM): 

When fi sh are counted for CVPIA monitoring, 

program managers differentiate between 

wild and hatchery fi sh; hatcheries mark 

a percentage of juveniles before they are 

released and when fi sh come back to spawn, 

the mark will indicate which were 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
APPENDIX A 111

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

APPENDIX B 113

ACID Anderson-Cottonwood Irrigation District

ADA Americans with Disabilities Act 

AF acre-feet

AFRP Anadromous Fish Restoration Program

AFSP Anadromous Fish Screen Program 

AIWD Atwell Island Water District

ALC American Land Conservancy 

ARRA American Recovery and Reinvestment Act

ASD Appraisal Services Directorate 

BA Biological Assessment

BDCP Bay-Delta Conservation Plan

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

CCASMP Clear Creek Anadromous Salmonid Monitoring Program

CDFG California Department of Fish and Game

CEQA California Environmental Quality Act

CFAMP Comprehensive Fisheries Assessment and Monitoring Program

CFS Cubic Feet per Second

CPAR CVPIA Program Activity Review

CVO Central Valley Operations Offi ce

CVP Central Valley Project

CVPIA (Act) Central Valley Project Improvement Act

CY Contract Year 

DIDSON Dual-frequency Identifi cation Sonar 

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

EC Electrical Conductivity

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

APPENDIX B: ACRONYMS
114 CENTRAL VALLEY PROJECT IMPROVEMENT – FISCAL YEAR 2009 ANNUAL REPORT

ESA Endangered Species Act

EWA Environmental Water Account

EWSOMP Ecosystems and Water Systems Operations Models Program

FERC Federal Energy Regulatory Commission

FFC Fisheries Foundation of California

FMP Fisheries Management Plan

FY Fiscal Year

GCID Glenn-Colusa Irrigation District

GIS Geographic Information System

GPM Gallons per Minute

GWD Grassland Water District

GGS Giant Garter Snake 

GUI Graphic Users Interface

HGS HydroGeoSphere

HRP Habitat Restoration Program

ID Irrigation District

IEP Interagency Ecological Program

IFIM Instream Flow Incremental Methodology

inSALMO Individual-Based Salmon Life-Cycle Framework 

IP Implementation Plan

IRWMT Interagency Refuge Water Management Team 

ISI Integrated Storage Investigation

JPP Jones Pumping Plant

LAWS Land Atmosphere Water Simulation

LED Light-Emitting Diode 

LRDP Land Retirement Demonstration Project

LRP Land Retirement Program

NEPA National Environmental Policy Act

NFH National Fish Hatchery

NMFS National Marine Fisheries Service

NOAA National Oceanic and Atmospheric Administration

NPS National Parks Service

NODOS North of Delta Offstream Storage

NRCS Natural Resources 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

PIMS Performance Information Management System

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

RPA Reasonable and Prudent Alternatives
APPENDIX B 115

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

SJBAPL San Joaquin Basin Action Plan Lands 

SJRA San Joaquin River Agreement 

SJRGA San Joaquin River Group Authority

SJRRP San Joaquin River Restoration Program

SJVDP San Joaquin Valley Drainage Program

SLDMWA San Luis & Delta Mendota Water Authority

SLT Shasta Land Trust

SNWR Sacramento National Wildlife Refuge

SWP State Water Project

SYRCL South Yuba River Citizens League

TCRCD Tehama County Resource Conservation District

T&E Threatened and Endangered 

TFCF Tracy Fish Collection Facility

TFFIP Tracy Fish Facility Improvement Program

TRRP Trinity River Restoration Program

USBR (Reclamation) Bureau of Reclamation 

USFWS (Service) US Fish and Wildlife Service

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

WSRCD Western Shasta Resource Conservation District

WTP Water Treatment Plant

WY Water Year

YOY Young-of-the-Year