U.S. Department of the Interior

Bureau of Reclamation 

U.S. Fish and Wildlife Service Finalized August 2016

Central Valley Project 

Improvement Act

Public Law 102-575

Annual Report

Fiscal Year 2014
Cover photographs:

Top: Shasta Lake during the 2014 drought conditions. 

Middle: A San Joaquin kit fox at Eastern Ciervo-Panoche Natural Area. Photo courtesy of US Fish & 

Wildlife Service.

Bottom: Juvenile fall run Chinook salmon rearing on the American River at Sailor Bar, California.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 iii

TABLE OF CONTENTS

TABLE OF CONTENTS

EXECUTIVE SUMMARY.............................................................................................................................................v

Introduction............................................................................................................................................................v

Water Management ...............................................................................................................................................v

Fish Resource Area ............................................................................................................................................. vii

Refuge Water Supply...........................................................................................................................................viii

Independent Programs ......................................................................................................................................... ix

CHAPTER 1 - INTRODUCTION .................................................................................................................................1

Purpose .................................................................................................................................................................1

Background............................................................................................................................................................1

Report Organization...............................................................................................................................................3

Funding..................................................................................................................................................................3

CVPIA Administration.............................................................................................................................................3

CHAPTER 2 - FISHERIES RESOURCE AREA..........................................................................................................7

Anadromous Fish Restoration Program, 3406 (b)(1).............................................................................................7

Tracy (Jones) Pumping Plant Program 3406 (b)(4).............................................................................................18

Clear Creek Restoration Program 3406 (b)(12)...................................................................................................20

Spawning and Rearing Habitat Restoration Program 3406 (b)(13).....................................................................24

Comprehensive Assessment and Monitoring Program 3406 (b)(16)...................................................................27

Anadromous Fish Screen Program 3406 (b)(21).................................................................................................29

CHAPTER 3 - WATER MANAGEMENT...................................................................................................................31

Contract Renewals 3404 (c) ................................................................................................................................31

Water Transfers 3405 ..........................................................................................................................................32

Dedicated 800,000 acre-feet Project Yield 3406 (b)(2)........................................................................................33

Water Acquisition Program – Instream Water 3406 (b)(3)...................................................................................35

CHAPTER 4 - REFUGES RESOURCE AREA .........................................................................................................37

Refuge Water Supply Program 3406 (d)(1), (2) & (5)..........................................................................................37

Refuge Water Acquisition 3406 (d)(2)..................................................................................................................39

Refuge Water Conveyance 3406 (d)(1), (2) & (5)................................................................................................40

Refuge Facilities Construction Component 3406 (d)(5).......................................................................................43

CHAPTER 5 - INDEPENDENT PROGRAMS...........................................................................................................45

Bay-Delta Activities 3406 (b)(1) ...........................................................................................................................45

Habitat Restoration Program for Other Adverse Environmental Impacts of the CVP Under 3406 (b)(1) ............46

Trinity River Restoration Program 3406 (b)(1) “Other” & (b)(23).........................................................................48

Ecosystem and Water Systems Operations Models 3406 (g) .............................................................................52

Land Retirement Program 3408 (h).....................................................................................................................54

San Joaquin River Restoration Program Public Law 111-11 ...............................................................................56

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA PERFORMANCE GOALS ..............................................57

APPENDICES ...........................................................................................................................................................63

Appendix A: Acronyms........................................................................................................................................63

Appendix B: Glossary of Terms ..........................................................................................................................64

Appendix C: CVPIA Title 34 of Public Law 102-575 ...........................................................................................67
TABLE OF CONTENTS

iv Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

LIST OF TABLES

LIST OF FIGURES

Figure ES-1: Ongoing Programs by Resource Area and Completed Programs.................................................. vi

Figure ES-2. FY 2014 Breakdown of Funding Obligations by Program Activity ................................................. xii

Figure ES-3. FY 2014 Breakdown of Funding Obligations by Fund Source....................................................... xii

Figure 1: Central Valley Project (CVP) System ....................................................................................................2

Figure 2: Program Financial Obligations By Action Category to Date (in $ millions)............................................4

Figure 3: Program Financial Obligations By Fund Source to Date (in $ millions).................................................4

Figure 4. FY 2014 Breakdown of Funding Obligations by Program Activity .........................................................5

Figure 5. FY 2014 Breakdown of Funding Obligations by Fund Source...............................................................5

Table ES-1. FY 2014 Breakdown of Funding Obligations by Program Activity.................................................... xi

Table 1. FY 2014 Breakdown of Funding Obligations by Program Activity...........................................................6

Table 2. Yearly Estimates of Natural Production of Anadromous Fish and the Average Natural

 Production by Species within Central Valley River and Streams, 1992-2013..................................................8

Table 3. Summary of Progress Towards Completing 289 Final Restoration Plan Actions and.............................9

Evaluations by Watershed, FY 1992-2014.......................................................................................................9

Table 4. Summary of Progress Towards 128 High and Medium Priority “Time Certain” Actions ........................11

 (53 Structural, 75 Non-Structural) .................................................................................................................11

Table 5. Average Natural Production Numbers in Each Watershed Compared to the AFRP

 Doubling Goal Targets, 1992-2013 ................................................................................................................12

Table 6. Summary of Progress Towards 23 Tracy Fish Facility Improvement Program Plan Actions.................19

Table 7. Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2014 ........................................26

Table 8: AFSP Projects by Watershed and Cubic Feet per Second (cfs) Screened, 1994-2014........................29

Table 9. Water Transfers under the CVPIA between 2012 and Fiscal Year 2014 (acre-feet).............................32

Table 10: Allocation Target and Use of (b)(2) Water, 2001-2014 ........................................................................34

Table 11: FY 2014 Use of (b)(2) Water by Location............................................................................................34

Table 12. Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 1994-2014................35

Table 13. Incremental Level 4 Acquisitions by Fiscal Year, 2002-2014 ..............................................................39

Table 14. Level 2 (L2), Incremental Level 4 (IL4) and Level 4 (L4) Water Deliveries by Water Service 

 Contract Years 2002-2013 .............................................................................................................................41

Table 15. Water Targets and Deliveries for Each Refuge (Contract Year 2013).................................................42

Table 16. Target FL4 Conveyance Capacity vs. Actual by Refuge .....................................................................44

Table 17: Projects Funded by the (b)(1) “Other” Program in 2014 .....................................................................47

Table 18: Approximate Acres of Habitat Protected and Restored by the (b)(1) “Other” Program, 

 1996-2014, Using HRP Funds .......................................................................................................................47

Table 19. FY 2013 Salmonid Production, Natural vs. Hatchery1 ........................................................................49

Table 20. Annual ROD Flows and Peak Releases to Trinity River, 2006-2014...................................................50

Table 21. Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2014.....................................50

Table 22. Rehabilitation Site Construction Summary, 2005-2014 ......................................................................51

Table 23: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2013......................................55
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 v

EXECUTIVE SUMMARY

EXECUTIVE SUMMARY

Introduction

This Annual Report for Fiscal Year (FY) 2014 

summarizes the actions authorized under the Central 

Valley Project Improvement Act (CVPIA or Act) 

through September 30, 2014 and addresses the 

requirement under Section 3408 (f) of the Act to submit 

an annual report to congress. This report summarizes 

funding levels, activities under the various provisions of 

the Act, and the status of metrics to measure progress. 

On October 30, 1992, President Bush signed Public 

Law 102-575, the Reclamation Projects Authorization 

and Adjustment Act of 1992. Title XXXIV amends 

previous authorizations of the CVP to include fish 

and wildlife protection, restoration, and mitigation as 

project purposes having equal priority with irrigation 

and domestic uses, and fish and wildlife enhancement 

as a project purpose equal to power generation. The Act 

established the Central Valley Project Restoration Fund 

(Restoration Fund) for donations from any source and 

revenues provided through payments by CVP water 

and power customers. The Bureau of Reclamation 

(Reclamation) and Fish and Wildlife Service (Service) 

jointly implement the CVPIA for the Department of the 

Interior (Interior) in collaboration with State and local 

governments, Tribes, non-governmental organizations, 

and stakeholders. 

The current focus of the CVPIA Program is on fish 

and wildlife restoration, water management, and 

conservation activities, authorized in Sections 3406 

and 3408 of the Act. Provisions under the CVPIA fall 

into four broad resource areas including Fisheries 

(Chapter 2), Water Management (Chapter 3), Refuges 

(Chapter 4), and Independent Programs (Chapter 5). 

Figure ES-1 shows the active CVPIA programs that 

contribute to each resource area as well as those 

provisions that are complete or inactive. Metrics 

developed under the CVPIA Program Activity Review 

(CPAR) Report and other efforts measure progress 

towards meeting the goals and objectives of the CVPIA 

(Chapter 6).

For FY 2014, $53.3 million was appropriated to the 

Restoration Fund to be derived from payments by 

water and power contractors. As a result of the drought, 

collections were lower than anticipated by $8.5 million 

and came later in the year. Reclamation and the Service 

adapted the 2014 work plans and used unappropriated 

revenues from prior years to partially mitigate the 

effects of the drought. Reclamation obligated a net total 

of $65.8 million including Water and Related Resources 

($20.7 million), state trust funds ($2.3 million), and 

Bay-Delta funds ($4.3 million). Table ES-1 shows the 

breakdown of funding obligations by program activity. 

Figure ES-2 shows the obligations by fund source and 

Figure ES-3 shows the obligations by category.

Administrative work products included the 2012 

Financial Report to Congress, Annual Report to 

Congress for Fiscal Year 2013, and the 2015 Annual 

Work Plans. These documents are available online 

at: http://www.usbr.gov/mp/cvpia. Work continues 

on a Structured Decision Making Framework for an 

Implementation Plan for the Fish Resource Area, a 

CVPIA Finance Plan to address power contractor 

concerns with collections for the Restoration Fund, 

negotiation of a cost-share agreement with the State to 

replace the expiring Sharing of Costs Agreement for 

Mitigation Projects and Improvements (SCAMPI), and 

planning actions to address recommendations from the 

2008 and 2009 Independent Review Panels.

Water Management

In changing the management of water, the CVPIA 

authorized the renewal of long-term water contracts, 

provided for water transfers, dedicated a portion of 

CVP yield to fish and wildlife, and mandated changes 

to CVP operations for fish habitat. 

Contract Renewals 3404 (c)

No changes occurred to contract renewals in 2014. 

Section 3404 (c) authorizes Interior to renew repayment 

and water service contracts for the delivery of water 

from the CVP. To date, 100 long term renewal contracts 

and 28 interim-renewal contracts have been executed 

within the various divisions of the CVP. Reclamation 

renewed 132 long term contracts with the Sacramento 

River Water Right Settlement contractors and one is 

pending renewal upon expiration in July 2020. 

Water Transfers, 3405 (a)

Reclamation approved the transfer of a total of 230,000 

acre-feet of CVP water in 2014. Prior to the CVPIA, 

the ability for CVP water contractors to transfer water 
EXECUTIVE SUMMARY

vi Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

supplies was limited depending upon the individual 

contracts. Section 3405 (a) authorizes Interior to 

approve the transfer of CVP water to other users within 

the state for any purpose recognized as beneficial 

under state law, subject to certain terms and conditions. 

Section 3405 (a)(1)(M) created the Accelerated Water 

Transfer Program (AWTP) for transfers between 

Central Valley Project contractors within counties, 

watersheds, or other areas of origin. Transfers 

authorized by the CVPIA in 2014 included:

• Sacramento Basin AWTP: 22,292 acre-feet

• Delta-Mendota Canal AWTP: 6,871 acre-feet

• Friant Division AWTP: 11,721 acre-feet

• North of Delta to South of Delta: 83,037 acrefeet

• South of Delta Non-AWTP: 106,545 acre-feet

Dedicated Yield 3406 (b)(2) and Operations for 

Fish Habitat, 3406 (9) and (19)

Consistent with Section 3406(b)(2) of the CVPIA 

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

water allocation was 600 thousand acre feet (TAF) 

during the 2014 water year. However, due to these 

Figure ES-1: Ongoing Programs by Resource Area and Completed Programs

Ongoing Programs Completed Programs

Fisheries Resources

Central Valley

3406 (b)(1) Anadromous Fish 

Restoration Program

3406(b)(2) Dedicated Project 

Yield

3406(b)(3) Instream Water 

Acquisition Program

3406 (b)(4) Tracy Pumping Plant 

Program

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)(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

P.L. 111-11 San Joaquin River 

Restoration Program

Refuge Resources

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

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

Other Resources

3404 Contract Renewals

3405 Water Transfers

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

Program

3408 (h) Land Retirement Program

CVP Water Operations Resources

3406 (b)(1)(B) Modified CVP 

Operations

3406 (b)(7) Flow Standards and 

Objectives

3406 (b)(8) Short Pulse Flows

3406 (b)(9) Flow Fluctuations

3406 (b)(19) Reservoir Storage

All Resource Areas

3406 (b)(5) Contra Costa Canal 

Pumping Plant

3406 (b)(6) Shasta Temperature 

Control Device 

3406 (b)(10) Red Bluff Diversion Dam

3406 (b)(11) Coleman National Fish 

Hatchery

3406 (b)(17) ACID Diversion Dam 

3406 (b)(20) Glenn-Colusa Irrigation 

District Program

3406 (b)(22) Waterfowl Incentive 

Program

3406(c)(1) San Joaquin River 

Restoration 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

3408 (i) Water Conservation Program

3408 (j) Water Augmentation (Yield 

Study)

* In FY 2012, the Red Bluff Diversion Dam Program substantially completed construction of the new, 2,500-cfs 

permanent pumping plant and fish screen. Fine tuning of the pumping plant equipment and monitoring of the riparian 

mitigation site continues to occur using sources other than Restoration Funds.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 vii

EXECUTIVE SUMMARY

historically dry hydrological conditions, Interior was 

only able to make approximately 400,000 AF of the 

600,000 AF of CVPIA (b)(2) water available. Under 

the Flow Fluctuations Program, the Sacramento River 

Stranding Project, a collaborative project with Golden 

Gate Salmon Association, began in FY 2013 to reduce 

fall chinook salmon redd dewatering post-irrigation 

season and was suspended again in FY 2014 due to 

unfavorable hydrologic conditions. The Reservoir 

Storage Program did not meet the carryover targets for 

Shasta and Trinity reservoirs due to drought.

Under the Dedicated Yield Program (b)(2), Reclamation 

and the Service dedicate and manage up to 800,000 

acre-feet of CVP yield with shortage provisions 

for critically dry years. The Flow Fluctuations and 

Reservoir Storage Program seeks to maintain carryover 

water storage and deliver appropriately timed flows and 

flows of adequate quality to support fisheries restoration 

and meet other project purposes.

Fish 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 fish 

in Central Valley rivers and streams will be sustainable, 

on a long-term basis, at levels not less than twice the 

average levels attained during the period of 1967-

1991....” The target established by this section of 

the Act is known as the “fish-doubling goal”, which 

pertains to Chinook salmon, rainbow trout (steelhead), 

striped bass, American shad, white sturgeon and green 

sturgeon; species believed to have been impacted by 

CVP construction and operation. The Final Restoration 

Plan for the Anadromous Fish Restoration Program 

(Service, 2001) identified 289 actions and evaluations 

that were determined to be reasonable given numerous 

technical, legal and implementation considerations. 

When the Plan’s actions are implemented in concert, 

they provide for comprehensive restoration that 

improves freshwater habitat for Chinook salmon and 

other anadromous fish species. The Fish Resource Area 

is divided up into programs reflecting the individual 

provisions of the Act. Completed fish resource area 

provisions include:

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

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

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

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

• Anderson-Cottonwood Irrigation District 

Diversion Dam, 3406 (b)(17)

• Glenn-Colusa Irrigation District Fish Screen, 

3406 (b)(20)

• Waterfowl Incentive Program, 3406 (b)(22)

Anadromous Fish Restoration Program 

(AFRP), 3406 (b)(1)

AFRP continued 38 various projects to address high 

priority limiting factors in 20 watersheds, including fish 

passage, entrainment, habitat restoration, and spawning 

gravel augmentation projects as well as variety 

of assessments and evaluations that are providing 

information critical for future projects. No structural or 

non-structural actions were completed in FY 2014,

The AFRP seeks to address the limiting factors in 

each watershed. On watersheds where the CVPIA 

substantially addressed most limiting factors, fish 

populations have exceeded the doubling goals. These 

watersheds include Clear Creek, Butte Creek, and 

Battle Creek. The AFRP continued progress toward 

actions and evaluations in the Sacramento and San 

Joaquin watersheds to enhance passage and habitat, and 

reduce loss of fish. About 23% of the 289 Restoration 

Plan actions and evaluations have been completed 

to date. Of the 128 “time certain” high and medium 

priority actions, forty-six (46%) have been completed.

Water Acquisition Program – Instream Water 

(Instream WAP), 3406 (b)(3)

Due to the severe drought no water was acquired in 

FY14 for instream flows.

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

Actions taken to improve the Tracy Fish Facility in FY 

2014 include continued work to improve the louver 

systems, the development of land for onsite research 

and fish protection, replacement of the secondary 

louvers, the continued work towards a third fish release 

site and various research studies that will improve fish 

capture and reintroduction capabilities.

Clear Creek Restoration Program (CCRP), 3406 

(b)(12)

The CCRP provided instream pulse flows and 

maintained temperature of flows to attract fish and 

promote upstream movement. The program added 

about 8,000 tons of gravel to four sites in 2014. The 

program also evaluated past spawning gravel placement 

and monitored the impacts of the 2008, 2012 and 2013 

wildfires in the South Fork Clear Creek tributary. The 

program continued monitoring fish populations with 

2013 escapement numbers for fall-run estimated at 

13,337.
EXECUTIVE SUMMARY

viii Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Spawning and Rearing Habitat Restoration 

Program, 3406 (b)(13)

The Gravel program worked on permitting for new 

habitat restoration project sites in the Sacramento River 

and created a 400 yard long side channel and placed 

10,000 tons of gravel just below Nimbus Dam on the 

American River. The program conducted spawning 

surveys and surveys of downstream movement of 

previously placed gravel on the Stanislaus River. 

Comprehensive Assessment and Monitoring 

Program (CAMP), 3406 (b)(16)

CAMP produced its 2014 annual report assessing the 

overall effectiveness of actions implemented pursuant 

to CVPIA section 3406(b) in meeting AFRP fish 

production targets. CAMP continues to support fish 

population evaluations through the development of 

the Rotary Screw Trap Platform, monitoring at several 

locales within the CVP area, marking and tagging of 

juvenile fall-run Chinook salmon at the Nimbus Fish 

Hatchery and Coleman National Fish Hatchery and 

studies on the Cottonwood and Battle Creeks. The 

program also supported the Science Based Management 

Framework in conjunction with the other fisheries 

programs to develop tools and a process that will enable 

a comprehensive and prioritized fisheries management 

approach CVPIA-wide.

Anadromous Fish Screen Program (AFSP), 

3406 (b)(21)

Construction was completed on the Yuba City (74 cfs) 

and Feather Water District North (78 cfs) and South 

(40 cfs) diversion fish screens on the Feather River. 

Fish screen construction was initiated for the Natomas 

Mutual Water Company Pritchard Lake diversion 

(150 cfs), and Reclamation District 2035/Woodland 

Davis Clean Water Agency Joint Intake (400 cfs) on 

the Sacramento River. In addition, the AFSP continued 

to support design, environmental compliance and 

permitting activities for the following fish screen 

projects: Colusa Indian Community Council Compton 

diversion (22 cfs) on the Sacramento River, South 

Sutter Water District Pleasant Grove Canal diversion 

(80 cfs) on Auburn Ravine, and the West Stanislaus 

Irrigation District Joint Use Intake (375 cfs) on the 

lower San Joaquin River.

Refuge Water Supply

Section 3406 (d) of the Act contributes to the 

maintenance, restoration and enhancements of wetlands 

and waterfowl habitat. The Act directs Interior 

to: provide, either directly or through contractual 

agreements with other appropriate parties, firm water 

supplies of suitable quality to maintain and improve 

wetland habitat areas on 19 federal, state and private 

lands, collectively referred to as “refuges.” The Refuge 

Water Supply Program (RWSP) goal is to provide 

555,515 AF of water annually, comprised of 422,251 

AF of Level 2 water, which also includes 26,007 AF 

of replacement water, and 133,264 AF of Incremental 

Level 4 water. Full Level 4 water is the sum of 

Level 2 and Incremental Level 4 water. The RWSP 

allocates water on a contract year starting in March 

and continuing through February of the next year. This 

report shows refuge water deliveries from March 2013 

through February 2014.

Water Acquisitions – Refuge Water (Refuge 

WAP), 3406 (d)(2)

In 2013, the RWAP purchased up to 33,925 AF of 

water for Water Year 2013 through contracts with 

Grasslands Water District, San Joaquin River Exchange 

Contractors Water Authority and Merced Irrigation 

District.

Refuge Water Conveyance Component 

(RWCC), 3406 (d)(1),(2) and (5)

The RWCC delivered an estimated 389,343 AF of 

Level 2 water and an estimated total of 48,096 AF 

of Incremental Level 4 water to the refuges during 

Contract Year 2013. Of the Level 2 water, a total of 

51,879 AF was delivered from diverse, non-CVP 

sources.

Reclamation delivered 100 percent of Level 2 water 

supplies scheduled by CVPIA refuges in Contract Year 

2013. The goal of delivering 422 TAF was not met for 

several reasons. Contributing factors to refuges not 

scheduling 100% of their L-2 allocation include:

• Conveyance capacity restrictions to certain 

refuges;

• Refuge internal distribution systems 

groundwater pump mechanical failures;

• Unexpected erosion around newly constructed 

alfalfa valves;

• Regionally, a few refuges received more 

precipitation than other refuges, reducing their 

demand for full Level 2 during certain months in 

Contract Year 2013; and

• Water schedules that are developed and 

implemented on a water-year basis versus a 

fiscal-year. Much of the RWSP is implemented 

and operated on a water-year basis, including the 

Refuge Water Supply Contracts and refuge water 

conveyance agreements. 

Refuge Facilities Construction Component 

(RFCC), 3406 (d)(5)

To date, 15 of the 19 CVPIA refuges have the external 

conveyance capacity to receive Full Level 4 water. 
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 ix

EXECUTIVE SUMMARY

In FY 2014, the RFCC focused construction efforts 

at the East Bear Pumping Plant located at the East 

Bear Creek Unit of the San Luis National Wildlife 

Refuge Complex, at Biggs-West Gridley Water District 

Facilities Improvement Project for the Gray Lodge 

Wildlife Area, and at the Gray Lodge and Pixley 

groundwater wells. Initial studies began to assess a 

water supply conveyance system for the Sutter National 

Wildlife Refuge.

Independent Programs

Habitat Restoration Program (HRP), 3406 (b)(1) 

“Other”

The HRP focuses on protecting and restoring native 

species and their habitats that have been directly and 

indirectly affected by the CVP’s construction and 

operation. This is accomplished through the purchase 

of fee title or conservation easements on lands where 

threats are significant, and through restoring lands 

to native habitat. The HRP also funds research, and 

captive propagation and reintroduction projects. The 

HRP contributes to the protection and/or restoration 

of lands and habitats affected by the construction and 

operation of the CVP. The 1999 State Water Resources 

Control Board Decision 1641 (SWRCB’s D-1641) 

requires that Reclamation provide compensation and 

habitat values to mitigate for impacts associated with 

the delivery of CVP water to lands previously outside 

the CVP Consolidated Place of Use. It identifies the 

HRP as one of three Reclamation programs suitable for 

fulfilling the mitigation plan. Pursuant to the SWRCB’s 

D-1641, Reclamation developed the Consolidated 

Place of Use, Habitat Mitigation Plan and Monitoring 

and Reporting Program (HMP) as a report/strategy for 

how the mitigation requirements will be addressed. 

The HMP identifies acquisition, maintenance, and 

restoration of 45,391 acres needing to occur as 

mitigation related to the CVP Consolidated Place of 

Use. To date, the program has protected 1,749 acres of 

land towards the D-1641 goal.

In fiscal year 2014, the HRP helped protect about 795 

acres on two parcels located on the eastern slope of the 

Ciervo Hills to benefit several federally listed species in 

western Fresno County. 

Land Retirement Program (LRP), 3408 (h)

The LRP goals include the purchase and retirement 

of land from agricultural production to improve water 

quality and provide for terrestrial habitat restoration. 

By ceasing irrigation of agricultural lands, the LRP 

reduces the volume of agricultural drainage produced, 

improving water quality and providing the opportunity 

to restore wildlife habitat. Specifically, the goal of the 

LRP is to retire 15,000 acres of agricultural lands by 

2014 for the Land Retirement Demonstration Project 

and to restore up to 400 acres of that land annually.

Ecosystem and Water Systems Operation 

Models (Modeling), 3406 (g)

The Modeling Program continued to develop models 

and supporting data to evaluate water management 

strategies for the CVPIA Programs. In FY 2014, 

the program continued ongoing development and 

modification of the following programs: CalSim II, 

the CalLite, CalSim 3.0, HEC-5Q based temperature 

model, C2VSIM (California Central Valley 

Groundwater-Surface Water Simulation Model), ANN, 

DSM2, inSALMO, and HydroGeoSphere (HGS). 

The program also prepared publications and provided 

support to model applications. 

San Joaquin River Restoration Program 

(SJRRP), Public Law 111-11

Section 10009 (b)(2) of Public Law 111-11 authorizes 

up to $2 million (indexed to 2006 funds) from the 

CVP Restoration Fund for implementation of the 

San Joaquin River Restoration Program (SJRRP). 

Activities, including planning and environmental 

studies aim to restore and maintain fish populations 

in “good condition” on the mainstem of the San 

Joaquin River while reducing or avoiding adverse 

water supply impacts to Friant Division long-term 

contractors. Specific actions to achieve these goals 

include reintroduction of spring-run Chinook salmon, 

restoration flow releases and recirculation of restoration 

flows back to Friant Division contractors. The Central 

Valley Project Restoration Fund supplements the 

program’s funding under PL 111-11.

The Restoration Fund contributes to the environmental 

analysis for the Reach 4B and Mendota Pool Bypass 

projects, as well as the Conservation Facility 

development. SJRRP accomplishments are reported at 

http://www.restoresjr.net.

Trinity River Restoration Program (TRRP), 3406 

(b)(1) “Other” and (b)(23)

The CVPIA includes provisions to authorize activities 

for the Trinity River Restoration Program (TRRP); 

Section 3406 (b)(23) for delivering flows and 3406 (b)

(1) for river restoration. The goal of the TRRP is to 

restore and sustain natural production of anadromous 

fish populations downstream of Lewiston Dam to 

pre-dam levels, and to facilitate dependent Tribal, 

commercial, and sport fisheries’ full participation 

in the benefits of restoration via enhanced harvest 

opportunities. This will be accomplished through 

restoring habitats for the anadromous fishery resources 

by implementing variable annual instream flows, 

rehabilitating the channel, and managing sediment, as 
EXECUTIVE SUMMARY

x Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

stipulated in the December 2000, Record of Decision 

(ROD), for the Trinity River Mainstem Fishery 

Restoration Final Environmental Impact Statement/

Environmental Impact Report (EIS/EIR).

A channel rehabilitation project was completed at 

Lower Junction City. Five watershed projects including 

watershed condition assessments and educational 

outreach activities were completed in FY 2013 that 

continue to keep approximately 15,500 CY of fine 

sediment out of the mainstem. The Program conducted 

monitoring and assessment of biological and physical 

conditions to determine project effectiveness and 

salmon production.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 xi

EXECUTIVE SUMMARY

Table ES-1. FY 2014 Breakdown of Funding Obligations by Program Activity

Section Activity

Water & 

Related 

Funds

Restoration 

Funds

State 

Funds

Bay 

Delta

Funds

ARRA

Funds

Total 

Funds

3405(a) Water Transfer Program 0 0 0 418,366 0 418,366

3406(b)(1) Anadromous Fish Restoration Program 0 7,765,338 0 0 0 7,765,338

3406(b)(1) Habitat Restoration Program 0 1,522,605 0 0 0 1,522,605

3406(b)(1) Bay-Delta Activity 682,654 0 0 3,474,149 0 4,156,803

3406(b)(2) Dedicated Project Yield 0 493,439 0 0 0 493,439

3406(b)(3) Water Acquisition 

Program - Instream 

Water

(2,570,000) 215,265 0 0 0 (2,354,735)

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

Plant Program

Tracy 

(Jones) 

Pumping 

Plant1

1,124,884 0 0 0 0 1,124,884

Two Gates 0 0 0 0 0 0

3406(b)(5) Contra Costa Pumping Plant No. 1 2,143,914 0 48 0 0 2,143,962

3406(b)(9) Flow Fluctuations 0 47,279 0 0 0 47,279

3406(b)(10) Red Bluff Diversion Dam 636,515 0 0 0 14,654 651,169

3406(b)(12) Clear Creek Restoration Program 0 655,320 0 0 0 655,320

3406(b)(13) Spawning Gravel 0 500,348 662,829 0 0 1,163,177

3406(b)(16) Comprehensive Assessment and 

Monitoring Program

2,531,125 3,137,377 0 0 0 5,668,502

3406(b)(20) Glenn Colusa Irrigation District 0 0 0 0 0 0

3406(b)(21) Anadromous Fish Screen Program 3,175,000 2,345,740 1,635,582 768,000 0 7,924,322

3406(b)(23) Trinity River Restoration 2,338,551 0 0 0 0 2,338,551

3406(b)(1) Trinity River Restoration Program 10,267,715 1,517,937 0 0 0 11,785,652

PL 111-11 San Joaquin River Restoration Program 0 1,936,297 0 0 0 1,936,297

3406(d)(1) Refuge Water Supply

3406(d)(2) Refuge Water Supply Level 4 0 1,083,628 0 (350,000) 0 733,628

3406(d)(5) Refuge Facilities 

Construction Program

Construction0 4,469,209 0 0 0 4,469,209

Wheeling 0 9,972,876 0 0 0 9,972,876

3406(d)(5) San Joaquin Basin Action Plan 340 36,006 0 0 0 36,346

3406(g) Ecosystem & Water System Operations 

Models

290,250 677,983 0 0 0 968,233

3408(h) Land Retirement Program 69,811 515,488 0 0 0 585,299

3407 CVPIA Administration 0 1,558,619 0 0 0 1,558,619

TOTAL FUNDING OBLIGATED 20,690,759 38,450,753 2,298,459 4,310,515 14,654 65,765,141

1 Prior year recoveries are included and may result in a negative or reporting of less than total FY 2014 obligation. See Cumulative chart
EXECUTIVE SUMMARY

xii Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Figure ES-2. FY 2014 Breakdown of Funding Obligations by Program Activity

Figure ES-3. FY 2014 Breakdown of Funding Obligations by Fund Source
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 1

CHAPTER 1 - INTRODUCTION

CHAPTER 1 - INTRODUCTION

Purpose

This Annual Report for Fiscal Year (FY) 2014 

summarizes the actions authorized under the Central 

Valley Project Improvement Act (CVPIA or Act) 

through September 30, 2014 and addresses the 

requirement under Section 3408 (f) of the Act to submit 

an annual report to congress. This report summarizes 

funding levels, activities under the various provisions of 

the Act, and the status of metrics to measure progress. 

Background

Authorized in 1935, construction of the Central Valley 

Project (CVP), California, resulted in 20 dams and 

reservoirs, 11 power plants, and 500 miles of canals and 

aqueducts. CVP facilities manage 9 million acre-feet 

of water storage and generate an average of 5.5 billion 

kilowatt-hours of electricity. The majority of the water 

supply for the Central Valley originates in the north 

within the Sacramento River Basin and is conveyed 

across the Sacramento-San Joaquin Delta to the San 

Joaquin Valley and further south (see Figure 1). Initial 

features of the project were built primarily to protect 

the Central Valley from crippling water shortages and 

menacing floods. Today, the CVP maintains Sacramento 

River navigation, supplies domestic and industrial 

water, generates electric power, conserves fish and 

wildlife, creates opportunities for recreation, and 

enhances water quality. This multiple-purpose project 

plays a key role in California`s economy, providing 

water for 6 of the top 10 agricultural counties in the 

nation`s leading farm state, approximately one-third of 

the agricultural land in California.

The benefits of the CVP did not come without costs. 

The construction of dams and the diversion of water 

affected the ecosystems of the Central Valley, Bay 

Delta Estuary, and Trinity River Basin. Populations 

of anadromous fish declined to levels resulting in the 

listing of some species under the Endangered Species 

Act. Conversion of historical wetlands to agricultural 

purposes reduced the habitat for migratory birds and 

other species, in some cases resulting in additional 

listings.

In 1992, the 102nd Congress passed, and President 

Bush signed, the multi-purpose water legislation 

known as the CVPIA. Officially Title XXXIV of 

Public Law 102-575, this legislation amends previous 

authorizations of the California Central Valley 

Project (CVP) to include fish and wildlife protection, 

restoration, and mitigation as project purposes having 

equal priority with irrigation and domestic uses; and 

fish and wildlife enhancement as a project purpose 

equal to power generation. The purpose of the CVPIA 

is expressed in six broad statements found in Section 

3402 of the Act: 

• To protect, restore, and enhance fish, wildlife, 

and associated habitats in the Central Valley and 

Trinity River basins of California;

• To address impacts of the CVP on fish, wildlife, 

and associated habitats; 

• To improve the operational flexibility of the 

Central Valley Project;

• To increase water-related benefits provided 

by the CVP to the State of California (State) 

through expanded use of voluntary water 

transfers and improved water conservation;

• To contribute to the State’s interim and longterm efforts to protect the San Francisco Bay/

Sacramento-San Joaquin Delta Estuary;

• To achieve a reasonable balance among 

competing demands for use of CVP water, 

including the requirements of fish and wildlife, 

agricultural, municipal and industrial, and power 

contractors.

The Secretary of the Department of Interior (Interior) 

assigned responsibility for implementing CVPIA’s 

provisions jointly to Reclamation and the Service. 

Reclamation and the Service coordinate with other 

federal agencies, tribes, the State, partner organizations, 

and other stakeholders during each fiscal year to plan 

and implement activities. The CVPIA operates in a 

complex environment and coordinates with actions 

to: operate the State and Federal water projects, 

comply with the State’s Water Quality Control Plan, 

implement Biological Opinions, support Endangered 
CHAPTER 1 - INTRODUCTION

2 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Figure 1: Central Valley Project (CVP) System
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 3

CHAPTER 1 - INTRODUCTION

Species Recovery Programs, continue water resources 

development, and further local projects, among other 

initiatives. Reclamation and the Service partner 

with entities that have the authority, interest, ability, 

expertise, and resources to implement CVPIA 

restoration actions using a variety of instruments 

such as interagency agreements, memoranda of 

understanding, grants, cooperative agreements, and 

contracts.

Report Organization

This Chapter 1 summarizes funding for the activities 

under the CVPIA and reports on administrative 

expenses. The specific activities under the CVPIA fit 

within four broad resource areas:

• Chapter 2 describes actions to improve fisheries, 

primarily the facility and habitat provisions 

under 3406(b) including the Anadromous Fish 

Restoration Program 3406(b)(1);

• Chapter 3 describes water operations including 

the contract renewal and transfer provisions 

of the CVPIA, sections 3404 and 3405 of the 

CVPIA. In addition, Chapter 2 reports on the 

use of water dedicated for fish and wildlife 

purposes and operations of the CVP, paragraphs 

3406(b)(2) and (9), and the Water Acquisition 

Program 3406(b)(3) for instream flows;

• Chapter 4 describes actions to provide water 

supplies for wetland habitat areas, Section 

3406(d);

• Chapter 5 describes the independent programs 

under the CVPIA including the Habitat 

Restoration Program 3406(b)(1), Federal 

Science Task Force 3406(b)(1), Land Retirement 

Program 3408(h), Ecosystem and Water 

Operations Modeling Program 3406(g), San 

Joaquin River Restoration Program (Title 

X of Public Law 111-11), and Trinity River 

Restoration Program 3406(b)(1) and (23),

• Chapter 6 summarizes the metrics measuring 

progress towards meeting the goals and 

objectives of the CVPIA.

Additional information on the completed projects and 

how they have contributed to the CVPIA restoration 

efforts may be found online at http://www.usbr.gov/mp/

cvpia. 

Funding

Funding to implement the CVPIA derives from multiple 

sources: CVP Restoration Fund (RF or Restoration 

Fund), Water and Related Resources (W&RR), BayDelta Fund, American Recovery and Reinvestment 

Act Fund (ARRA), and the State of California (State). 

Figure 2 shows the historical breakdown of funding 

from the different sources. Figure 3 shows the historical 

obligation by category of expenditure.

The Restoration Fund, established by Section 3407 

of the CVPIA, is an account in the Treasury of the 

United States (U.S.) to be available for deposits of 

donations and revenues provided under the CVPIA. The 

Restoration Fund is authorized for up to $50 million 

(1992 price levels) to be derived from the revenue 

sources provided by the Act. The majority of revenues 

for the Restoration Fund derive from Mitigation 

and Restoration payments by CVP water and power 

contractors. Paragraph 3407(d) limits Mitigation and 

Restoration Payments to no more than $30 million 

(1992 price level) on a three-year rolling average basis. 

The rolling average results in a cyclical funding pattern 

with high, medium, and low collection years. Use of 

the Restoration Fund requires collections in advance of 

expenditures.

For FY 2014, $53.3 million was appropriated to the 

Restoration Fund to be derived from collections from 

CVP water and power beneficiaries. As a result of 

the drought, collections were lower than anticipated 

by $8.5 million and came later in the year. Revenues 

did not reach the levels anticipated by appropriations 

and many actions were initiated behind schedule. 

Unappropriated revenues from prior years provided 

some small ability to mitigate the effects of the drought. 

Figure 5 shows a total of $65.8 million in obligations 

with the addition of Water and Related Resources 

($20.7 million), state cost share funds ($2.3 million), 

and Bay-Delta funds ($4.3 million). Table 1 shows a 

breakdown of funding for each CVPIA Program activity 

in FY 2014. Additional financial reporting is posted 

online at http://www.usbr.gov/mp/cvpia. 

CVPIA Administration

CVPIA Administration addresses activities necessary 

for implementation, but that cannot be reasonably 

attributed to the other more specific sections of the 

Act. Administration provides for developing and 

implementing the overall budget, collecting revenues 
CHAPTER 1 - INTRODUCTION

4 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Figure 2: Program Financial Obligations By Action Category to Date (in $ millions)

Figure 3: Program Financial Obligations By Fund Source to Date (in $ millions)
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 5

CHAPTER 1 - INTRODUCTION

Figure 4. FY 2014 Breakdown of Funding Obligations by Program Activity

Figure 5. FY 2014 Breakdown of Funding Obligations by Fund Source
CHAPTER 1 - INTRODUCTION

6 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Table 1. FY 2014 Breakdown of Funding Obligations by Program Activity

for the Restoration Fund, reporting, coordination 

between the individual CVPIA activities, and oversight 

of activities. Charges include accounting and budget 

staff, CVPIA Administrators, administration support 

staff, and Regional Office management for both the 

Service and Reclamation.

Specific products included the 2012 Financial Report 

to Congress, Annual Report to Congress for Fiscal 

Year 2013, and the 2015 Annual Work Plans. These 

documents are available online at: http://www.usbr.

gov/mp/cvpia. In addition to managing execution of 

the budget, work continued on a Structured Decision 

Making Framework for an Implementation Plan for the 

Fish Resource Area, a CVPIA Finance Plan to address 

power contractor concerns with collections for the 

Restoration Fund, negotiation of a cost-share agreement 

with the State to replace the expiring Sharing of Costs 

Agreement for Mitigation Projects and Improvements 

(SCAMPI), and continued actions to address 

recommendations from the 2008 and 2009 Independent 

Review Panels.

Section Activity

Water & 

Related 

Funds

Restoration 

Funds

State 

Funds

Bay 

Delta

Funds

ARRA

Funds

Total 

Funds

3405(a) Water Transfer Program 0 0 0 418,366 0 418,366

3406(b)(1) Anadromous Fish Restoration Program 0 7,765,338 0 0 0 7,765,338

3406(b)(1) Habitat Restoration Program 0 1,522,605 0 0 0 1,522,605

3406(b)(1) Bay-Delta Activity 682,654 0 0 3,474,149 0 4,156,803

3406(b)(2) Dedicated Project Yield 0 493,439 0 0 0 493,439

3406(b)(3) Water Acquisition 

Program - Instream 

Water

(2,570,000) 215,265 0 0 0 (2,354,735)

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

Plant Program

Tracy 

(Jones) 

Pumping 

Plant1

1,124,884 0 0 0 0 1,124,884

Two Gates 0 0 0 0 0 0

3406(b)(5) Contra Costa Pumping Plant No. 1 2,143,914 0 48 0 0 2,143,962

3406(b)(9) Flow Fluctuations 0 47,279 0 0 0 47,279

3406(b)(10) Red Bluff Diversion Dam 636,515 0 0 0 14,654 651,169

3406(b)(12) Clear Creek Restoration Program 0 655,320 0 0 0 655,320

3406(b)(13) Spawning Gravel 0 500,348 662,829 0 0 1,163,177

3406(b)(16) Comprehensive Assessment and 

Monitoring Program

2,531,125 3,137,377 0 0 0 5,668,502

3406(b)(20) Glenn Colusa Irrigation District 0 0 0 0 0 0

3406(b)(21) Anadromous Fish Screen Program 3,175,000 2,345,740 1,635,582 768,000 0 7,924,322

3406(b)(23) Trinity River Restoration 2,338,551 0 0 0 0 2,338,551

3406(b)(1) Trinity River Restoration Program 10,267,715 1,517,937 0 0 0 11,785,652

PL 111-11 San Joaquin River Restoration Program 0 1,936,297 0 0 0 1,936,297

3406(d)(1) Refuge Water Supply

3406(d)(2) Refuge Water Supply Level 4 0 1,083,628 0 (350,000) 0 733,628

3406(d)(5) Refuge Facilities 

Construction Program

Construction0 4,469,209 0 0 0 4,469,209

Wheeling 0 9,972,876 0 0 0 9,972,876

3406(d)(5) San Joaquin Basin Action Plan 340 36,006 0 0 0 36,346

3406(g) Ecosystem & Water System Operations 

Models

290,250 677,983 0 0 0 968,233

3408(h) Land Retirement Program 69,811 515,488 0 0 0 585,299

3407 CVPIA Administration 0 1,558,619 0 0 0 1,558,619

TOTAL FUNDING OBLIGATED 20,690,759 38,450,753 2,298,459 4,310,515 14,654 65,765,141

1 Prior year recoveries are included and may result in a negative or reporting of less than total FY 2014 obligation. See Cumulative chart.

 Note: Numbers have been rounded.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 7

CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

CHAPTER 2 - FISHERIES RESOURCE AREA

Anadromous Fish Restoration 

Program, 3406 (b)(1)

The Anadromous Fish Restoration Program (AFRP) is 

the overarching program to address anadromous fish 

doubling in the Central Valley. The Act specifically 

directs Interior to:

“... implement a program which makes all reasonable 

efforts to ensure that, by the year 2002, natural 

production of anadromous fish in Central Valley rivers 

and streams will be sustainable, on a long-term basis, 

at levels not less than twice the average levels attained 

during the period of 1967-1991...”

Subsequent to CVPIA’s passage, the AFRP developed 

a series of planning reports that culminated in the 

Final AFRP Restoration Plan (Final Restoration Plan)

(FRP) in 2001. 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 evaluation of restoration actions

• Integrate habitat restoration efforts with harvest 

and hatchery management 

• Involve partners in implementing and evaluating 

restoration actions

Performance Measures 

Central Valley rivers and streams were defined in the 

January 9, 2001, Final Restoration Plan (FRP) for the 

AFRP as all rivers, streams, creeks, sloughs and other 

watercourses, regardless of volume and frequency 

of flow, that drain into the Sacramento River basin, 

the San Joaquin River basin downstream of Mendota 

Pool, or the Sacramento-San Joaquin Delta upstream 

of Chipps Island. The 22 rivers and streams are 

specifically called out within Appendix B of the FRP 

and are listed in Appendix B of this report.

The anadromous fish natural production targets pertain 

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.

Table 5 below lists the doubling target by species. The 

AFRP implements actions and evaluations that will 

contribute to the doubling of the natural production 

of anadromous fish populations. To achieve the fishdoubling goal, the AFRP has identified 289 actions and 

evaluations that support Fisheries restoration (Table 3). 

The CVPIA Program Activity Review (CPAR) Report 

identified 128 Restoration Plan high and medium 

priority actions that are “time certain”, structural (53), 

such as fish screens or passage obstacles and nonstructural actions (75), such as flow fluctuations or 

studies (Table 4). 

FY 2014 Accomplishments 

The AFRP obligated $7.8 million from the Restoration 

Fund in FY 2014. 

The AFRP continued progress toward programmatic 

actions and evaluations throughout Central Valley 

rivers and streams to enhance passage and habitat, and 

reduce loss of fish. Table 2 presents the average natural 

production estimate by species since 1992, including 

the most recent data available (2013 or earlier, 

depending on species).

The Central Valley Chinook salmon (all races) natural 

production average from 1992-2013 was 396,881 fish 

which dropped below the 1967-1991 baseline average 

Chinook salmon production of 497,054. Average 

Chinook salmon natural production for the period 

1992-2013 has exceeded the watershed doubling goal 

target on Clear Creek, Butte Creek, and Battle Creek, 

and in 2012 and 2013 the Mokelumne River observed 

high returns (12,660 and 11,482 naturally produced 

fish respectively; Table 5). Substantial gains in fish 

populations have been observed where investment 

in flow and passage has occurred. Clear Creek and 

the Mokelumne River have also had a substantial 

investment in habitat restoration. Winter-run Chinook 
CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

8 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Table 2. Yearly Estimates of Natural Production of Anadromous Fish and the Average Natural

Production by Species within Central Valley River and Streams, 1992-2013

Year Steelheada

American 

Shadb

Striped 

Bassc

Green 

Sturgeond

White 

Sturgeone

Chinook 

Salmon 

Run

--------------

Fall

Chinook 

Salmon 

Run

--------------

Late Fall

Chinook 

Salmon 

Run

------------

Winter

Chinook 

Salmon 

Run

------------

Spring

Baseline 6,546 2,129 1,252,259 983 5,571 374,049 34,192 54,439 34,374

Target 13,000 4,300 2,500,000 2,000 11,000 750,000 68,000 110,000 68,000

1992 4,086 2,012 777,293 N/A N/A 192,117 27,778 3,167 4,463

1993 5,155 656,505 68 692 316,846 2,411 1,060 4,229

1994 1,317 599,770 N/A 6,392 382,650 1,063 505 7,811

1995 6,808 N/A N/A N/A 709,299 764 4,284 36,884

1996 4,270 1,043,239 N/A N/A 485,160 453 2,160 6,309

1997 2,590 N/A 1,306 11,689 601,000 1,350 2,079 3,866

1998 4,137 1,356,412 470 8,971 272,337 83,027 5,680 49,676

1999 715 N/A N/A N/A 399,951 17,299 5,472 11,163

2000 764 1,591,419 N/A N/A 658,688 19,933 2,657 11,643

2001 763 N/A 7,098 5,129 527,391 27,756 9,938 18,424

2002 1,916 945,878 1,688 2,775 539,052 56,737 9,195 19,839

2003 9,355 829,111 N/A N/A 521,646 9,144 10,911 13,331

2004 947 1,352,335 N/A N/A 509,017 21,343 14,862 21,638

2005 1,742 1,058,679 2,557 2,898 397,755 20,838 21,511 26,099

2006 2,304 N/A 3,144 6,991 227,985 15,600 19,712 11,659

2007 552 752,275 1,530 10,559 107,253 30,508 4,142 13,138

2008 271 1,116,062 1,330 6,257 39,236 4,806 2,555 4,508

2009 624 830,641 10,272 6,258 30,604 4,350 4,070 2,492

2010 683 693,288 N/A N/A 121,132 5,860 1,534 2,244

2011 894 895,774 N/A N/A 170,805 5,654 899 3,688

2012 414 744,604 N/A N/A 297,294 5,600 3,804 17,668

2013 309 N/A N/A N/A 404,269 8,838 7,798 20,015

Average

% of Goal

N/A

N/A

2,206

51%

952,705

38%

2,946

147%

6,237

57%

359,613

48%

16,869

25%

6,273

5.7%

14,127

21% 

a Insufficient data are available to estimate natural production of steelhead in the Central Valley other than upstream of Red Bluff

Diversion Dam Operational changes at Red Bluff Diversion Dam after 1994 preclude the ability to collect comparable post

baseline data for this taxon.

b Mid-water trawl index for young-of-the-year American shad in the Sacramento-San Joaquin River Delta and San Pablo and 

Suisun bays, 1992-2013.

c Estimated abundance of adult striped bass in the Central Valley’s anadromous waters, 1992-2013. Estimates for 2007-2013 

are preliminary and subject to change. Years with missing data is due to CDFW survey frequency which is based upon funding.

d Estimated abundance of green sturgeon >40 inches in total length, 1992-2013. Estimates for 2006, 2007, 2008, and 2009 are 

preliminary and subject to change. Years with missing data is due to CDFW survey frequency which is based upon funding.

e Estimated abundance of 15-year-old white sturgeon, 1992-2013. Estimates for 2006, 2007, 2008, and 2009 are preliminary 

and subject to change.

N/A indicates: (a) data were not collected that year, or (b) indicates the data that are needed to calculate a production estimate 

using historical methodologies is currently unavailable.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 9

CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

Watershed

Total actions and 

evaluations in 

Final 

Restoration Plan

Actions and 

evaluations

completed to date

Actions 

and 

evaluations 

addressed 

in 2013

% of actions 

and evaluations 

completed to 

date

American River 13 2 1 15

Antelope Creek 2 0 1 0

Battle Creek 12 8 3 67

Bear Creek 2 0 0

Bear River 8 0 1 0

Big Chico Creek 10 3 30

Butte Creek 39 32 82

Calaveras River 6 0 1 0

Central Valley-Wide 15 1 4 7

Clear Creek 7 5 71

Colusa Basin Drain 2 0 0

Cosumnes River 9 2 2 22

Cottonwood Creek 5 1 2 20

Cow Creek 4 0 2 0

Deer Creek 5 0 1 0

Elder Creek 2 0 0

Feather River 12 0 1 0

Merced River 8 0 4 0

Mill Creek 5 1 1 20

Miscellaneous Small 

Tributaries

 1 0 0

Mokelumne River 13 1 1 8

Ocean 3 0 0

Paynes Creek 2 0 0

Upper Mainstem 

Sacramento River

 22 8 2 36

Sacramento-San 

Joaquin Delta

 29 0 4 0

Mainstem San Joaquin 

River

 13 0 1 0

Stanislaus River 9 1 4 11

Stoney Creek 1 0 0

Thomes Creek 6 2 33

Tuolumne River 10 0 2 0

Yuba River 14 0 4 0

All Watersheds1 289 67 42 23

1

 Actions to be implemented CVP-wide via tools identified in AFRP Final Restoration Plan.

Table 3. Summary of Progress Towards Completing 289 Final Restoration Plan Actions and

Evaluations by Watershed, FY 1992-2014
CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

10 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Salmon natural production numbers were higher in 

2013 (7,798 naturally produced fish) than during the 

recent trend related to poor returns from 2007-2012 (6-

year average of 2,834 naturally produced fish). In 2013, 

Spring-run Chinook Salmon natural production (20,015 

naturally produced fish) reached the highest level since 

2005. In recent years, Fall-run Chinook Salmon natural 

production had decreased to below baseline levels due 

to the recent stock collapse observed from 2007-2010 

however, the 2013 natural production estimate (404,269 

naturally produced fish) is the highest since 2004 and 

brings the doubling period average nearly back to the 

baseline value. Late fall-run Chinook Salmon natural 

production averaged 5,254 fish between 2008 and 2012, 

but a modest increase in production was observed in 

2013 (8,838 naturally produced fish). 

Table 2 shows the yearly estimate of natural production 

for each anadromous fish species since 1992 and 

Table 5 shows the average natural production estimate 

of Chinook Salmon in each watershed from 1992-

2013. Available data are insufficient to estimate 

natural production of steelhead in the Central Valley. 

Monitoring data for white and green sturgeon in San 

Pablo and Suisun bays are available for eleven years 

and ten years, respectively, between 1992 and 2009. 

The FRP production target for 15-year-old white 

sturgeon was met once while the production target for 

green sturgeon >40 inches (total length) was met in 

2001, 2005, 2006, and 2009. The California Department 

of Fish and Wildlife midwater trawl index for juvenile 

American shad in the Sacramento-San Joaquin River 

Delta and San Pablo and Suisun bays suggests the FRP 

production target for this species was met in three of 

21 years between 1992 and 2013. The 2013 midwater 

trawl index for this species (309) decreased from 2012 

(414), and the 2013 index was markedly below the 

1967-1991 baseline average of 2,129 shad and the FRP 

production target of 4,300 shad. Monitoring of legalsize striped bass in the Central Valley’s anadromous 

waters has occurred in 16 out of 21 years between 1992 

and 2012 and the FRP production target has not been 

met in any of those years. 

About 23% of all Final Restoration Plan actions and 

evaluations (67/289) have been completed between 

1992 and 2013 (Table 3). Of the 105 projects identified 

by the Program Assessment Rating Tool (PART) 

as high and medium priority structural actions and 

evaluations in the Restoration Plan, 73 (70%) have 

been completed. Of the 128 actions identified in 

CPAR, forty-six (36%) have been completed (Table 4). 

One structural action, identified as one of the 105 

PART actions, was completed in FY2014 with the 

completion of construction at the Merced River 

Ranch Floodplain and Channel Restoration Project 

in November 2013. Although no other structural or 

non-structural actions were completed in FY2014 due 

to the limited availability of funds, 38 separate actions 

and evaluations to address high priority limiting factors 

in 20 separate watersheds continued, including fish 

passage, entrainment, habitat restoration, and spawning 

gravel augmentation projects as well as variety 

of assessments and evaluations that are providing 

information critical for future projects.

Accomplishments in the Sacramento Basin

American River

Work to further refine a structured decision making 

(SDM) prototype model continued to assist in 

selecting the best actions for restoration given existing 

conditions (e.g., spawning versus rearing habitat 

restoration). Additional spawning and side channel 

habitat was restored in FY2014 with the addition of 

gravel and improvement of approximately 1.5 acres of 

spawning habitat. Additionally, a 350-yard-long side 

channel was created along the south side of the river 

to provide juvenile rearing habitat. These efforts are 

co-implemented with the 3406(b)(13) program, U.S. 

Fish and Wildlife Service (USFWS), U.S. Bureau of 

Reclamation, U.S. Army Corps of Engineers (ACOE), 

California Department of Fish and Wildlife (CDFW), 

and the Sacramento Area Water Forum.

Antelope Creek

The Juvenile Fish Passage Improvement Project at 

Edwards Diversion Dam (Central Valley Evaluation 11) 

will prevent out-migrating salmonids from becoming 

entrained in the two diversion canals. The Technical 

Advisory Committee has met with the diverters to 

determine the most feasible alternative. Substantial 

progress on a final report of the project’s history and 

documentation of data gaps discovered during detailed 

design discussions was made in 2014. This project is 

a cooperative effort between the USFWS, National 

Marine Fisheries Service (NMFS), CDFW, and the 

Tehama County Resource Conservation District.

Battle Creek

The Battle Creek Salmon and Steelhead Restoration 

Project will restore approximately 42 miles of habitat 

in Battle Creek and an additional 6 miles of habitat in 

its tributaries. AFRP staff is heavily involved in the 

coordination and planning of the larger restoration 

efforts and individual related projects and planning 

actions. Of the nine Bureau of Reclamation (USBR) 

contracts that constitute Phase 1A and 1B, seven have 

been awarded. At the Wildcat Dam & Canal site, both 

the dam & canal have been removed and the associated 

road repair is completed. A new fish screen and bypass 

is in place at Eagle Canyon Dam (Actions 2, 6, and 7). 

The additional pending work has been delayed to be 

completed until 2016. This project is a cooperative 

effort among the U.S. Department of the Interior, 
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 11

CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

Watershed 53 Structural Actions 75 Non-structural Actions

Number of 

structural actions 

completed in FY 

2014

Number of 

structural 

actions completed 

since 1992

Number of 

non-structural 

actions completed 

in FY 2014

Number of 

non-structural actions 

completed since 1992

American River 1 1

Battle Creek 3 2

Big Chico Creek 1 1

Butte Creek 13 17

Clear Creek 1

Cosumnes River 1

Cottonwood Creek 1

Mill Creek 1

Stanislaus River 1

Thomes Creek 2

All Watersheds 21 25

* NOTE: Although structural or non-structural actions were not completed in FY 2014, work continued on 20 watersheds 

throughout the Central Valley.

Table 4. Summary of Progress Towards 128 High and Medium Priority “Time Certain” Actions

(53 Structural, 75 Non-Structural) 
CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

12 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Watershed Species

Doubling 

Goal Target

1992-2013 Average 

Natural Production 

Numbers Percent of Target

American River* Fall-Run 160,000 104,296 65.2

Antelope Creek Fall-Run 720 0 0

Battle Creek* Fall-Run 10,000 17,564 175.6

Bear River Fall-Run 450 N/A N/A

Big Chico Creek Fall-Run 800 N/A N/A

Butte Creek Fall-Run 1,500 2,288 152.5

Clear Creek Fall-Run 7,100 10,956 154.3

Cosumnes River Fall-Run 3,300 768 23.3

Cottonwood Creek Fall-Run 5,900 2,145 36.4

Cow Creek Fall-Run 4,600 2,117 46.0

Deer Creek Fall-Run 1,500 898 59.9

Feather River* Fall-Run 170,000 94,314 55.5

Merced River* Fall-Run 18,000 6,484 36.0

Mill Creek Fall-Run 4,200 1,896 45.1

Miscellaneous Creeks Fall-Run 1,100 78 7.1

Mokelumne River* Fall-Run 9,300 8,731 93.9

Paynes Creek Fall-Run 330 N/A N/A

Sacramento River Fall-Run 230,000 69,069 30.0

Stanislaus River Fall-Run 22,000 5,167 23.5

Tuolumne River Fall-Run 38,000 6,474 17.0

Yuba River Fall-Run 66,000 30,670 46.4

Central Valley Wide Fall-Run 750,000 359,613 47.9

Battle Creek* Late-fall-Run 550 676 122.9

Sacramento River Late-fall-Run 68,000 16,964 24.9

Central Valley Wide Late-fall-Run 68,000 16,869 24.8

Butte Creek Spring-Run 2,000 10,327 516.3

Deer Creek Spring-Run 6,500 1,949 30.0

Mill Creek Spring-Run 4,400 1,198 27.2

Sacramento River Spring-Run 59,000 653 1.1

Central Valley Wide Spring-Run 68,000 14,127 20.8

Calaveras River Winter-Run 2,200 0 0

Sacramento River* Winter-Run 110,000 6,273 5.7

Central Valley Wide Winter-Run 110,000 6,273 5.7

TOTAL All races 990,000 396,881 40.1

* Watersheds that contain a fish hatchery.

Table 5. Average Natural Production Numbers in Each Watershed Compared to the AFRP

Doubling Goal Targets, 1992-2013
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 13

CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

USBR, USFWS, NMFS, CDFW, and the Pacific Gas 

and Electric Company (PG&E).

Bear River

The quality of anadromous salmonid habitat and 

presence of passage barriers were assessed in a 

4-mile reach of Dry Creek beginning at the Beale 

AFB boundary and moving upstream. Mesohabitat 

units were identified and mapped, and shapefiles 

were generated. The percentage of spawning gravel 

and percentage of bank with woody cover for each 

mesohabitat was recorded. Results are documented and 

discussed in a final report. Additionally, AFRP staff is 

investigating a recent report of the potential occurrence 

of an acoustically-tagged White Sturgeon entering the 

watershed and will proceed accordingly if the report is 

confirmed. 

Cottonwood Creek

In 2014, AFRP staff finalized plans and required 

permitting for the South Fork Cottonwood Creek 

Fish Passage Improvement Project (Central Valley 

Evaluation 11). The project was planned to be 

implemented in late FY2014, but has been delayed 

due to the limited availability of helicopter support 

needed to move equipment (delay is related to wildfires 

throughout the region during this time). This project is a 

cooperative effort between the USFWS, CDFW, USBR, 

NMFS, and the landowner. 

Significant work on the Cottonwood Creek Sediment 

Budget and accompanying report was made during 

FY2014 and a draft report is anticipated by the end of 

the calendar year.

The Cottonwood Creek non-native (invasive) plant 

management and control was completed in 2014. 

Additional treatments were implemented in South Fork 

Cottonwood Creek and a final report for the entire 

project has been submitted.

Cow Creek

Substantial field work was completed on the Cow 

Creek Riparian Assessment Project. A draft final report 

including restoration recommendations is expected 

during fall 2014. This is a cooperative project with the 

USFWS, CDFW, and the Cow Creek Watershed Group. 

Work continued on the Cow Creek anadromous 

fish passage barrier assessment originally funded in 

2011. Field surveys continued in 2014 as additional 

landowner access allowed. A barrier database, GIS 

layers and draft final report are ongoing. This is a 

cooperative project with the USFWS, CDFW, Cow 

Creek Watershed Group, and the Western Shasta 

Resource Conservation District.

AFRP staff remain engaged in the Clover Creek Fish 

Passage/Millville Diversion Dam Restoration Project. 

The design and initial permitting for this project was 

completed in 2013 and additional efforts to finalize and 

compete implementation are underway. This project 

will open up 10 miles of historic habitat to fall-run 

Chinook salmon and steelhead (Action 3). This is 

a cooperative project with the USFWS, CDFW, the 

California Department of Water Resources (CDWR), 

the Natural Resources Conservation Service, and the 

Millville Ditch Association. 

Deer Creek

A design alternatives report for the Lower Deer Creek 

Falls Fish Passage Improvement Project (Phase 1) 

was submitted for review by the project’s Technical 

Advisory Group in 2014. The grant recipient is working 

closely with the National Marine Fisheries Service 

hydraulic engineer to best address the complexity of 

the site but still meet ladder passage criteria. A new 

alternative design is anticipated in late summer/fall of 

2014. This project is a cooperative effort between the 

USFWS, NMFS, USBR, CDFW, and the Deer Creek 

Irrigation District.

A cooperative agreement was finalized in late 2013 

to begin work on the Deer Creek Irrigation District 

Dam Fish Passage Project. In 2014, local landowners 

were contacted and facilities access agreements were 

initiated.

Feather River

Monitoring activities targeting green sturgeon did not 

occur in 2014 due to low water conditions. As a result, 

an additional year of monitoring was added and will 

occur in 2015 as conditions allow. This is a cooperative 

project between the USFWS and CDWR. Additionally, 

AFRP staff remain heavily involved in planning efforts 

on the Feather River and serve an integral role in 

coordinated management decisions in this watershed.

Mill Creek

The Mill Creek fish passage assessment and restoration 

project was funded in FY2011 and additional funding 

to complete the environmental permitting was modified 

into the agreement on September 2013 (Evaluation 1). 

In 2014, 90% designs are in process for the siphon and 

Ward Dam sites. Agreement on the proposed alternative 

for both sites has been made. The Upper Dam still 

has to have agreement on the screening alternative 

which should be reached by the end of FY2014. Once 

this is agreed upon, 50% designs will be submitted 

for the Upper Dam fish ladder and screens. This is a 

cooperative project between the USFWS, CDFW, Los 

Molinos Mutual Water Company, and the Mill Creek 

Conservancy.
CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

14 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Substantial field work was completed in 2014 on 

the Mill Creek Riparian Assessment Project. A draft 

final report including restoration recommendations 

is expected during fall 2014. This is a cooperative 

project with the USFWS, CDFW, and the Mill Creek 

Conservancy. 

An Interagency Agreement was established in 2013 

to set up a network of acoustic receivers in the Mill 

and Deer Creek tributaries to the Sacramento River 

and implement a study that will assess reach specific 

survival rates of juvenile Chinook salmon from the 

Upper Sacramento River to the Delta. In 2014, Battle 

Creek was added to the study and juvenile salmon were 

collected and tagged in the spring on both Mill Creek 

and Battle Creek. Data from the receivers has been 

downloaded and is under analysis. This study is being 

co-implemented by the USFWS, NMFS, the CDFW 

Ecosystem Restoration Program, and UC Santa Cruz. 

Sacramento River

The mainstem Sacramento River redd monitoring 

project provided managers the ability to make 

management recommendations to prevent dewatered 

redds on nearly a “real-time” basis. Seventy-three miles 

of the mainstem Sacramento River were monitored 

for redd dewatering and juvenile stranding. Based on 

population estimates, about 0.2% winter, 3.1% fall/

spring mixed, and 1.2% late-fall-run Chinook salmon 

redds were dewatered to various degrees. Maintaining 

stable flows during egg incubation and emergence 

are important to reduce negative impacts to fall run 

and late-fall run Chinook salmon and steelhead fry 

production on the mainstem Sacramento River. This 

project is a cooperative effort between the USFWS, 

CDFW, CDWR, and Pacific States Marine Fisheries 

Commission.

Additionally, substantial progress has been made 

on efforts to determine the potential impacts, and/or 

the degree of impact, to northern California aquatic 

resources, specifically anadromous fish, posed by 

illegal marijuana cultivation activities. In the summer of 

2014, site visits and data collection were completed on 

multiple upper Sacramento River tributaries. 

Yuba River 

Monitoring growth and survival of the 5 acres of 

cottonwood and willow pole cuttings planted on 

Hammon Bar in FY2012 and FY2013 continued in 

FY2014. Water depths and velocities during inundation 

also were measured. A draft long-term monitoring 

plan was developed that is intended to assess plant 

survivorship and structure, sediment and organic 

material deposition, understory plant composition, 

groundwater and surface water patterns, and fish 

and macroinvertebrate abundance and diversity. The 

planting area is intended to flood periodically under 

moderate flows and thus provide juvenile salmonids 

with improved rearing habitat (Evaluation 4). This 

project is a cooperative effort between the USFWS, 

CDFW, Bureau of Land Management (BLM), 

Americorps, Western Aggregates, PG&E, and the South 

Yuba River Citizens League. PG&E is cost sharing 

$50,000 of the total project cost.

The Yuba River Study Utilizing the Spawning Habitat 

Integrated Rehabilitation Approach (SHIRA) has led to 

a detailed map and 2-D model of the lower Yuba River. 

Mapping of the final reach (i.e., the Narrows) was 

completed as part of a related AFRP project. Reports 

assessing the 2013 data were presented at the Lower 

Yuba River Accord Symposium on July 15, 2014. 

AFRP staff continued to be an active participant on the 

Yuba Accord RMT providing technical expertise on 

anadromous fish habitat restoration and guiding future 

restoration efforts with the SHIRA model. This project 

is a collaborative effort between the USFWS, NMFS, 

Army Corps of Engineers (ACOE), Yuba County Water 

Agency (YCWA), and the University of California 

at Davis. ACOE provided $100,000 and YCWA 

contributed $30,000 in cost-share to further refine the 

model. 

Vaki Riverwatcher systems continue to be operated 

on the north and south fish ladders at Daguerre Point 

Dam in the lower Yuba River. The collection of fish 

passage data continues to improve understanding about 

the timing, abundance, population trends, and response 

to changing flow and temperature conditions of adult 

spring and fall-run Chinook salmon and steelhead. 

Reports assessing the 2013 data were presented at the 

Lower Yuba River Accord Symposium on July 15, 

2014. AFRP staff continued to be an active participant 

on the Yuba River Management Team providing 

technical expertise on anadromous fish population 

monitoring. This project is a collaborative effort 

between the USFWS, NMFS, ACOE, CDFW, YCWA, 

and the Pacific States Marine Fisheries Commission. 

YCWA provided $120,000 for in-kind services to 

operate and maintain the fish counting systems on both 

ladders at Daguerre Point Dam. 

Accomplishments in the San Joaquin Basin

Calaveras River

In-water work at the Caprini Low Flow Crossing 

Fish Passage Project was completed last fiscal year 

in September 2013 and additional project elements 

were completed during October 2013. Passage 

opportunities were limited during FY2014 due to low 

water conditions but steelhead were observed passing 

the site without delay on the one occasion when the 
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 15

CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

river was reconnected to a degree that allowed them to 

enter the system. This project restored access to about 

6 miles of habitat (Action 3). Additional design work 

was required at the California Central Traction Railroad 

crossing site due to safety concenrs. Additional funding 

has been obligated and the project is scheduled to be 

implemented in 2015. The Calaveras River projects 

are a cooperative effort between the USFWS, CDFW, 

CDWR, Stockton East Water District, Fisheries 

Foundation of California, and the University of the 

Pacific. Stockton East Water District is cost-sharing 

$200,000 of the total project cost. 

The 4th annual Calaveras River Education and 

Appreciation Day was held on November 2nd, 2013. 

Approximately 35 students from A.A. Stagg School in 

Stockton attended the event. Additionally, more than 

10 local experts in a wide array of natural resource 

disciplines were able to interact with the students in 

a variety of educational activities. This is an annual 

cooperative effort by USFWS, USACE, Friends of 

the Lower Calaveras River, Defenders of Wildlife, 

University of the Pacific, Fisheries Foundation of 

California, A.A. Stagg High School, and local Audubon 

and Sierra Club chapters.

Cosumnes River

Unexpected delays related to adjacent landowner 

responses to the NEPA permitting for the Cougar 

Wetland Floodplain Restoration Project have 

caused a delay in implementation until FY15. Those 

concerns are being addressed by the project team and 

implementation is expected to start in summer 2015. 

Aquatic and terrestrial habitat assessments occurred 

in FY14. This project is a cooperative effort between 

the USFWS, CDWR, Ducks Unlimited, ACOE, and 

BLM. Ducks Unlimited and the ACOE cost shared an 

estimated $800,000.

Merced River

AFRP staff continued to administer the rotary screw 

trap monitoring agreement with Merced Irrigation 

District. This project documented the number of 

juvenile salmon and steelhead that outmigrated from 

the Merced River in 2014. Estimates of juvenile 

salmonid production were calculated and the existing 

outmigration database was updated. Additional data to 

assess effectiveness of flow management and habitat 

restoration projects was collected. 

Designs and permitting for the Merced River floodplain 

and channel restoration project at Snelling (Action 3) 

were completed in 2013. The objective of the project 

is to improve spawning and rearing habitat for juvenile 

salmonids on the Merced River by restoring areas 

degraded by gold mining operations. Due to lack of 

funding in 2014 construction was delayed until 2015, 

permit required monitoring was continued. This project 

is a cooperative effort between the USFWS, CDFW, 

and Merced County.

The final construction activities on the Merced River 

Ranch Project were completed in November 2013. Post 

project monitoring was scheduled to occur in 2014 

but was delayed due to lack of funding. This project 

is a cooperative effort between the USFWS, CDFW, 

Merced County, and the Merced Irrigation District.

The AFRP continued to participate in the FERC 

proceedings for the Merced Falls (P-2467) and Merced 

River Hydroelectric (P-2179) Projects (Actions 1 and 2; 

Evaluations 1 and 3). AFRP participated in multiple 

relicensing meetings in FY2014. Staff reviewed and 

provided comments on the Updated Study Report 

and various Technical Memorandums on channel 

armoring, IFIM habitat modeling, temperature criteria, 

water balance operations models, and egg viability. 

AFRP is actively participating in the Merced River 

Technical Advisory Committee and developing 

ongoing partnerships with numerous stakeholders in the 

watershed. 

Mokelumne River

Ongoing habitat assessments and modeling of the 

treatment reaches and downstream affected areas has 

been completed for the Mokelumne River Spawning 

Habitat Improvement Project (Actions 2 and 7). This 

project area is rigorously characterized and monitored 

each year for spawning use, bed form and function and 

provides a foundation project for the Spawning Habitat 

Integrated Rehabilitation Approach (SHIRA). The final 

report for the 2009-2013 activities was completed in 

early FY2014. Due to limited funding availability, this 

project has yet to be funded in FY14 and no new gravel 

placement has occurred. Ongoing habitat assessments 

and modeling of the treatment reaches and downstream 

affected areas has been completed. Additional sources 

of appropriate gravel have been identified during FY14 

and final permitting is nearly complete for up to 5 

years of additional implementation. This project is a 

cooperative effort between the USFWS and the East 

Bay Municipal Utility District (EBMUD). 

In FY2014, AFRP staff worked with the EBMUD 

and other signatories of the Lower Mokelumne Joint 

Settlement Agreement to adaptively manage the system 

and coordinate fall pulse flows (about 5,000 acre feet) 

with Delta Cross Channel (DCC) operations in an 

effort to improve adult Chinook salmon returns (Delta 

Evaluation 5). The DCC gates were not closed in 

October of 2013 due to low flow conditions and water 

quality concerns in the South Delta. This project is a 

cooperative effort between the USFWS, NMFS, CDFW, 

Woodbridge Irrigation District, and the EBMUD. 
CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

16 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

San Joaquin River

AFRP staff partnered with the CDFW to maintain 

VEMCOTM acoustic receivers in the San Joaquin River 

and continue an annual white sturgeon population 

assessment. AFRP deployed egg mats to identify 

sturgeon spawning habitat. No eggs were collected 

during the 2014 sampling season and it is likely 

that very little or no spawning occurred in the study 

area. This may be due to the low river discharge, 

high water temperatures, and a lack of spring rains. 

Understanding the conditions that result in sturgeon 

spawning continues to be an active area of research 

and will allow us to develop better water management 

recommendations needed to increase recruitment and 

abundance of this important CVPIA focus species. 

Additionally, 15 white sturgeon were captured and 

implanted with acoustic transmitters in the spring of 

2014. Movements of these fish were tracked to learn 

more about the spatial and temporal distribution of 

white sturgeon in the San Joaquin River. Also, the 

AFRP partnered with USGS to map habitat-related 

physical characteristics along the San Joaquin River 

with a multibeam sonar, acoustic Doppler current 

profiler, and RTK-GPS, unfortunately due to low water 

levels the habitat mapping could not take place. 

A manuscript has been developed and submitted for 

peer-review describing the evaluation of effects of fin 

ray removal on growth, survival and swim performance 

of White Sturgeon. Fin rays continue to be collected 

from angler-harvested fish and those captured by 

CDFW during annual bay monitoring efforts. When 

funding becomes available, these rays will be used to 

evaluate population age and growth characteristics, 

previous life history information, and inform restoration 

and management actions. Fin rays, stomachs, gonads, 

and blood samples were collected from 26 angler 

harvested fish and are being analyzed for histology, 

contaminants, and age and growth. Analyses are 

on hold due to lack of FY14 funding. Results of 

all analyses will be used to identify and prioritize 

restoration and management actions.

Stanislaus River

FY 2014 accomplishments included the collection of 

both juvenile and adult passage data via rotary screw 

trapping (juveniles)(CAMP) and a fish counting weir 

(adults) operated in partnership with Tri-Dam. A report 

summarizing the FY13 salmonid production data was 

completed. The third year of the Chinook salmon 

juvenile acoustic study was completed this year and 

the annual report was submitted. Juvenile salmon were 

radio tagged and tracked using both fixed and mobile 

detectors. The study will identify geographic sources of 

mortality for juvenile salmonids within the migratory 

corridor and evaluate the effectiveness of improving 

survival with a spring pulse flow. These studies 

assist with evaluating benefits resulting from habitat 

restoration actions. Tri-Dam cost shared about $150,000 

for the operation of the rotary screw traps from January 

1st to June 15th, 2013 and the fish counting weir from 

September 11, 2012 to June 30, 2013.

A construction summary report of the Lancaster Road 

Floodplain and Side-channel Restoration Project 

was completed in late 2013. Additional post-project 

monitoring was undertaken and results were presented 

at professional conferences in FY2014. Post-project 

monitoring which included vegetation surveys, channel 

velocity and depth profiles, channel bathymetry 

and floodplain topographic surveys, benthic macroinvertebrate sampling, fish population monitoring, and 

substrate quality assessments were also completed for 

the Honolulu Bar Floodplain Restoration Project. These 

projects were designed to increase juvenile salmonid 

rearing habitat and decrease predation (Action 2). The 

Stanislaus River floodplain restoration projects were 

implemented in partnership with ACOE, Oakdale 

Irrigation District, Cramer Fish Sciences, FishBio, 

River Partners, and CDFW. 

Planning documents and design alternatives were 

developed for the Knights Ferry Floodplain Restoration 

Project and the Buttonbush Floodplain Restoration 

Project (Action 2). Pre-project monitoring data was 

collected to characterize the pre-project habitat 

conditions including water depth and velocities, 

substrate size distribution, and biological data.

Topographic and bathymetric surveys were also 

completed to be used to further refine design 

alternatives. These projects are a cooperative effort 

between the USFWS and the ACOE. 

The Fifth Annual Stanislaus River Salmon Festival 

was held on October 26, 2013 at the Knights Ferry 

Recreation Area, with AFRP staff heavily involved 

in the organization and implementation of the event. 

An estimated 1,800 attendees joined in the multiple 

activities offered as part of the event. The East 

Stanislaus Resource Conservation District, Modesto 

Junior College, Great Valley Museum, FishBio, U.S. 

Army Corps of Engineers, and both Oakdale and 

Knights Ferry schools played key roles in organizing 

the event.

Tuolumne River

Post-project monitoring at the Bobcat Flat Restoration 

Project sampled fish through snorkel and seine 

surveys and benthic macro-invertebrate sampling 

in the constructed floodplain and side-channel in 

the Tuolumne River (Action 2). The Bobcat Flat 

Restoration Project restored 8 acres of highly disturbed 

floodplain and about 1.6 miles of fall run Chinook 

salmon and Central Valley steelhead spawning and 
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 17

CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Restoration Program 3406 (b)(1)

rearing habitat in 2011. Adult and juvenile salmon 

were observed using the improved habitat October 

2013 - May 2014. The Final Report was completed in 

2014. This project was a collaborative effort between 

USFWS, CDFW Ecosystem Restoration Program, and 

Friends of the Tuolumne River.

The AFRP continued to participate in the FERC 

proceedings for the Don Pedro Hydroelectric Project 

(P-2299) (Actions 1 and 6; Evaluations 1, 2, 3, and 4). 

AFRP participated in multiple relicensing meetings in 

FY2013 and submitted study proposals for Floodplain 

Habitat Modeling, juvenile Chinook salmon and 

predator acoustic telemetry studies, and a predator 

mark and recapture study. Staff also provided detailed 

comments on the Don Pedro FERC Initial Study Report 

and on the Don Pedro Chinook Population Model. 

AFRP is collaborating with numerous stakeholders 

in the watershed through the relicensing process to 

develop conceptual models and evaluate the limiting 

factors and fishery resources in the Tuolumne River.
CHAPTER 2 - FISHERIES RESOURCE AREA | Tracy (Jones) Pumping Plant Program 3406 (b)(4)

18 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Tracy (Jones) Pumping Plant 

Program 3406 (b)(4)

The Tracy (Jones) Pumping Plant’s six pumps, each 

capable of pumping between 800 - 1000 cfs into the 

Delta Mendota Canal, are powerful enough to alter 

stream flow in the Delta and the San Joaquin River 

Basin. This disorients migratory fish and draws them 

toward the pumps where they can become entrained, or 

trapped. 

To mitigate entrainment, the Tracy Fish Collection 

Facility (TFCF), located upstream of the pumping plant, 

collects migratory fish and transports them to the Delta 

where they can resume outmigration to the ocean. The 

focus of the (b)(4) program is to improve fish protection 

and salvage through development of new technologies. 

Ongoing monitoring of the program’s effectiveness 

helps define best practices that inform decision-making 

and long-term planning at Tracy and other South Delta 

facilities. 

Performance Measures 

The Tracy (Jones) Pumping Plant program (TPPP) 

develops and implements actions to mitigate impacts to 

fisheries, targeting the 23 actions included in The Tracy 

Fish Facility Improvement Program Plan, as shown in 

Table 6. As of this year 17 of the 23 actions have been 

completed.

FY 2014 Accomplishments 

The program obligated $1,125,000 from Water & 

Related Resources fund for the TFCF, with no funds 

contributed from the Restoration Fund. 

Actions to Improve Tracy Fish Collection 

Facility 

By far the greatest accomplishment was the Secondary 

Louver Replacement project, Action 18, awarded at 

the end of last fiscal year and implanted in the Spring/

Summer 2014. Installation of the secondary channel fish 

screen and debris handling system was completed in 

July 2014, in effect becoming a prototype for Action 17. 

Also, work continued on design details towards 

eventual completion of Action 19, which will result in 

the development of land to better Reclamation’s ability 

to conduct research onsite and improve fish protection 

at the TFCF. Replacement of the secondary transfer 

system, Action 20, to improve hydraulic control and 

fish transfer will be delayed to 2018, accommodating 

the new screening system testing and the need for RAX 

Program funding. 

The program continued assessments, search of land 

records and initial reconnaissance was conducted in 

support of Action 23, the third release site. In addition 

Reclamation partnered with the State of California on 

the physical modeling of fish release pipe configuration 

at the DTSC. This research will be incorporated into the 

ultimate design for the third release site.

In addition to the 23 actions listed in Table 6, the 

program also completed a number of studies that will 

improve fish capture and reintroduction capabilities. 

The studies include a continuation of data evaluation 

related to the salvage efficiency tests for salmon, and 

evaluation of predatory impacts within the secondary 

system of the TFCF. Predation studies continued 

with the evaluation of the use of carbon dioxide as 

an alternative predator removal technique to decrease 

TFCF predator numbers as well as the investigation 

of the use of fish traps and bait attraction of predator 

fish. The research group advanced the state of the art of 

acoustic tag technology by evaluating the influence of 

tags on susceptibility to predation and evacuation rate 

in several species. 

Reclamation also evaluated the holding tank screen 

retention efficiency for juvenile delta smelt. The 

research group also completed studies of the effects of 

fish density on water quality in the haul-out bucket and 

fish-haul trucks at the TFCF.

Some of these studies are related to specific RPA 

action items and some are included in the facility 

assessment program. The facility assessment program 

is needed in order to understand present day operational 

characteristics so as to have a baseline to compare 

improvements to and also figure out which technologies 

and concepts to apply to the eventual physical 

improvements.

Tracy Fish Facility Improvement Program Publication 

for FY2014:

• Tracy Technical Bulletin 2014-1

Zachary A. Sutphin and Connie Svoboda. 

2014. Effects of Life-Stage and Origin (Wild or 

Hatchery) on Delta Smelt Secondary Channel 

Efficiency at the Tracy Fish Collection Facility. 

25 pp.

• Tracy Technical Bulletin 2014-2

Zachary A. Sutphin. 2014. Effects of Removing 

Primary Channel Adult Striped bass on Delta 

Smelt Salvage Efficiency. 29 pp.

• Tracy Technical Bulletin 2014-3

Brandon J. Wu and Brent B. Bridges. 2014. 

Retention Efficiency of the Tracy Fish Collection 

Facility Holding Tank Screens for 20–30 mm 

Fork Length Juvenile Delta Smelt during 

30-Minute Fish Counts. 35 pp.
CHAPTER 2 - FISHERIES RESOURCE AREA | Tracy (Jones) Pumping Plant Program 3406 (b)(4)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 19

Actions Start Date

Completion 

Date

 1 Implemented periodic predator removals 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 fish taxonomic work 1999 1999

 9 Added air system to fish haul trucks 2000 2000

10 Upgraded fish count area to accommodate DNA sampling & fish ID 2000 2000

11 Updated fish identification key for training of operators 2000 2000

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

13 Replaced fish transfer bucket with new/improved fish transfer 

bucket

2006 2008

14 Replaced fish haul trucks with new/improved fish 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 Replace primary louvers/cleaners with new primary louvers/

cleaning system

2006 2017*

18 Replace secondary louver/cleaners with new secondary louvers/

cleaning system

2006 2014

19 Develop land onsite to improve ability to conduct research and 

operate the facility

2006 2018*

20 Construct new secondary screening and transfer system 2010 2018*

21 Construct new aquaculture facility onsite 2012 2020*

22 Automate velocity control pumps for the fish bypass system 2013 2016*

23 Construct third fish release site 2014 2016*

* Estimated Completion Date

Table 6. Summary of Progress Towards 23 Tracy Fish Facility Improvement Program Plan 

Actions

• Tracy Research Series Volume 49

Brandon J. Wu and Brent B. Bridges. 2014. 

Evaluating the Use of Carbon Dioxide as an 

Alternative Predator Removal Technique to 

Decrease Tracy Fish Collection Facility Predator 

Numbers and Improve Facility Operations. 61 

pp.

• Tracy Research Series Volume 50

Brandon J. Wu and Brent B. Bridges. 2014. 

Evaluation of a New Technique to Remove 

Debris from Holding Tanks at the Tracy Fish 

Collection Facility. 33 pp.

• Tracy Research Series Volume 51

Zachary A. Sutphin, Rene C. Reyes, and 

Brandon J. Wu. 2014. Predatory Fishes in 

the Tracy Fish Collection Facility Secondary 

System: An Analysis of Density, Distribution, 

Re-colonization Rates, and Impact on 

Salvageable Fishes. 69 pp.
CHAPTER 2 - FISHERIES RESOURCE AREA | Clear Creek Restoration Program 3406 (b)(12)

20 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Clear Creek Restoration Program 

3406 (b)(12)

Clear Creek suffered widespread degradation through 

the 20th century due to several factors, including 

construction of McCormick-Saeltzer Dam in 1903, 

construction of Whiskeytown Dam in the 1960s, and 

aggregate and gold mining activities. These actions led 

to precipitous drops in Chinook salmon and steelhead 

spawning, and juvenile production. Section (b)(12) 

calls for a restoration program to improve instream 

habitat, allowing greater spawning and rearing success.

Performance Measures

The Clear Creek Restoration Program (CCRP) focuses 

on the following areas and uses the following goals 

to track progress: fish passage; erosion control; gravel 

placement (creation of spawning habitat); channel 

restoration; instream flow and temperature of flow 

releases. All of these goals are in support of the overall 

CCRP objective of restoring fish populations in Clear 

Creek, and increasing natural production, to meet the 

annual target of 7,100 for fall-run Chinook in Clear 

Creek. Although there is no doubling target for spring 

run Chinook on Clear Creek, restoration actions will 

also help increase spring-run Chinook populations, 

contributing to the CVPIA’s Central Valley-wide goals.

Fish Passage – The fish passage target was achieved in 

2000, when McCormick-Saeltzer Dam was removed, 

opening 12 additional miles of habitat to fish passage 

and upstream spawning.

Erosion Control – The erosion control target was 

achieved ahead of schedule. All feasible and cost 

effective erosion control projects initially identified 

were completed by 2001 and at that time, the necessity 

for further work would be subject to future needs. Since 

that time, the Clear Creek watershed has experienced 

two major wildfires, the Moon Fire in 2008, and the 

Dale Fire of July 2012. The federal and state lands 

affected by the Dale Fire have been subject to some 

post-fire stabilization measures such as grass-seeding, 

straw mulching, replanting, and other erosion reduction 

efforts. The Clover Fire of September 2013 affected the 

Cottonwood Creek drainage and also burned a smaller 

area within the Clear Creek watershed. There were 

no major conflagrations during the summer of 2014. 

The potential impacts to Clear Creek are not yet fully 

known.

Gravel Placement (Creation of Spawning Habitat) – 

The CCRP attempts to replenish Clear Creek spawning 

habitat areas with 25,000 tons of gravel every year. 

Clear Creek spawning gravel replenishment goal was 

erroneously reported in the Final CPAR, 2009 as 17,000 

tons annually. This unit of measure should have been 

cubic yards. Applying a conversion factor, 17,000 cubic 

yards of spawning gravel equates approximately to 

25,000 tons. This correction first occurred in the 2012 

Accomplishment Report and therefore, the percentage 

of annual goal for this year forward will appear smaller 

than past years of the same amounts of gravel. Gravel 

placement contributes to the restoration of the 347,288 

square feet of spawning habitat that existed before the 

construction of Whiskeytown Dam. 

Channel Restoration – The CCRP is restoring 2 miles 

of stream channel to support successful spawning and 

rearing.

In-stream Flows and Temperature of Flow 

Releases – The CCRP provides instream flows, 

depending on hydrology and biological conditions, to 

ensure that flow volumes and temperature meet habitat 

needs for successful spawning and rearing. Using (b)

(2) water and coordinating with operators, the CCRP 

aims to provide water at 60°F June 1–September 15, 

and 56°F September 16–October. The goal is to meet 

these targets at least 98% of days, with no more than 

two consecutive days of releases when exceeding the 

temperature target. The timing of flows benefit both 

spring run and fall run Chinook but are especially 

important to spawning spring run Chinook as they 

can only spawn in water cold enough to sustain eggs 

through their incubation period. 

Since 1999, studies have been undertaken by CVPIA 

and CALFED to develop channel maintenance flows, 

which are vital for providing and maintaining spawning 

and rearing habitat in Clear Creek. In 2008 FWS and 

CALFED contracted to facilitate a pilot re-operation 

of Whiskeytown reservoir to achieve the channel 

maintenance flow prescription. This Environmental 

Water Program prescription calls for the re-operation 

of Whiskeytown Dam, between March 1 and May 15, 

to produce a Glory Hole spill event that results in a 

minimum target release of 3,250 cfs for a one-day 

duration. This event would occur seven times in a 

ten-year period. Flows of this magnitude and duration 

could reactivate various fluvial geomorphic processes to 

re-create and maintain diverse instream and floodplain 

habitat required to support and recover aquatic and 

riparian species. This flow prescription is also required 

in the NMFS OCAP BO.

FY 2014 Accomplishments

In FY 2014, the CCRP obligated $655,000 from the 

Restoration Fund and no funding from the Water and 

Related Resources fund.
CHAPTER 2 - FISHERIES RESOURCE AREA | Clear Creek Restoration Program 3406 (b)(12)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 21

Chinook Salmon Populations - Although the springrun population numbers have been in decline, the 

numbers of spring-run Chinook (SCS) increased from 

8 in 2011 to 68 in 2012, and 652 were observed in 

2013, the highest since monitoring efforts began in 

1998. For 2013, a record number of SCS redds were 

counted (142), which was the 3 times the average of the 

previous ten years.

Gravel Placement (Creation of Spawning Habitat) – 

Spawning gravel was not placed in Clear Creek during 

FY 2013 due to limited funding, however, for 2014, 

about 8,000 tons of gravel were placed at four sites.

The second annual evaluation of spawning gravel 

implementation and monitoring was previously 

submitted to NMFS as a requirement under the OCAP 

BO. As a result of studies in 2011 suggesting that gravel 

sizes specification should be modified in future years to 

improve use by spring Chinook, a new specification was 

developed and implemented for the 2012 injections. 

The FWS conducts on-going monitoring of the 

spawning gravel and documents the areas being used 

by salmonids for spawning. These efforts will evaluate 

the efficacy of the new criteria, and identify whether the 

criteria needs to be adaptively changed. The monitoring 

efforts also provides a scientifically-based basis for 

determining future injection locations and amounts.

Channel Restoration – Phase 3C, the last phase 

of the restoration project, will be considered for 

implementation in future years. FWS and BOR began 

initial efforts to garner funding support from the CVPIA 

program managers, and the approval of the Clear Creek 

Technical Team (CCTT) to begin planning efforts 

for this final phase. The FWS and BOR will start by 

working on the feasibility design aspects of the project. 

Thereafter, FWS and BOR will develop a Performance 

Work Statement to begin the process of securing a 

contractor to work on the NEPA/CEQA environmental 

compliance requirements.

Instream Flows and Temperature of Flows – The 

CCRP met its goal of providing base flows of 200 cfs 

between October 1–May 31. 

The pulse flows conducted in Clear Creek are 

beneficial in attracting salmon and promoting upstream 

movement. In the spring of 2014, two pulse flows 

were provided to help attract spring-run Chinook to 

Clear Creek. The first event (peak of 423 cfs) began on 

April 14, 2014 and ended on April 21, 2014. Scheduling 

complications due to drought contingency operations 

hindered our ability to conduct monitoring during the 

first pulse flow event. The second pulse flow began on 

June 20, 2014, and reached a maximum of 1,110 cfs. 

Pre- and post-flow fish-passage monitoring was 

collected during the second higher flow event, and 74 

spring Chinook were counted prior to the flow event, 

and 123 were counted after the flow event, for a relative 

increase of 66%. Similar flows will occur in future 

years, as directed by the NMFS OCAP BO.

Water temperature targets were only met 70% of the 

time due to reduced diversions from the Trinity River 

Division to the Sacramento River due to widespread 

drought in California. During the spring Chinook 

salmon holding period, targets were met 100% of the 

time, but spawning and incubation period targets from 

September 15 to October 31 were never met.

In 2012, the juvenile salmonid flow habitat 

relationships Instream Flow Incremental Methodology 

(IFIM) draft report was released for peer review. Work 

continued on bio-validation of the models. The resulting 

14 IFIM flow-habitat models is being synthesized 

(integrated) as the “synthesis report” with population, 

temperature, and restoration information in 2012 to 

provide flow prescriptions that optimize habitat needs 

for all species, runs and life stages of salmonids in the 

different reaches of Clear Creek, throughout the year. 

This “synthesis report’ is currently in draft form, and 

upon its completion, the CCTT will provide the report 

and its recommendations to Reclamation. Reclamation 

will then submit their recommendations to NMFS for 

review and approval.

Instream Flows, Environmental Water Program – In 

FY 2011, CCRP entered into contracts to further the 

Environmental Water Program which aims to identify 

and discuss data gaps and uncertainties, understand 

operational tools, identify resources needed, ensure 

safety-of-dams considerations, and mitigate for 

foregone power revenues. Three workshops were 

conducted during FY 2012. During FY 2013, draft 

Technical Memorandum documents were provided to 

the CCRP for initial review. FWS, Reclamation, and 

CDFW will need to complete formal reviews of these 

documents to enable their finalization. During FY14, 

the Core Monitoring and Adaptive Management Plan 

(CMAMP) was completed by Stillwater Sciences. This 

CMAMP document will serve as the monitoring plan 

for the EWP pilot flow release and for longer-term 

monitoring needs of future EWP flow releases. With the 

completion of the CMAMP and eventual review of the 

Technical Memorandums by Reclamation, it is expected 

that Reclamation will begin formal development of the 

NEPA/CEQA process.
CHAPTER 2 - FISHERIES RESOURCE AREA | Clear Creek Restoration Program 3406 (b)(12)

22 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Adaptive Management and Monitoring

Spawning gravel-size specifications improved 

based on monitoring – Past spawning ground surveys 

and spawning habitat suitability surveys identified 

that Chinook were no longer using the spawning 

gravel provided by the program in the reach directly 

downstream of Whiskeytown Dam. Gravel-size 

distributions suggested that only smaller size gravel 

was being delivered to spawning areas due to reduced 

high flows from Whiskeytown Reservoir, and that the 

size specifications being used for restoration in this 

area did not contain enough larger material. Therefore 

gravel size specifications were increased for projects 

implemented in 2012. Further monitoring will be 

needed to complete the adaptive management cycle and 

verify if Chinook use the new gravel. Spawning studies 

conducted by FWS and geomorphic studies conducted 

by Graham Matthews and Associates (GMA) also 

indicated that some spawning gravel projects performed 

better than others. These results were used to improve 

projects conducted in 2012 and to prioritize sites for 

future spawning gravel augmentations. As gravel 

placement did not take place in 2013, future project 

efforts will be monitored to evaluate the efficacy of the 

size criteria which was developed in concert with the 

CCTT. In 2013, GMA completed the final report for 

the 2010-2013 Clear Creek Geomorphic Monitoring 

work. The report contains valuable information that 

confirms the importance of the seasonal pulse flows 

in supporting sediment/gravel transport, and provides 

recommendations on the gravel injection locations, 

tonnage, and injection frequencies. 

Also, GMA re-established a stream gaging station at 

the “P4” location, which provides strategically valuable 

information on stream turbidity and flows in the 

“restoration reach” of lower Clear Creek.

Phase 3b restoration, pedestrian bridge, and 

Lower Clear Creek Aquatic Habitat and Mercury 

Abatement Project (LCCAHMAP; formerly longterm gravel supply project) – In 2013, planning 

activities continued to obtain permits to conduct 

decommissioning of roads used during habitat 

restoration activities within the Phase 3B areas, 

and planting riparian and upland areas. The future 

decommissioning of roads will reduce the amount of 

habitat fragmentation. Also, the Horsetown pedestrian 

bridge was completed. The LCCAHMAP made notable 

progress during 2014, with the completion of the final 

EA/EIS. The Initial Study-EA/EIS underwent review 

in the State “Clearinghouse” by trust agencies, and the 

public, and several comments were received. Presently, 

a Biological Asssessment for the LCCAHMAP is under 

preparation. Final environmental compliance permits 

and consultation with NOAA Fisheries are anticipated 

to be completed during latter 2014.

The Long-term Programmatic Permits project also 

made substantial progress in FY 2014. A Biological 

Opinion was issued by NOAA-Fisheries, and an Initial 

Study/Mitigated Negative Declaration (IS/MND) 

document was submitted to the State “Clearinghouse” 

for review. Minor comments were received and the 

CEQA lead agency, the California Regional Water 

Quality Control Board (CRWQCB) is expected to 

formally adopt the IS/MND in the fall of 2014.

Monitoring the impacts of wildfire will guide erosion 

control – The aforementioned 2008 wildfire in the 

South Fork Clear Creek tributary, and subsequent 

salvage logging and road building contributed to 

a significant instream sediment problem. These 

observations led to topographic surveys to quantify the 

amount of fine sediment delivered to the creek, bulk 

sampling to estimate changes in sediment size, and 

snorkel surveys to locate the downstream extent of sand 

deposition in pools. These actions indicated that the fine 

material has been progressively moving downstream 

and out of the Clear Creek system. It appears possible 

that the amount of fine sediment has been decreased, 

perhaps by the multiple pulse flows that have occurred 

since the fire. Since the 2008 fires, the juvenile 

productivity of steelhead and spring and fall Chinook 

had decreased, although it is was not understood why. 

Recent monitoring by the FWS has indicated that 

productivity of juvenile salmonids may be increasing. 

Since the recent 2012 Dale Fire, and the Clover Fire 

of 2013, monitoring efforts need to continue in Clear 

Creek system to guide future restoration actions. 

Fish and geomorphic monitoring results may 

improve future pulse flows – Results of past and 

recent pulse flows suggested that higher flows would 

provide more favorable geomorphic outcomes. In 

addition, it was determined that higher flows could 

have been provided without impacting the ability 

of the Clear Creek Community Services District to 

receive water. The CCTT has assisted in adaptively 

modifying pulse flows in an effort to move more 

sediment downstream, as well as attracting Spring-run 

Chinook and stimulating their upstream movement. 

Therefore in 2013, and 2014, both higher and lower 

pulse flows were provided. The Clear Creek Technical 

Team requested that NOAA-Fisheries modify the 

OCAP RPA I.1.1 to provide more flexibility and aid in 

adaptive management. The proposal would allow the 

Clear Creek Technical Team to recommend to NOAAFisheries and Reclamation, changes in the timing, 

magnitude and duration of the spring attraction flows to 
CHAPTER 2 - FISHERIES RESOURCE AREA | Clear Creek Restoration Program 3406 (b)(12)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 23

better meet objectives of the Clear Creek RPA actions, 

additional ecosystem goals, operational constraints, and 

adaptive management. This proposal was prompted by 

the results from on-going fish, geomorphic, avian and 

riparian monitoring.

Fish Population Monitoring Suggests Program 

Success – Monitoring continues to document the 

overall success of the Clear Creek Restoration Program. 

No other Central Valley watershed has survived the 

Chinook fishery collapse nearly as well as Clear 

Creek. This may be due to increased resilience of the 

watershed due to CVPIA’s habitat restoration. In 2011, 

fall-run Chinook escapement was 4,841 compared to 

the average baseline escapement of 1,689 between 

1967 and 1991. Escapement appeared lower in 2011 

than in the previous 10-years (average of 8,825), in 

part because the method for estimating escapement 

was changed. The 2012 fall-run estimate was 7,631. 

The 2013 escapement was an impressive 13,337; 

approaching double the AFRP production target (7,100) 

for Clear Creek. 

In addition, populations of threatened spring-run 

Chinook and steelhead have been re-established 

in the Clear Creek watershed. The recent CDFW 

Central Valley Steelhead Monitoring Plan and Central 

Valley Chinook Monitoring Plan recommended that 

a counting weir be used in Clear Creek to monitor 

adult populations of salmon and steelhead. In 2012 

CVPIA partnered with CDFW to build and install a 

fish counting weir in Clear Creek near the confluence 

with the Sacramento River. The weir was in operation 

during 2013 by CDFW, using video and DIDSON 

sonar technology for fish counts. The CDFW GrandTab spring-run estimate for 2013 was 659, the highest 

count recorded in Clear Creek. Also, as previously 

noted, a record 142 SCS redds were counted in 2013. In 

2014, the steelhead redd index was 328, which is 67% 

higher than the 10-year average. In addition, 68% of all 

steelhead redds were found in injected gravels, which 

represents a doubling of the steelhead redds over the 

past 12 years.

Whiskeytown Oak Bottom Temperature Control 

Curtain (OBTCC) – The OBTCC has deteriorated in 

recent years and is no longer functional. Reclamation 

will be removing the OBTCC during the fall of 

2014. To date, there are no definitive plans for the 

replacement of the OBTCC, although it is anticipated 

that Reclamation will be listing the replacement action 

in its RAX (replacement, addition, and extraordinary) 

system.

The (b)(12) program also supported the development 

of the inSALMO Salmon Model Project, which was 

completed in FY 2014, and a peer reviewed paper was 

produced in the Canadian Journal of Fisheries and 

Aquatic Science, “Facultative anadromy in salmonids: 

linking habitat, individual life history decisions, and 

population-level consequences”. This paper was 

prepared by Steven F. Railsback, Brett C. Harvey, and 

Jason L. White.
CHAPTER 2 - FISHERIES RESOURCE AREA | Spawning and Rearing Habitat Restoration Program 3406 (b)(13)

24 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Spawning and Rearing Habitat 

Restoration Program 3406 (b)(13)

In a free-flowing river, rocks, gravel, dirt and other 

substrates are continually moving downstream, 

providing suitable habitat for successful spawning and 

juvenile rearing. The construction of CVP dams has had 

a dramatic impact on streams by impeding this natural 

process. 

The (b)(13) program represents a continuous effort to 

restore spawning and rearing habitat in three Central 

Valley streams:

• Upper Sacramento River, from Keswick Dam to 

the Red Bluff Diversion Dam

• American River downstream of Nimbus Dam 

• Stanislaus River downstream of Goodwin Dam

The Spawning and Rearing Habitat Program (SRHP) 

focuses on sites that are thought to have the most 

potential to increase the quality and quantity of 

spawning and rearing habitat. Two criteria guide the 

identification of gravel placement sites: the need for 

spawning and rearing habitat; and accessibility to the 

river by heavy equipment, helicopter or sluice to deliver 

gravel or modify the channel.

Aerial photos, redd (fish egg “nests”) surveys, snorkel 

surveys and boat surveys are used to identify areas 

for gravel augmentation. Prior to placing gravel or 

improving rearing habitat, baseline data is collected 

using aerial photos, topographic surveys, spawning 

surveys and rearing surveys. Once the projects are 

implemented, the SRHP monitors the spawning and 

rearing occurring at and near the restored sites and 

makes comparisons to pre-project conditions and 

control sites to determine the program’s effectiveness. 

The SRHP relies on other river-wide monitoring to 

evaluate population level effects. This consists of adult 

escapement surveys (all Reclamation funded) conducted 

by the California Department of Fish and Wildlife 

(CDFW) in the Sacramento, American and Stanislaus 

rivers; juvenile production monitoring conducted 

by FWS in the Sacramento River (Reclamation 

funded), FWS and the Pacific States Marine Fisheries 

Commission in the American River (CVPIA funded), 

and private contractor in the Stanislaus River (CVPIA 

funded). Adult escapement and juvenile production 

monitoring provides information on the number of 

juvenile emigrants produced per spawner.

Performance Measures

The SRHP places gravel in the Sacramento, Stanislaus 

and American rivers on an annual basis to improve 

spawning and rearing habitat (see Table 11). The annual 

program targets for gravel placement are 10,000 tons 

on the Sacramento River, 3,000 tons on the Stanislaus 

River, and 7,000 tons on the American River. 

The program monitors the effectiveness of gravel 

placement by surveying for several indicators. The 

number of redds per square meter indicates whether 

salmon find the gravel appropriate for spawning (0.03 

redds/square meter is a standard guideline). The level 

of egg retention in females indicates whether fish 

are successfully finding suitable sites to spawn and 

are spawning (less than 10% retention is a standard 

guideline). The percentage of salmon using emplaced 

gravel indicates whether the program is providing 

habitat that is suitable (the program aims for 10% on 

the Stanislaus River and 25% on the Sacramento and 

American rivers).

FY 2014 Accomplishments 

In FY 2014, the SRHP obligated $500,000 from the 

Restoration Fund and $683,000 from Water and Related 

currently accounted for under Bay Delta Activities.

Sacramento River

In 2014, the program continued work on permitting 

new sites for placing gravel and providing enhanced 

rearing habitat. No gravel has been placed in 2014. A 

significant stockpile of nearly 30,000 tons of gravel 

remains just below Keswick Dam awaiting higher flows 

to distribute the material downstream. Redd surveys 

funded separately by Reclamation showed that 71% 

of the winter-run Chinook salmon spawning occurred 

upstream of the Anderson Cottonwood Irrigation 

District diversion dam in 2014. This is the reach 

affected by gravel injections at Keswick Dam and the 

section of river with the coolest water to support egg to 

fry survival.

Stanislaus River

In 2014, no projects were implemented by the program 

in the Stanislaus River. Monitoring conducted by the 

program consisted of redd surveys and surveys of 

downstream movement of previously placed gravel 

During redd surveys in November and December of 

2013, 242 Chinook salmon redds were mapped on the 

gravel placed in Goodwin Canyon at the float tube pool 

and cable crossing sites and 54 redds were mapped on 

the Knights Ferry placement sites. The peak river-wide 

redd counts on the days that redd mapping occurred 

totaled 1,261 redds. The redds on these sites made up 

23% of the river-wide count. In addition, high densities 

of rearing juvenile rainbow trout/steelhead, a threatened 

species in the Stanislaus, were documented rearing at 

the Goodwin gravel placement sites during snorkel 

surveys throughout the year. The primary source of 

gravel to Goodwin Canyon since Goodwin Dam was 
CHAPTER 2 - FISHERIES RESOURCE AREA | Spawning and Rearing Habitat Restoration Program 3406 (b)(13)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 25

built has been the recent gravel placements (over the 

last 15 years or so) so the cumulative movement of 

this material can be visually monitored with snorkel 

surveys in the canyon. A 2013 survey showed gravel 

accumulations creating spawning habitat 0.2 mile 

downstream of the placement reach. No gravel has 

reached the downstream end of the large pool at the 

old stream gauge site located 0.5 mile downstream of 

the gravel placement site and one mile downstream of 

Goodwin Dam.

American River

In 2014, the SRHP placed 10,000 tons of gravel and 

created 400 yards of side channel habitat in Nimbus 

Basin, directly below Nimbus Dam. The gravel 

placement represented 143% of the annual target of 

7,000 tons. This project was funded by SRHP and 

AFRP and included participation by multiple agencies 

including Reclamation, Fish and Wildlife Service, 

the Water Forum, City of Sacramento, CDFW, and 

Sacramento County Regional Parks. The project 

included a designed channel spanning gravel placement 

(creating approximately 7,200 square yards of improved 

spawning habitat) and created a side channel with 

floodplain habitat to provide Chinook and steelhead 

spawning and rearing habitats designed to be usable 

over a range of flows. Woody debris was installed in 

the channel to enhance rearing habitat for juvenile 

salmonids. 

The program continued development of a decisionsupport model using the Structured Decision Making 

approach to help determine the most efficient use of 

management resources to maximize the number and 

condition of juvenile salmonids leaving the American 

River. We improved on the predictive model created in 

FY12 by quantifying the model functions using data 

and empirical models and will continue to update the 

model through focused project monitoring. The finished 

model is intended to be used as a decision support tool 

to assist in prioritization of sites for restoration (inchannel, side channel, and floodplain) and the type of 

restoration action (gravel injection, gravel placement, 

in-channel or out-of-channel rearing habitat restoration) 

that will provide the greatest benefit to increase the 

number of juvenile outmigrants. 

Monitoring, using a before-after control-impact 

framework, was conducted to evaluate the effectiveness 

of the projects including: hyporheic water chemistry, 

flow and temperature; gravel movement and river bed 

changes; Chinook and steelhead spawning habitat 

use; juvenile salmonid habitat preferences; macro 

invertebrate production; and floodplain inundation.
CHAPTER 2 - FISHERIES RESOURCE AREA | Spawning and Rearing Habitat Restoration Program 3406 (b)(13)

26 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Sacramento 

River 

(10,000 Ton 

Target)

%

Target

Stanislaus 

River

(3,000 Ton 

Target)

%

Target

American 

River

(7,000 Ton 

Target)

%

Target

1997 31,000 310 2,000 67 0

1998 23,000 230 3,000 100 0

1999 25,000 250 0 6,000 86

2000 32,000 320 1,300 43 0

2001 0 500 17 0

2002 15,000 150 4,000 133 0

2003 8,800 88 0 0

2004 8,500 85 1,200 40 0

2005 7,200 72 2,500 83 0

2006 6,000 60 2,500 83 0

2007 6,000 60 4,100 137 0

2008 8,300 83 0 7,000 100

2009 9,900 99 0 10,600 151

2010 5,500 55 0 16,000 229

2011 5,000 50 5,000 167 20,770 297

2012 15,00 150 3,000 100 24,510 350

2013 14,000 140 0 6,000 86

2014 0 0 10,000 143

TOTAL 220,000 130 29,100 54 100,880 80

Table 7. Gravel Placed by Year in CVP Streams, and Percent of Target, 1997-2014
CHAPTER 2 - FISHERIES RESOURCE AREA | Comprehensive Assessment and Monitoring Program 3406 (b)(16)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 27

Comprehensive Assessment and 

Monitoring Program 3406 (b)(16)

Pursuant to CVPIA section 3406 (b)(16), the 

Comprehensive Assessment and Monitoring Program 

(CAMP) was established to assess the biological results 

and effectiveness of actions implemented by CVPIA in 

support of the AFRP’s fish production targets. CAMP 

produces annual reports that compile and synthesize 

anadromous fish production data from the Central 

Valley. These data are used to assess the effectiveness 

of habitat restoration actions such as water management 

modifications, structural modifications, habitat 

restoration, and fish screens. CAMP annual reports 

provide data for 22 Central Valley watersheds, and a 

broader area that includes San Pablo Bay, Suisun Bay, 

and the Sacramento-San Joaquin River Delta.

The CAMP depends on other programs and agencies 

that provide information that the CAMP then 

synthesizes and summarizes in its annual report. 

To optimize its program budget, CAMP works with 

partners whenever possible to complete high-priority 

monitoring projects.

The CAMP Implementation Plan was developed 

in 1997. That document describes methods for 

monitoring nine anadromous fish taxa in California’s 

Central Valley, and provides procedures for assessing 

the biological results and effectiveness of different 

categories of restoration activities. The nine 

anadromous fish taxa in the Plan are: Chinook salmon 

(fall-, late-fall-, winter-, and spring-run), steelhead, 

striped bass, American shad, white sturgeon and green 

sturgeon.

CAMP focuses on three program objectives:

• Objective #1 – Assess the overall effectiveness 

of actions implemented pursuant to CVPIA 

section 3406(b) in meeting AFRP fish production 

targets.

• Objective #2 – Assess the relative effectiveness 

of categories of CVPIA section 3406 (b) 

actions (e.g., water management modifications, 

structural modifications, habitat restoration, 

and fish screens) toward meeting AFRP fish 

production targets.

• Objective #3 – Establish a data management 

program to manage CVPIA data (a resource 

available to all interested parties), provide 

training in data management, ensure compliance 

with relevant federal laws and regulations, and 

ensure the effective and economical management 

of resources.

Performance Measures

The CAMP has one performance measure. That 

measure requires that the program produce one report 

each year.

The CAMP Implementation Plan identifies 82 

monitoring elements that are required to assess progress 

toward the AFRP fish production targets (CAMP 

Objective #1). The Plan also provides a framework 

to assess the biological response to, and effectiveness 

of, restoration actions (CAMP Objective #2). The 

program’s goals have recently been expanded to 

consolidate, standardize, and enhance the collection 

of data related to the CVP ecosystems (CAMP 

Objective #3).

FY 2014 Accomplishments

In FY 2014, the CAMP received $3,137,000 from 

the Restoration Fund and $2,531,000 from Water and 

Related.

The CAMP accomplishments that were completed in 

FY 2014 are listed below; the accomplishments have 

been grouped according to the three CAMP objectives. 

For the CAMP-funded projects where a report was 

completed, the reports can be accessed on the CAMP 

website at: http://www.fws.gov/sacramento/Fisheries/

CAMP-Program/Documents-Reports/Documents/2014_

CAMP_Annual_Report.pdf.

CAMP Objective #1

CAMP Annual Report

CAMP produced its 2014 annual report assessing the 

overall effectiveness of actions implemented pursuant 

to CVPIA section 3406(b) in meeting AFRP fish 

production targets.

Constant Fractional Marking Program

Marking and tagging of juvenile fall-run Chinook 

salmon at the Nimbus Fish Hatchery and Coleman 

National Fish Hatchery was completed during the 

spring of 2014. A report describing this activity is 

being developed and will be posted on the CAMP 

website when it is finalized. The data from the marking 

and tagging program is used to quantify the relative 

proportion of hatchery vs. wild adult Chinook salmon 

observed during escapement surveys, which in turn 

leads to the development of more accurate natural 

production estimates for Chinook salmon.

Quantify Escapement of Adult Steelhead and 

Spring-run Chinook salmon on Battle Creek

Escapement levels of adult steelhead and springrun Chinook salmon in Battle Creek at the Coleman 

National Fish Hatchery weir in late fall, 2013, were 
CHAPTER 2 - FISHERIES RESOURCE AREA | Comprehensive Assessment and Monitoring Program 3406 (b)(16)

28 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

monitored. A report documenting the results of that 

activity will be produced in 2014.

Quantify Escapement of Adult Winter-run Chinook 

Salmon on the Sacramento River

Escapement levels of adult winter-run Chinook salmon 

in the Sacramento River in 2014 were monitored. A 

report documenting the results of that activity will be 

produced in 2014 or 2015.

CAMP Objective #2

CAMP Rotary Screw Trap Platform

Development of the CAMP RST Platform continued 

in 2014. The Platform is now able to produce juvenile 

Chinook salmon production estimates from the 

American River, Stanislaus River, and Feather River. 

Data from the Mokelumne River and Sacramento River 

at the Red Bluff Diversion Dam have been imported 

into the Platform and are being modified so they can be 

analyzed with the Platform’s analytical routines.

Monitor Juvenile Chinook Salmon Production on 

the Stanislaus River at Caswell State Park

Rotary screw traps were operated at Caswell State Park 

on the Stanislaus River during the 2014 rotary screw 

trap field season. A report documenting those operations 

will be completed in the fall of 2014.

Monitor Juvenile Chinook Salmon Production on 

the American River

Rotary screw traps were operated on the American 

River during the 2014 rotary screw trap field season. A 

report documenting those operations will be completed 

in the fall of 2014.

Monitor Juvenile Chinook Salmon Production on 

Battle Creek

Rotary screw traps were operated on Battle Creek 

during the 2014 rotary screw trap field season. A report 

documenting those operations will be completed at 

some future date.

Monitor Juvenile Chinook Salmon Production on 

the Sacramento River at the Red Bluff Diversion 

Dam

Rotary screw trap operations on the Sacramento River 

at the Red Bluff Diversion Dam were conducted during 

FY 2014. An annual report documenting those results 

will be developed in 2015.

Sacramento River/San Joaquin River Delta Juvenile 

Chinook Salmon Delta Survival Study

Juvenile Chinook salmon were tagged with acoustic 

tags and released to assess their survival through 

different portions of the Sacramento River/San Joaquin 

River Delta. The results will be documented in a 

forthcoming report, and quantify salmon survival in 

context with the historic drought currently occurring in 

the state of California. 

CAMP Objective #3

Performance Goals and Accomplishments

The storage media used to document various program 

goals and annual accomplishments was converted from 

a Microsoft Excel spreadsheet format to an Access 

database format in 2014. That conversion is expected 

to markedly improve the ability to track and analyze 

annual accomplishments across multiple years because 

the ability to query data from a single media (data 

source) has been created.

Develop a Science Based Management Framework

Staff from the U.S. Geological Survey finished 

developing a computerized tool and a framework in 

2014 that will be used to: (1) revisit CVPIA Program 

objectives and performance measures with State 

and Federal agencies as well as other stakeholders. 

Reframe the objectives and performance measures 

where appropriate, with explicitly stated hypotheses 

with measurable criteria; (2) update/develop a systemwide conceptual/quantitative model for an area that 

includes the Bay-Delta and Central Valley headwater 

tributaries to help guide Program decisions; (3) reassess 

monitoring and evaluation efforts within the context of 

revised objectives and a system-wide model; and (4) 

incorporate scientific reviews into the organizational 

structure of the Program to evaluate the Program’s 

progress. 
CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Screen Program 3406 (b)(21)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 29

Anadromous Fish Screen Program 

3406 (b)(21)

The Anadromous Fish Screen Program (AFSP) works 

together with the State of California to construct, 

replace and rehabilitate fish screens throughout the 

Central Valley and Sacramento-San Joaquin Delta. 

The AFSP strives to improve the effectiveness and 

efficiency of fish screens, and collaborates with other 

agencies to encourage the dissemination of fish screen 

related information. The program also seeks to reduce 

the overall cost of fish screens. These efforts support 

the CVPIA fish doubling goal by protecting juvenile 

Chinook salmon, steelhead, and green sturgeon from 

entrainment at priority water diversions. 

The AFSP can provide matching cost share funds for 

state and local funding, providing up to 50% of the cost 

of a fish screen project. The AFSP conducts monitoring 

at many diversions and fish screens to determine the 

critical factors related to fish losses, and to assure 

the effectiveness of constructed fish screens. Fish 

screen projects are often complex and are sometimes 

constructed in phases over several years. The three 

key project phases include feasibility, design, and 

construction. Once a screen is constructed, the diverter 

is solely responsible for its ongoing operation and 

maintenance.

Performance Measures

The AFSP’s key performance measure is to assist the 

State of California in developing and implementing 

measures to avoid juvenile anadromous fish losses 

resulting from unscreened or inadequately screened 

diversions. This is accomplished primarily by 

installation of fish screens. Progress is measured in 

the number of fish screens constructed, with a target 

of screening the priority unscreened diversions on 

prescribed watersheds. The AFSP and the State of 

California have conducted fish entrainment monitoring 

at representative unscreened diversions on the 

Sacramento River to evaluate potential fish screening 

benefits and to help determine the highest priority 

diversions for screening.

FY 2014 Accomplishments 

The AFSP obligated funding from the Restoration Fund 

in the amount of $2,346,000, along with $768,000 

from Bay-Delta funds and $3,175,000 from Water and 

Related funds. 

Screening Diversions

Construction was completed on the Yuba City Fish 

Screen for a 74 cfs diversion on the Feather River. 

This screen consisted of an inclined flat-plate fish 

screen with an air-burst cleaning system. In addition, 

fish screens were installed for the north (78 cfs) and 

south (40 cfs) Feather Water District diversions on the 

Feather River. These screens are located near the west 

bank of the river and are cleaned using an external 

rotating brush. All three of the completed screens on 

the Feather River provide protection for out-migrating 

Chinook salmon, steelhead and green sturgeon as well 

as resident fish. 

Fish screen construction was initiated for the Natomas 

Mutual Water Company’s Pritchard Lake Diversion 

(150 cfs) and Reclamation District 2035/Woodland 

Davis Clean Water Agency Joint Intake (400 cfs) on the 

Sacramento River. These fish screens are targeted for 

completion in 2015 and 2016, respectively. In addition, 

the AFSP continued to support design, environmental 

compliance and permitting activities for the following 

fish screen projects: Colusa Indian Community Council 

Compton Diversion (22 cfs) on the Sacramento River; 

South Sutter Water District Pleasant Grove Canal 

diversion (80 cfs) on Auburn Ravine, and the West 

Stanislaus Irrigation District Joint Use Intake (375 cfs) 

on the lower San Joaquin River.

See Table 8 for fish screen projects constructed, by 

watershed, using AFSP cost share funding.

Table 8: AFSP Projects by Watershed

and Cubic Feet per Second (cfs) Screened, 

1994-2014

Watershed

Number of

 Fish Screens

Flow

(cfs)

Sacramento 26 4,783

American 1 310

Feather 3 192

Yuba 1 65

Butte 4 257

Delta 7 137

San Joaquin 2 455

TOTAL 44 6,199
CHAPTER 2 - FISHERIES RESOURCE AREA | Anadromous Fish Screen Program 3406 (b)(21)

30 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

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CHAPTER 3 - WATER MANAGEMENT | Contract Renewals 3404 (c)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 31

CHAPTER 3 - WATER MANAGEMENT

Purposes of the CVPIA included improving the 

operational flexibility of the CVP and increasing 

the water-related benefits provided by the CVP 

through voluntary water transfers and improved 

water conservation as well as providing for fish and 

wildlife. Section 3404(c) of the Central Valley Project 

Improvement Act (CVPIA or Act) authorized and 

directed the Secretary to renew repayment and water 

service contracts for the delivery of water from the 

Central Valley Project (CVP). Prior to the passage 

of the CVPIA, the ability for Central Valley Project 

(CVP) water contractors to transfer water supplies 

depended upon their individual authorizations and 

contracts. Section 3405 of the Act authorized transfers 

for all water service, water repayment, and settlement 

contracts, at the time of the passage of the Act, to both 

CVP and non-CVP customers and established criteria 

for water transfers. Specific provisions within Section 

3406(b) provide for water releases and management to 

support fisheries and the acquisition of additional water.

Contract Renewals 3404 (c)

All interim and long-term contracts have been renewed. 

These include 100 long term renewal contracts and 28 

interim-renewal contracts have been executed within 

the various divisions of the CVP. 132 long term 

contracts have been renewed with the Sacramento 

River Water Right Settlement contractors and 1 is 

pending renewal upon expiration in July 2020. Long 

term execution of the interim-renewal contracts and the 

remaining unexpired contracts is pending completion of 

final biological opinions required to support operation 

of the CVP. Reclamation will continue to implement 

interim contract renewal consistent with CVPIA until 

such time that all environmental requirements have 

been satisfied, including the completion of a new 

biological opinion on the overall operations of the CVP, 

upon which time, Reclamation intends to complete long 

term contract renewal.
CHAPTER 3 - WATER MANAGEMENT | Water Transfers 3405

32 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Water Transfers 3405

Water transfers are a means by which water supplies 

under contract can be reallocated from one user to 

another on a short term or long term basis, to assist 

in meeting existing and future water needs within 

California. Water transfers create flexibility in the place 

and timing of water deliveries that sustain agriculture, 

municipal and industrial health and safety and provide 

environmental and recreational benefits. Section 3405 

authorizes individuals and districts who held a contract 

at the time of the Act to transfer all or a portion of that 

water to other users within the state for any purpose 

recognized as beneficial under state law, subject to 

certain terms and conditions. 

The CVPIA adopted the transfer criteria under 

section 1725 of the California water code including 

requirements for historic use, section 3405(a)(1)(A) 

and a reduction in consumptive use, section 3405(a)(1)

(I). Additionally, section 3405(a)(1)(M) determined 

that transfers between CVP contractors within a basin 

shall be deemed to meet historic and consumptive use 

provisions. Section 3405(a)(1)(M) provides the basis 

for the Accelerated Water Transfer Program (AWTP).

Reclamation approved a total of 23,000 acre-feet of 

CVP water in fiscal year 2014. Table 9 shows historical 

transfers from 2012 through fiscal year 2014.

Table 9. Water Transfers under the CVPIA between 2012 and Fiscal Year 2014 (acre-feet)

Year

Sacramento 

Basin AWTP

DeltaMendota 

Canal 

AWTP

Friant 

Division 

AWTP

North of 

Delta to 

South of 

Delta

South of 

Delta NonAWTP Refuges

2012 64,866 121,239 71,311 0 25,000 38,480

2013 95,716 68,822 108,037 0 92,171 26,756

2014 22,292 6,871 11,721 83,037 106,545 0
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 33

CHAPTER 3 - WATER MANAGEMENT | Dedicated 800,000 acre-feet Project Yield 3406 (b)(2)

Dedicated 800,000 acre-feet Project 

Yield 3406 (b)(2)

CVPIA authorizes a portion of the CVP project yield 

to be dedicated and managed for the benefit of fish and 

other wildlife. Interior has the responsibility to annually 

dedicate and manage up to 800,000 AF of CVP (b)(2) 

water for fish, wildlife and habitat restoration purposes. 

This water includes both CVP releases and decreased 

CVP export pumping, relative to a hypothetical preCVPIA baseline operation. This accounting is applied 

specifically to 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. The 

management of (b)(2) water is partially informed by the 

Anadromous Fish Restoration Plan (AFRP) developed 

per Section (b)(1), and the results of Instream Flow 

Incremental Methodology (IFIM) studies, undertaken as 

part of Section (b)(1)(B), which identify optimal flow, 

temperature needs, and timing for the life stages of 

anadromous fish.

The Dedicated Yield Program (DYP) actions affecting 

fish fall into the following categories: 

• Instream flow augmentations on CVP-controlled 

streams intended to protect salmon and 

steelhead, as well as contribute toward meeting 

Anadromous Fish Restoration Program (AFRP) 

Final Restoration Plan flow objectives

• Increased releases from Goodwin Reservoir 

to help meet the Water Quality Control Plan 

(WQCP) requirements for San Joaquin River 

flows at Vernalis for fish and wildlife standards

• Increased releases from Keswick and/or Nimbus 

reservoirs to help meet the WQCP fish and 

wildlife standards

• Export reductions at the CVP Jones pumps to 

protect at-risk fish species, notably salmon, 

steelhead and delta smelt, and to help meet the 

WQCP Delta standards

Performance Measures

Annual contribution – Reclamation annually contributes 

up to 800,000 AF of water from CVP facilities. In 

dry years, the target is reduced by up to 100,000 AF. 

In critically dry years, the target is reduced by up to 

200,000 AF.

Contribution to fisheries habitat goal – The 800,000 

AF of water contributes towards the 1,000,000 AF 

fishery habitat goal. The Section (b)(3) Instream Water 

Acquisition Program contributes the balance, up to 

200,000 AF, towards this goal, as described in the 

CVPIA record of decision (ROD).

FY 2014 Accomplishments 

The program obligated $493,000 from the Restoration 

Fund in FY 2014. 

The Water Year (WY) type is a designation that is 

based on hydrologic indices for the Sacramento and 

San Joaquin Valleys. Water Year type is either Wet, 

Above Normal, Below Normal, Dry or Critical. Water 

year type is largely determined by precipitation and is 

therefore indicative of local and regional conditions that 

influence climate, snowpack and runoff. 

WY 2014 has been one of the driest in decades and 

follows two consecutive dry years throughout the state. 

This three year period has set a new record for low 

statewide precipitation accumulation totals in the 

historical record, which has manifested in very low 

reservoir levels and dry soil.

The final WY 2014 classification was Critical for both 

the Sacramento Valley and the San Joaquin Valley. 

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

Interior’s May 2003 (b)(2) Policy, the total (b)(2) water 

allocation was 600 thousand acre feet (TAF) during 

the 2014 water year. However, due to these historically 

dry hydrological conditions, Interior was only able to 

make approximately 400,000 AF of the 600,000 AF of 

CVPIA (b)(2) water available. The specific uses and 

locations are shown in Table 11.

This program activity partially funds real-time fish 

monitoring which informs when and where fish actions 

should be taken. On a weekly basis, fishery biologists 

from the Sacramento, San Joaquin and Delta regions 

report on fish movements to a B2 Interagency Team 

(Team). The Team, including fishery biologists from 

FWS, USBR, NOAA, CDFW, and DWR, evaluate the 

data and collaboratively decide where to apply CVPIA 

(b)(2) water. Interior provides detailed accounting of 

(b)(2) fish actions at http://www.usbr.gov/mp/cvo.
34 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 3 - WATER MANAGEMENT | Dedicated 800,000 acre-feet Project Yield 3406 (b)(2)

Table 10: Allocation Target and Use of (b)(2) Water, 2001-2014

Year

Water Year 

Type*

Allocation of (b)(2) Water

-------------------------------

(b)(2) Allocation Target

(acre-feet)

Use of (b)(2) Water

------------------------

Allocated

Flow** (acre-feet)

Use of (b)(2) Water 

-------------------- 

Unused**

(acre-feet)

Use of (b)(2) Water 

--------------------

Banked

(acre-feet)

2001 Dry 800,000 798,000

2002 Dry 800,000 793,000

2003 Above Normal 800,000 796,000

2004 Below Normal 800,000 800,000

2005 Above Normal 800,000 672,000 128,000

2006 Wet 800,000 422,000 183,000 195,000

2007 Dry 800,000 798,000

2008 Critical 600,000 600,000

2009 Dry 600,000 600,000

2010 Below Normal 800,000 800,000

2011 Wet 800,000 348,800 451,200

2012 Below Normal 800,000 800,000

2013 Dry 700,000 700,000

2014*** Critical 600,000 600,000

* Water Year Type is based on the Sacramento Valley Index.

** 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 finding by the Secretary, the Secretary is authorized to make such water available for other 

project purposes.

*** 2014 water data is estimated.

River Action Timeframe Results

American (b)(2) water used 

to provide spring 

outmigration pulse flows

Mar – Apr 2014 Contributed toward AFRP Final Restoration 

Plan flow objectives and provided pulse flows 

for juvenile steelhead and fall-run Chinook 

rearing and outmigration.

Clear Creek (b)(1) and (b)(2) water 

used to augment 

would-be base flows 

throughout water year 

2013

Nov 2013 – Apr 2014 Contributed to AFRP Final Restoration 

Plan flow objectives and improved instream 

conditions for fall-run Chinook, spring-run 

Chinook and steelhead during spawning, 

incubation, rearing and downstream 

migration.

(b)(2) water was used to 

provide short pulse flows

Apr and Jun 2014 Contributed to AFRP Final Restoration Plan 

flow objectives and provided pulse flow to 

attract adult spring-run Chinook salmon to 

suitable spawning areas.

Sacramento None N/A N/A

Stanislaus (b)(2) water used to 

provide a fall attraction 

pulse flow, two winter 

instability pulse flows, 

and spring outmigration 

pulse flow

Oct – Nov 2013 

Jan – Feb 2014 

Apr - May 2014

Contributed toward AFRP Final Restoration 

Plan flow objectives and provided pulse 

flows for adult fall-run Chinook and steelhead 

attraction, juvenile steelhead and fall-run 

Chinook rearing and outmigration, and 

steelhead juvenile rearing.

CVP Jones 

Pumping Plant

(b)(2) water used to 

reduce CVP exports 

pursuant to both the 

NMFS BO and the 

SWRCB WQCP

Nov - Dec 2013 

Feb – Apr 2014

Benefitted outmigrating salmon and steelhead 

smolts and pre-spawning adult delta smelt 

within the lower Sacramento and San Joaquin 

Rivers and Sacramento-San Joaquin Delta.

Table 11: FY 2014 Use of (b)(2) Water by Location
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 35

CHAPTER 3 - WATER MANAGEMENT | Water Acquisition Program – Instream Water 3406 (b)(3)

Water Acquisition Program – 

Instream Water 3406 (b)(3)

The Water Acquisition Program – Instream Water 

(WAP-Instream) acquires water to supplement the 

800,000 acre-feet (AF) of CVP yield that is dedicated 

to fisheries. The increased instream flows benefit 

numerous resident and anadromous fish species, but 

primarily benefit Central Valley Chinook salmon, the 

majority of salmon produced in California. 

Water acquisition for CVPIA-designated refuges and 

wildlife management areas is discussed in Section 3406 

(d)(2), Refuge Water Supply Program (RWSP).

Performance Measure

Acquire up to 200,000 AF per year to supplement the 

800,000 AF dedicated from CVP yield to meet the 

fisheries flow objective of 1,000,000 AF (per ROD, 

CVPIA Final PEIS, Jan 2001).

FY 2014 Accomplishments 

In FY 2014, $215,000 was obligated for the purpose 

of administering the program. Prior year funds from 

Water and Related were deobligated. Due to the severe 

drought no water was acquired this year.

Central Valley rivers and streams were defined in the 

January 9, 2001, Final Restoration Plan (FRP) for the 

AFRP as all rivers, streams, creeks, sloughs and other 

watercourses, regardless of volume and frequency 

of flow, that drain into the Sacramento River basin, 

the San Joaquin River basin downstream of Mendota 

Pool, or the Sacramento-San Joaquin Delta upstream 

of Chipps Island. The 22 rivers and streams are 

specifically called out within Appendix B of the FRP 

and are listed in Appendix B of this report.

The anadromous fish production targets pertain 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.

Table 12. Annual (b)(3) Instream Water Acquisitions, Toward 200,000 Acre-Feet Target, 

1994-2014

Year AF Acquired

% of 200,000 

AF Target

1994 76,441 38

1995 0 0

1996 16,161 8

1997 155,983 78

1998 80,000 40

1999 224,498 112

2000 108,880 54

2001 109,785 55

2002 68,105 34

2003 91,526 46

2004 98,211 49

2005 38,500 19 

2006 38,500 19

2007 114,645 57

2008 106,490 53

2009 38,500 19

2010 62,480 31

2011 38,500 19

2012 25,714 13

2013 0 0

2014 0 0

Average 71,091 36
36 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 3 - WATER MANAGEMENT | Water Acquisition Program – Instream Water 3406 (b)(3)

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Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 37

CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Water Supply Program 3406 (d)(1), (2) & (5)

CHAPTER 4 - REFUGES RESOURCE AREA

Refuge Water Supply Program 

3406 (d)(1), (2) & (5)

The Refuge Water Supply Program (RWSP) is 

comprised of three components: 

• 3406 (d)(2) Refuge Water Acquisition – 

Acquisition of Incremental Level 4 quantities 

specified in 3406 (d)(2).

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

Conveyance – Delivery of Level 2 water and 

Incremental Level 4 water in quantities specified 

in 3406 (d) (1 & 2).

• 3406 (d)(5) Refuge Facilities 

Construction – Infrastructure construction to 

provide conveyance capacity for the delivery of 

full Level 4 water supplies to the boundary of 

the CVPIA refuges.

The RWSP was established to implement Section 

3406(d), providing for the delivery of water to 19 

specific state wildlife areas, federal wildlife refuges 

and privately owned/managed wetlands (hereinafter 

referred to as refuges) identified in the Report on 

Refuge Water Supply Investigations (March 1989) 

and the San Joaquin Basin Action Plan/Kesterson 

Mitigation Plan (December 1989). The RWSP’s goal is 

to ensure that all CVPIA refuges annually receive water 

of specified quantity, of suitable flow rate and timing, 

and suitable quality to support their wetland and aquatic 

environments. 

Most of the RWSP’s activities are based on 

Reclamation’s Mid-Pacific Region’s water service 

contract year (Contract Year), including administration 

of conveyance and water supply contracts, refuge water 

allocation delivery schedules, and related accounting 

of water deliveries. A Contract Year is the period 

beginning March 1st of each calendar year through 

the last day of February of the following calendar 

year. Obligations show Fiscal Year 2014 activities 

and water delivery data in this report represents 

Contract Year 2013 (March 1, 2013, thru February 28, 

2014) in correlation with water delivery activities, 

which concluded during the middle of FY 2014. The 

RWSP components—acquisition, conveyance, and 

construction—work together to implement the goals of 

CVPIA related to refuges. 

The RWSP’s two water targets are defined in CVPIA as 

Level 2 (L2) water and Level 4 (L4) water.

• L2 is the amount of water required for minimum 

wetlands and wildlife habitat management based 

on historic average annual water use before 

1989. Reclamation is required to provide full 

Level 2 water supplies annually. The L2 annual 

water delivery target is 422,251 acre-feet (AF), 

including 26,007 acre-feet of “replacement 

water”. Replacement water represents specific 

quantities of refuge water supplies originally 

provided by tailwater and groundwater to certain 

refuges and later replaced with Central Valley 

Project supplies under pre-CVPIA Reclamation 

contracts. Replacement water was included in 

Level 2 water supply allocations in the refuge 

water supply contracts subsequent to CVPIA.

• L4 is the total annual amount of water 

identified for each refuge in CVPIA as required 

for optimum wetlands and wildlife habitat 

development and management. The L4 water 

delivery target for the 19 refuges is 555,515 AF.

To achieve the L4 target, however, the RWSP must 

acquire the incremental difference between the L2 

and L4 water supplies, which amounts to 133,264 

AF of water. This quantity of water is referred to as 

Incremental Level 4 (IL4) water and is made available 

either through direct purchase, exchange, conservation, 

conjunctive use, lease, donations, or other similar 

activities. Each year, Reclamation strives to deliver 

full quantities of L2 supplies based on the schedules 

of those refuges where sufficient existing conveyance 

capacity allows. Reclamation also strives to acquire 

as much as possible of IL4 supplies for delivery to the 

refuges. 

Long-Term Supply Contracts Provide Stability 

for Refuge Managers 

To ensure reliability for refuge managers, Reclamation 

entered into long-term water supply contracts with 

the three refuge managing agencies: CDFW, the 

Service, and Grassland Water District (GWD). These 

contracts have a performance period of 25 years and are 

renewable, representing Reclamation’s obligation under 

CVPIA to provide identified quantities of water to these 

refuges in the Central Valley. 
38 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Water Supply Program 3406 (d)(1), (2) & (5)

Each year in February and monthly thereafter through 

May, Reclamation’s Central Valley Operations Office 

announces the water supply allocation available to the 

CVP contractors and CVPIA refuges (Level 2 water) for 

the current contract year. Each year between February 

and March, the RWSP provides the Interagency 

Refuge Water Management Team (IRWMT) with an 

initial projection of anticipated Incremental Level 4 

water purchases for that contract year. The IRWMT 

determines the allocation of the projected Incremental 

Level 4 supplies. The IRWMT is comprised of 

representatives from Reclamation, the Service, 

CDFW, GWD, and the Central Valley Joint Venture. 

The creation of this team was established through a 

provision in the long-term water supply contracts. 

Concurrent to this process, the three refuge managing 

agencies develop their initial annual water delivery 

schedules for each refuge by March 1.

Use of Groundwater for Refuge Water Supplies 

The RWSP strives to broaden its water supply sources. 

For example, the RWSP pursues groundwater projects 

in partnership with local water districts. Groundwater 

is acquired at a lower cost than surface water, and 

frequently does not require external conveyance if the 

source can be located at or near a refuge. The lower 

cost of groundwater is also an advantage, although 

downsides include groundwater of lesser quality in 

some locations, particularly in the San Joaquin Valley; 

threat of aquifer depletion; and land subsidence. The 

RWSP coordinates with refuge managers for monitoring 

of groundwater quality for toxins, pollutants and 

salinity so as not to degrade the general quality of water 

on the refuges. 

During Contract Year 2013, several refuges relied at 

least in part on groundwater supplies, including Gray 

Lodge Wildlife Area (WA), Merced and Pixley National 

Wildlife Refuges (NWR) and Grassland Resource 

Conservation District (GRCD). 

Refuge Benefits

Numerous biological benefits 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 benefits early arriving migrant 

waterfowl and shorebirds; habitat is also provided for 

resident wildlife and their young during the spring 

and summer, when wetland habitat can be particularly 

limited by hydrology. Introducing water for semipermanent and permanent wetland habitat in the spring 

and summer directly benefits the recovery of special 

status species such as the giant garter snake, and 

tricolored blackbirds. 

Wintering wildlife also benefit from this habitat 

diversity, as seasonal wetlands are now managed to 

coincide with peak migration times of shorebirds and 

waterfowl. Timely de-watering and irrigations promote 

the germination and irrigation of important moist-soil 

food plants, such as swamp timothy and watergrass. 

These plants provide a high-energy food source 

through both their seeds and associated invertebrate 

communities.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 39

CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Water Acquisition 3406 (d)(2)

Refuge Water Acquisition 

3406 (d)(2)

The Refuge Water Acquisition Component (RWAC) is 

responsible for the acquisition of IL4 Water for critical 

wetland habitat supporting resident and migratory 

waterfowl, threatened and endangered species, and 

wetland dependent aquatic biota on the refuges.

IL4 water consists of annual purchases from willing 

sellers from both surface and groundwater supplies. 

In 1998 and 2005 the RWAC acquired a total of 

9,300 AF of permanent IL4 surface water supplies. 

The RWAC also acquires a portion of water supplies 

at no cost, including 215 water, and water delivered 

under a mitigation agreement with the Federal Energy 

Regulatory Commission. 

The RWAC continues to use groundwater to lower 

costs and increase reliability of providing IL4 refuge 

water supplies with acquisitions from GWD and by 

other groundwater wells including two groundwater 

wells constructed at the Volta Wildlife Area under the 

American Recovery and Reinvestment Act through 

a pilot project. The groundwater wells will increase 

water supply reliability and the ARRA funded wells 

help to diversify L2 water sources. It is anticipated 

that together these wells will produce up to 10,000 AF 

annually.

Performance Measures 

Acquisition - The RWAC’s goal is to acquire enough 

water to deliver 133,264 acre-feet (AF) of IL4 water to 

refuge boundaries annually (i.e. 133,264 AF plus any 

additional water needed to cover conveyance losses).

FY 2014 Accomplishments 

The RWCP obligated $1,084,000 from the Restoration 

Fund FY 2014. Funds were used primarily for water 

purchases, ground water assessment, and program 

administration.

The RWAC entered into contracts with the following 

contractors to purchase a total amount of 33,925 AF 

of IL4 water to be delivered in water year 2013: San 

Joaquin River Exchange Contractors (19,500 A/F), 

Merced Irrigation District (7,256 A/F), and Grassland 

Water District (7,169 A/F of groundwater). In addition, 

permanent surface water of 5,858 AF, mitigation water 

of 2,500 AF, Volta well water of 1,146 A/F and Pixley 

well water of 102 A/F were acquired at no additional 

cost for the water and increased the amount of IL4 

to 41,531 AF, which includes water to account for 

conveyance losses such as seepage and evaporation (see 

Table 13). 

In Contract Year 2013 approximately 42,243 AF of 

IL4 water was delivered to the refuges. See the next 

section on Conveyance for more information on water 

deliveries.

Table 13. Incremental Level 4 Acquisitions by 

Fiscal Year, 2002-2014

Fiscal Year*

Gross Incremental 

Level 4 

Water Acquired (AF)**

2002 94,690

2003 79,300

2004 77,010

2005 85,538

2006 94,622

2007 51,911

2008 41,108

2009 42,526

2010 74,038

2011 102,565

2012 59,197

2013 50,281

2014 22,579

* A water year is the period beginning March 1st of each

calendar year through the last day of February the following

calendar year.

** Water acquired is from all sources (purchased and non

purchased).
CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Water Conveyance 3406 (d)(1), (2) & (5)

40 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Refuge Water Conveyance 3406 (d)

(1), (2) & (5)

The Refuge Water Conveyance (Wheeling) Component 

(RWCC) is responsible for providing long-term, firm 

and reliable water deliveries to the 19 CVPIA refuges 

located in the Central Valley of California. The RWCC 

has two primary performance goals, specifically, 

starting with Water Year 2002 forward, based on 

established refuge allocations for each of the two water 

types: 

• Annually provide/deliver Level 2 (L2) water 

supplies by specified amounts to the refuges 

totaling 422,251 acre-feet; and

• Annually deliver IL4 acquired water supplies by 

specified amounts to the refuges totaling 133,264 

acre-feet.

The RWCC delivers L2 and IL4 water supplies to the 

refuges through agreements with water conveying 

entities. 

Reclamation entered into five long-term water supply 

contracts with GWD (1), the Service (2), and CDFW 

(2) which established Reclamation’s commitment to the 

CVPIA delivery mandates. 

Reclamation currently has eight long-term (15-50 

years) conveyance agreements that are administered by 

the RWCC, along with one Service 40-year conveyance 

agreement, also administered under the RWCC. The 

RWCC utilizes cooperative agreements to reimburse 

delivering entities for costs of conveying L2 and IL4 

water supplies through federal, state, and private water 

distribution systems to the refuges. The RWCC also 

uses agreements to reimburse costs for groundwater 

pumping.

Performance Measures 

The RWCC goal is to deliver L2 water supplies of 

422,251 acre-feet (AF) per year; and IL4 water of 

133,264 AF per year to the boundary of the refuges.

A portion of L2 water supplies is provided from nonCVP diverse sources, which assists in minimizing 

possible adverse effects on other CVP contractors.

FY 2014 Accomplishments 

The RWCC obligated $9,973,000 from the Restoration 

Fund.

In Contract Year 2013, an estimated 387,611 AF of L2 

water was delivered to the refuges, representing 92% of 

the target (Table 18).

Approximately 42,243 AF of IL4 water was delivered, 

representing 32% of the target. Table 15 shows the 

targets and deliveries for each refuge in Contract Year 

2013.

Of the estimated total of 270,915 AF of L2 

water delivered in Contract Year 2013, a total of 

approximately 57,030 AF was delivered from diverse 

sources (i.e. non-CVP sources), including riparian water 

rights water, pre-1914 water rights water, groundwater, 

and water provided under Merced Irrigation District’s 

existing mitigation agreement with the Federal Energy 

Regulatory Commission.
CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Water Conveyance 3406 (d)(1), (2) & (5)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 41

Water 

Service 

Contract 

Year* L2 Delivered

% 422,251 

AF L2 

Goal** IL4 Delivered

% 133,262 

AF Inc L4 

Goal***

Total 

Delivered

% 555,515 

AF L4 

Goal

2002 383,842 91% 82,262 62% 466,104 84%

2003 391,636 93% 78,657 59% 470,293 85%

2004 385,732 91% 68,262 51% 453,994 82%

2005 388,803 92% 83,211 62% 472,014 85%

2006 380,073 90% 90,545 68% 470,618 85%

2007 388,521 92% 45,049 34% 433,570 78%

2008 398,010 94% 37,066 28% 435,076 78%

2009 383,739 91% 41,313 31% 425,052 77%

2010 378,086 90% 71,743 54% 449,829 81%

2011 380,688 90% 99,612 75% 480,300 86%

2012 382,628 91% 50,782 38% 433,410 78%

2013 387,611 92% 42,243 32% 429,854 77%

2014 249,987 59% 16,020 12% 266,007 48%

* Water Service Contract Year (WY) is the period from and including March 1 of each calendar year through the last day of 

February of the following calendar year.

** This includes approximately 26,000 AF of replacement water.

*** Does not include replacement water

Table 14. Level 2 (L2), Incremental Level 4 (IL4) and Level 4 (L4) Water Deliveries by Water 

Service Contract Years 2002-2014
CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Water Conveyance 3406 (d)(1), (2) & (5)

42 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Table 15. Water Targets and Deliveries for Each Refuge (Contract Year 2013)

Water Allocation Targets WY 2013 Deliveries % Target Achieved

Refuge Name & 

Region

Level 2 

Water 

(AF)*

IL4 Water 

(AF)**

Full Level 

4 Water 

(AF) 

(= L2+IL4)

Level 2 

Water 

(AF)

IL4 Water 

(AF)

Total 

Delivered 

(AF) 

(= L2+IL4)

Level 2 

Water (%)

IL4 Water 

(%)

Grassland Water District (private) — San Joaquin Valley

Grassland RCD 125,000 55,000 180,000 128,233 25,010 153,243 103% 45%

CA Department of Fish and Wildlife — Sacramento Valley

Gray Lodge WA 35,400 8,600 44,000 29,889 0 29,889 84% 0%

CA Department of Fish and Wildlife — San Joaquin Valley

Volta WA 13,000 3,000 16,000 9,064 0 9,064 70% 0%

Los Banos WA 16,670 8,330 25,000 17,155 2,489 19,644 103% 30%

Salt Slough Unit 6,680 3,340 10,020 6,336 2,150 8,486 95% 64%

China Island Unit 6,967 3,483 10,450 4,932 1,875 6,807 71% 54%

Mendota WA 27,594 2,056 29,650 28,508 0 28,508 103% 0%

U.S. Fish and Wildlife Service — Sacramento Valley

Sacramento NWR 46,400 3,600 50,000 40,498 0 40,498 87% 0%

Delevan NWR 20,950 9,050 30,000 21,377 2,550 23,927 102% 28%

Colusa NWR 25,000 0 25,000 17,421 0 17,421 70% N/A

Sutter NWR 23,500 6,500 30,000 13,570 0 13,570 58% 0%

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

San Luis Unit 19,000 0 19,000 18,824 0 18,824 99% N/A

Kesterson Unit 10,000 0 10,000 10,991 0 10,991 110% N/A

West Bear Creek 

Unit

7,207 3,603 10,810 7,207 0 7,207 100% 0%

Freitas Unit 5,290 0 5,290 4,982 0 4,982 94% N/A

Merced NWR 13,500 2,500 16,000 13,492 2,500 15,992 100% 100%

East Bear Creek 

Unit

8,863 4,432 13,295 3,902 0 3,902 44% 0%

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

Kern NWR 9,950 15,050 25,000 9,950 5,567 15,517 100% 37%

Pixley NWR 1,280 4,720 6,000 1,280 102 1,382 100% 2%

TOTAL 422,251 133,264 555,515 387,611 42,243 429,854 92% 32%

* This includes approximately 26,000 AF of replacement water.

* * Does not include replacement water
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 43

CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Facilities Construction Component 3406 (d)(5)

Refuge Facilities Construction 

Component 3406 (d)(5)

The Refuges Facilities Construction Component 

(RFCC) provides the necessary infrastructure with 

sufficient conveyance capacity to support long-term 

delivery of firm, reliable water supplies to the boundary 

of the CVPIA refuges, as identified in the Act. The 

RFCC is responsible for the delivery of water to those 

lands identified in the Report on Refuge Water Supply 

Investigations (March 1989) (Report) and the San 

Joaquin Basin Action Plan/Kesterson Mitigation Action 

Plan (December 1989)(Plan). 

The need to upgrade conveyance facilities is a result of 

capacity constraints in existing delivery systems and/or 

the lack of existing systems. The goal of the RFCC is 

to have the necessary facilities in place for delivery of 

L4 water supplies to the CVPIA refuges, meeting their 

timing and scheduling requirements. A L4 water supply 

will support optimum wildlife habitat over a broad 

range of species including targeted Threatened and 

Endangered species. 

The RFCC identified a total of 46 major structures 

and/or actions (Projects) necessary to provide needed 

capacity for the delivery of FL4 surface supplies to 

these refuges. These infrastructure improvements can 

be divided into two categories:

• Modify existing facilities – Existing conveyance 

facilities can be upgraded to overcome capacity 

constraints, and

• Construct new facilities – New facilities are 

constructed where there is no existing system, or 

where modifications to an existing system would 

not be sufficient to meet demand. 

Twenty of the Projects are located on refuge lands 

identified in the Plan and 26 Projects are associated 

with refuges identified in the Report. Those refuges 

still requiring conveyance facility improvements are: 

Gray Lodge and Mendota WAs, and Sutter and Pixley 

NWRs. 

An Implementation Plan for refuges identified in the 

Plan was completed in April 1998, and cooperative 

agreements with the San Luis Canal Company, GWD, 

and Central California Irrigation District to convey 

water to these refuges were completed in summer 

1998. Reclamation is currently administering the 

cooperative agreements, which include construction and 

rehabilitation of facilities to accommodate the needs of 

these refuges. 

RFCC activities include project integration and 

coordination with the associated Refuge Water 

Conveyance Component (RWCC) and Refuge 

Water Acquisition Component (RWAC) to ensure 

continuity of methodologies and approaches 

towards executing and achieving RFCC objectives. 

Interagency coordination activities are included in 

this element as well as budget formulation, tracking, 

and management activities. Additional activities 

are coordinating planning, design, and construction 

efforts between agencies and water purveyors (water 

districts). Reclamation’s Mid-Pacific Construction 

Office (MPCO) provides assistance to the RFCC 

by administering design and construction contracts/

agreements including construction contract award, 

facilities construction activities, construction inspection 

and management, and coordination as appropriate with 

other agencies regarding permit requirements.

Performance Measures 

The goal of the RFCC is to ensure that all 19 CVPIA 

refuges have the external conveyance capacity to 

receive L4 Water, totaling 555,515 acre-feet (AF), on an 

annual basis.

FY 2014 Accomplishments 

In FY 2014, the RFCC obligated $4,469,000 from the 

Restoration Fund in support of refuges identified in the 

Plan. 

In FY 2014, the RFCC extended the period of 

performance period on the contract for services to 

provide ongoing repairs to the East Bear Pumping 

Plant located at the East Bear Creek Unit of the San 

Luis National Wildlife Refuge. In addition, the RFCC 

initiated a solicitation to repair Pump #2 at the pumping 

facility. A contract for this repair was awarded and 

obligated in FY 2014.

In FY 2014, the RFCC solicited for the repair of 

erosion problems encountered at the Pixley NWR’s 

groundwater wells. Prior repair work on the alfalfa 

valves was not effective. A contract for this repair was 

awarded and obligated in FY 2014. 

In FY 2014, a contract for a feasibility study was 

executed for the Sutter NWR. The study is to assess 

both an interim solution and identify a long-term 

comprehensive solution for a permanent reliable water 

supply conveyance system. The study is expected to be 

completed in early FY 2015.
44 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 4 - REFUGES RESOURCE AREA | Refuge Facilities Construction Component 3406 (d)(5)

In FY 2014, the RFCC solicited to complete data 

assessment and for the three-year demonstration 

project as part of the Volta Wildlife Area Level 2 

Diversification/Incremental Level 4 Development Pilot 

Project Monitoring Plan. A contract for this project was 

awarded and obligated in FY 2014.

In FY 2014, the RFCC began construction on the 

Biggs-West Gridley Water District (BWGWD) 

Facilities Improvement Project. Construction is 

expected to be completed in FY 2019. When completed, 

BWGWD will have sufficient conveyance capacity for 

L4 water deliveries to the Gray Lodge WA. 

For each of the 19 CVPIA refuges, the conveyance 

target and actual conveyance capacity are shown in 

Table 16.

Table 16. Target FL4 Conveyance Capacity vs. Actual by Refuge

Refuge Name - Region

Target FL4 

Capacity 

(in acre-feet)

Actual 

Conveyance 

Capacity (in 

acre-feet) % of Target

Expected 

Date for 

Completed 

Conveyance 

Construction

Grassland Water District (private) – San Joaquin Valley

Grassland Resource Conservation 

District

180,000 180,000 100

CA Department of Fish and Wildlife – Sacramento Valley

Gray Lodge Wildlife Area 44,000 18,000 41 2019

CA Department of Fish and Wildlife – San Joaquin Valley

Volta Wildlife Area 16,000 16,000 100

Los Banos Wildlife Area 25,000 25,000 100

Salt Slough Unit 10,020 10,020 100

China Island Unit 10,450 10,450 100

Mendota Wildlife Area 29,650 26,000 91 2030

U.S. Fish and Wildlife Service – Sacramento Valley

Sacramento National Wildlife Refuge 50,000 50,000 100

Delevan National Wildlife Refuge 30,000 30,000 100

Colusa National Wildlife Refuge 25,000 25,000 100

Sutter National Wildlife Refuge - Lift 

Station

30,000 0 0 2018

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

San Luis Unit 19,000 19,000 100

Kesterson Unit 10,000 10,000 100

West Bear Creek Unit 10,810 10,810 100

Freitas Unit 5,290 5,290 100

Merced National Wildlife Refuge 16,000 16,000 100

East Bear Creek Unit 13,295 13,295 100

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

Kern National Wildlife Refuge 25,000 25,000 100

Pixley National Wildlife Refuge 6,000 1,280 21 2020
CHAPTER 5 - INDEPENDENT PROGRAMS | Bay-Delta Activities 3406 (b)(1)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 45

CHAPTER 5 - INDEPENDENT PROGRAMS

Bay-Delta Activities 3406 (b)(1)

Reclamation’s Bay-Delta Office (BDO) coordinates 

with the CVPIA office to respond to the urgent needs 

of species in the Bay-Delta. As such, projects typically 

include those which address CVP operations and the 

Reasonable and Prudent Alternatives (RPA) prescribed 

by the regulating agencies. 

FY 2014 Accomplishments

The BDO obligated $3,474,000 from the Bay-Delta 

Fund in FY14. 

BDO carried out several projects to benefit fish 

through the CVPIA. A network of about 30 tidal flow 

and continuous water quality monitoring stations 

were maintained throughout the Delta to measure fish 

habitat quality, to inform hydrodynamic and sediment 

modeling efforts, and to provide CVP/SWP operators 

with an early warning system for the arrival of turbidity 

plumes containing delta smelt. These data are posted in 

near-real time on the US Geological Survey NWIS web 

site. The BDO program also funded the fourth and final 

year of the ‘first flush’ study. This study documents 

the response of delta smelt to tidal flow and turbidity 

during the first high flow event of the winter. Some of 

the results of this study have been published in a peerreviewed journal article.

The BDO also continued funding for the six-year 

study of juvenile steelhead survival in the south Delta 

(required under the NMFS Biological Opinion).
CHAPTER 5 - INDEPENDENT PROGRAMS | Habitat Restoration Program 3406 (b)(1) “Other”

46 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Habitat Restoration Program for 

Other Adverse Environmental 

Impacts of the CVP Under 

3406 (b)(1)

The Habitat Restoration Program (HRP) benefits 

federally listed Central Valley species and habitats 

impacted by construction and operation of the CVP. 

Habitat loss and fragmentation occurred across a 

large part of the Central Valley as a result of CVP 

construction and operation, and the program is charged 

with contributing to the habitat mitigation requirements 

for this loss.

The HRP’s priorities include purchase of fee title or 

conservation easements on lands where threats to listed 

species are significant. The program also focuses on 

restoration of CVP-affected habitats, and research 

to facilitate species recovery. In addition, the HRP 

supports captive propagation and reintroduction of 

federally listed species affected by the CVP. 

Performance Measures

Since fiscal year 1996, the HRP has provided significant 

contributions by funding 121 diverse and valuable 

projects to benefit a multitude of federally listed and 

other special status species that were impacted by the 

CVP. Federally listed species which have benefitted 

include the San Joaquin kit fox, giant kangaroo rat, 

riparian brush rabbit, blunt-nosed leopard lizard, 

giant garter snake, bay checkerspot butterfly, Lange’s 

metalmark butterfly, vernal pool plant and invertebrate 

species, and gabbro and serpentine soils species. 

The HRP provides leveraging of funds by attracting 

additional funding partners which decreases the amount 

of HRP funds needed to implement a project; partners 

have contributed about 85 percent of total project costs. 

Land acquisition projects currently have the highest 

priority and receive at least 50 percent of the available 

funding. 

Protection and Restoration

The program contributes to the protection and 

restoration of threatened and endangered species 

habitats affected by the construction and operation 

of the CVP. Protection includes acquisition of lands 

through fee title or conservation easements. Since 

1996, over 109,000 acres have been acquired and over 

6,000 acres have been restored with HRP funds along 

with funds from partners (see Table 18). Various habitat 

types throughout the Central Valley have benefitted 

including alkali sink/scrub, valley grassland, riparian, 

vernal pools and other wetlands, serpentine soils, and 

chaparral.

The 1999 State Water Resources Control Board 

Decision 1641 (SWRCB’s D-1641) requires that 

Reclamation provide compensation and habitat values 

to mitigate for impacts associated with the delivery 

of CVP water to lands previously outside the CVP 

Consolidated Place of Use. It identifies the HRP as one 

of three Reclamation programs suitable for fulfilling 

the mitigation plan. Pursuant to the SWRCB’s D-1641, 

Reclamation developed the Consolidated Place of Use, 

Habitat Mitigation Plan and Monitoring and Reporting 

Program (HMP) as a report/strategy of how the 

mitigation requirements will be addressed. The HMP 

identifies acquisition, maintenance, and restoration of 

45,391 acres needing to occur as mitigation related 

to the CVP Consolidated Place of Use. To date, the 

program has protected and restored 7,600 acres of 

habitat within the CVP Consolidated Place of Use.

Research and Captive Propagation and 

Reintroduction

The program also supports the recovery of threatened 

and endangered species through stabilization and 

improvement of species populations by funding 

research and captive propagation and reintroduction 

activities. In part, research projects ultimately 

contribute important information towards increasing 

current and future protection and/or restoration of 

species or habitats impacted by the CVP. Research 

has included vernal pool mapping, assessing the 

potential for listed species reintroductions, and 

numerous genetics analyses. Captive propagation and 

reintroduction have benefitted two critically endangered 

species as well as other federally listed species.

FY 2014 Accomplishments 

In 2014, $1,523,000 was allocated to the program from 

the Restoration Fund to achieve the following: 

• Protection. HRP funding helped protect 

795 acres of land through fee title acquisition in 

Fresno County. (See Table 17 for 2014 project 

accomplishments, and Table 18 for approximate 

acres protected and restored from 1996 through 

2014 using HRP funds as well as partners’ 

funds). All 795 of these acres count towards the 

SWRCB’s D-1641 requirements.
CHAPTER 5 - INDEPENDENT PROGRAMS | Habitat Restoration Program 3406 (b)(1) “Other”

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 47

Name of Project Activity Description

Latitude and 

Longitude

Eastern Ciervo-Panoche Natural 

Area Habitat Protection Project 

(Mouren Cattle Company 

property)

Fee title acquisition of 2 parcels located on the 

eastern slope of the Ciervo Hills to protect San 

Joaquin kit fox, giant kangaroo rat, blunt-nosed 

leopard lizard, and San Joaquin woolly-threads in 

western Fresno County. 

Parcel 1: 

Lat: 36°29’41.01”N; 

Long: 120°33’36.27”W

Parcel 2: 

Lat: 36°33’49.37”N

Long: 120°33’36.13”W

Table 17: Projects Funded by the (b)(1) “Other” Program in 2014

Year Acreage Protected Acreage Restored

Cumulative Acreage of Protection 

and Restoration

1996 3,018 0 3,018

1997 284 617 3,919

1998 74,146 0 78,065

1999 1,180 0 79,245

2000 1,426 206 80,877

2001 2,831 0 83,708

2002 2,211 0 85,919

2003 2,866 0 88,785

2004 719 432 89,936

2005 755 3,370 94,061

2006 193 731 94,985

2007 1,603 122 96,710

2008 0 700 97,410

2009 5,165 0 102,575

2010 3,404 48 106,027

2011 5,384 129 111,540

2012 2,310 0 113,850

2013 1,873 0 115,723

2014 3,042 0 118,765

Total 112,410 6,355 118,765

Table 18: Approximate Acres of Habitat Protected and Restored by the (b)(1) “Other” Program, 

1996-2014, Using HRP Funds
CHAPTER 5 - INDEPENDENT PROGRAMS | Trinity River Restoration Program 3406 (b)(1) “Other” & (b)(23)

48 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Trinity River Restoration Program 

3406 (b)(1) “Other” & (b)(23)

The Trinity River Restoration Program (TRRP) is 

dedicated to the improvement of anadromous fishery 

resources in the Trinity River Basin. The program uses 

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

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

delivering flows.

The Trinity River Mainstem Fishery Restoration Final 

Environmental Impact Statement (FEIS) completed 

in October 2000, and the Record of Decision 

(ROD), signed on December 19, 2000, established a 

comprehensive science-based adaptive management 

program to restore the fishery resources of the Trinity 

River. The 2009 Master Environmental Impact Report 

(Master EIR) on channel rehabilitation and sediment 

management for remaining sites established the 

regulatory requirements for implementing physical river 

work required by the ROD. 

The program is based upon the goal of restoring the 

naturally produced anadromous fishery resources 

of the Trinity River by restoring the attributes of a 

healthy, alluvial river system through implementing 

variable annual instream flows, physical channel 

rehabilitation, sediment management, watershed and 

riparian rehabilitation and floodplain infrastructure 

improvements. Together, these actions will increase 

and enhance habitats for all life stages of anadromous 

salmonids, increase juvenile production and lead 

to increased spawning escapement and harvest 

opportunities of dependent fisheries. Since the ROD 

was signed, the TRRP has focused its physical 

restoration activities—such as gravel placement and 

channel rehabilitation activities—on the upper 40 miles 

of the Trinity River between Lewiston Dam and the 

confluence with the North Fork of the Trinity River as 

well as flow releases and sediment transportation that 

benefit the entire riverine system.

Performance Measures

The overall success of the program is gauged by 

naturally produced spawner escapement numbers 

relative to the goal (target) set for each species, and 

contributions to dependent tribal and non-tribal 

fisheries. Annual targets are found in Table 19. To 

achieve this overall goal, the program implements 

actions in several key areas that support the 

establishment of a healthy riverine system. Actions 

include scheduling annual flow of water, placement 

of coarse sediment, reduction of fine sediment 

delivery from watersheds by implementing watershed 

rehabilitation activities and physical channel restoration 

projects. 

Flows

The program releases between 369,000 and 815,000 

AF each year, in accordance with the ROD. The annual 

volume target and peak flow varies according to the 

water year type. 

Placement of Coarse Sediment

The program may place up to 10,000 tons (7000 CY) of 

coarse sediment annually. 

Fine Sediment Delivery and Storage

The program aims to reduce fine sediment delivery from 

tributary watersheds by 10,000 to 20,000 CY annually. 

Additionally, the goal for fine sediment management is 

to transport as much or more fine sediment downstream 

as is delivered to the upper river from tributary 

watersheds to reduce in-channel storage.

Channel Rehabilitation

The goal of the channel rehabilitation component of 

the program is to restore functioning alluvial river 

attributes and increase salmonid freshwater habitat. 

The ROD calls for 44 bank rehabilitation projects 

and 3 side channels, which combine to make 47 sites. 

Channel restoration progress is currently measured by 

the number of completed sites. The final measure of the 

success of channel rehabilitation projects will be their 

effectiveness of promoting a dynamic alluvial river 

in conjunction with high flows and coarse sediment 

augmentation to increase salmonid habitat and restore 

the Trinity River fishery resources. This is being 

evaluated through the Program’s adaptive management 

process.

Other

In addition to the action oriented performance measures 

listed above, the TRRP has developed performance 

measure documents that provide information pertaining 

to key metrics that are used to evaluate status and 

trends of these parameters. These Include: Temperature 

Target Performance; Chinook and Coho Salmon 

Rearing Habitat; Abundance of Naturally Produced 

Juvenile Chinook Salmon; Spawning Escapement of 

Naturally Produced Salmonids; Proportion of Natural 

Origin Salmonids Contributing to Total In-River 

Run; Distribution of Natural-Origin Chinook Salmon 

Spawners; Abundance Patterns Over Time of Riverine 

Birds; Abundance Patterns Over Time for Riparian 

Birds; and Comparison of Turtles on the South Fork 

Trinity and Mainstem Trinity. All program products can 

be found on the online data portal: http://www.odp.trrp.

net/

FY 2014 Accomplishments

In FY 2014, the Trinity River Restoration Program 

obligated $2,339,000 from the Water & Related 
CHAPTER 5 - INDEPENDENT PROGRAMS | Trinity River Restoration Program 3406 (b)(1) “Other” & (b)(23)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 49

Resources Fund (b)(23), $10,268,000 from the Water & 

Related Resources Fund (b)(1) “other” and $1,518,000 

from CVP Restoration Funds. 

Flows

Water Year 2014 was a Critically Dry Water Year. 

Water temperature, channel rehabilitation construction, 

juvenile salmonid numbers and available habitat and 

riparian vegetation issues were considered in flow 

scheduling. The ROD prescribed flow for a critically 

dry water year is 369,000 AF. Water volume peak flow 

at 1500 cfs was released from April 24 through May 30, 

2014 with flows decreasing to 450 cfs by June 26, 2014. 

Course Gravel and Channel Rehabilitation

A channel rehabilitation project was implemented at 

Lower Junction City completing one more of 47 sites 

included in the ROD for a total of 31 sites completed. 

The program also continued planning and engineering 

designs for the next four channel rehabilitation projects. 

Monitoring and Assessment

Approximately 12 science and monitoring activities 

were accomplished in FY 2014 to include stream 

gaging, sediment transport, course and fine sediment 

budgets, smolt outmigration population size and timing, 

adult spawning escapement separated by natural 

and hatchery, sport and tribal harvest, system wide 

habitat assessment, evaluation of habitat produced 

through construction, riparian vegetation recruitment 

and encroachment and system wide bird abundance. 

Results from salmon production monitoring are below 

in Table 19. Other results are included in the TRRP 

performance measures documents mentioned above 

as well as in reports located on the TRRP Online Data 

Portal (http://www.odp.trrp.net/).

Fall 

Chinook4

Spring 

Chinook5

Fall 

Steelhead6 Coho7

Fall 

Chinook4

Spring 

Chinook5

Fall 

Steelhead6 Coho7

Target 62,000 6,000 40,000 1,400 9,000 3,000 10,000 2,100

2010 14,715 5,093 3,786 817 13,335 4,314 4,468 5,852

2011 17,158 6,739 6,900 1,205 27,534 5,351 14,044 4,113

2012 35,540 9,613 8,267 1,774 31,238 14,472 11,745 13,494

2013 16,689 3,144 9,119 4,305 12,785 5,835 6,816 14,782

Average 21,025 6,147 7,018 2,025 21,223 7,493 9,268 9,560 

1

 All table entries reflect final numbers reported by CDFW. 

2

 Estimates of naturally-produced adult salmonid spawner escapement for combined natural and hatchery spawning areas.

3

 Estimates of hatchery-produced adult salmonid spawner escapement for combined natural and hatchery spawning areas.

4

 Fall Chinook estimates upstream of Willow Creek weir. Trinity River Basin estimate assumes no straying of hatchery produced 

spawner escapement downstream of Willow Creek weir.

5

 Spring Chinook estimates upstream of Junction City weir combined with dive counts for the South Fork Trinity River and 

miscellaneous tributaries. 

6

 Fall-run steelhead estimates upstream of Willow Creek weir for all years of data collected. Does not include summer- or winter run 

steelhead estimates.

7

 Coho estimates upstream of Willow Creek weir.

Table 19. Salmonid Production, Natural vs. Hatchery1

Naturally Produced Adult Spawner Escapement2

Trinity River Hatchery Produced Adult 

Spawner Escapement3
CHAPTER 5 - INDEPENDENT PROGRAMS | Trinity River Restoration Program 3406 (b)(1) “Other” & (b)(23)

50 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Table 20. Annual ROD Flows and Peak Releases to Trinity River, 2006-2014

Fiscal 

Year Water Year Type ROD Flow Target

ROD Flow 

Provided*

Peak Releases 

(cfs)

2006 Extremely wet 815,000 AF 809,900 AF 10,100

2007 Dry 453,000 AF 453,700 AF 4,750

2008 Normal 647,000 AF 648,700 AF 6,470

2009 Dry 453,000 AF 445,500 AF 4,410

2010 Normal 647,000 AF 656,700 AF 6,840

2011 Wet 701,000 AF 721,800 AF 11,600

2012 Normal 647,000 AF 647,000 AF 6,080

2013 Dry 453,000 AF 453,000 AF 4,500

2014 Critically Dry 369,000 AF 369,000 AF 1,500

 * Computed flow volume ± 5% based on stream flow measurement accuracy.

Table 21. Placement of Coarse Gravel by Year (7,000 Cubic Yard Target), 2003-2014

Fiscal 

Year Gravel Augmentation Location Gravel * (CY)

Total per Year* 

(CY)

2003 Cableway 2,000 2,000

2006 Hatchery 1,600 1,600

2007 Hatchery 4,300 4,300

2008 High Flow Injections 2,300 12,300

Lewiston-Dark Gulch 10,000

2009 High Flow Injections 2,300 8,000

Sawmill 5,700

2010 High Flow Injections 3,100 13,500

Lowden Ranch Area and Reading Creek 10,400

2011 High Flow Injections 5,300 5,300

2012 Upper Junction City 0 0

Lower Steiner Flat 0

2013 High Flow Injections 200 1,700

Saw Mill Dry Placement 1,500

2014 Lower Junction City 3,620 3,620

Total 52,320

 * Volume for mobile coarse gravel only. Reported volumes do not included oversized gravel or structural gravel to build permanent 

in-river features.
CHAPTER 5 - INDEPENDENT PROGRAMS | Trinity River Restoration Program 3406 (b)(1) “Other” & (b)(23)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 51

Table 22. Rehabilitation Site Construction Summary, 2005-2014 

Fiscal 

Year Rehabilitation Site

Number 

of Sites Earth-work (CY)

Feet of Large 

Wood Habitat 

Structures

River 

Miles

Acres 

Treated

2005 Hocker Flat (complete) 1 83,000 0 1.0 26

2006 Canyon Creek Sites 

(complete)

 4 91,000 100 1.7 40

2007 Indian Creek Sites 

(complete)

 3 77,800 200 2.8 31

2008 Lewiston and Dark 

Gulch Sites (complete)

 8 56,900 200 3.7 42

2009 Sawmill and Steel 

Bridge Day Use* 

(complete)

 2 87,750 260 0.8 25

2010 Lowden, Trinity House 

Gulch, Reading Creek 

 5 202,600 300 2.4 36

2011 Wheel Gulch 

(complete)

 1 48,000 200 0.3 7

2012 Upper Junction City, 

Lower Steiner Flat

 4 63,900 400 1.2 45

2013 Lorenz Gulch and 

Lower Douglas City

 2 56,400 525 1.4 52

2014 Lower Junction City 1 34,580 250 0.5 52

Total 31 801,930 2,435 15.8 356

* The No-Action alternative was chosen for the Steel Bridge Day Use Project Site.
CHAPTER 5 - INDEPENDENT PROGRAMS | Ecosystem and Water Systems Operations Model 3406 (g)

52 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

Ecosystem and Water Systems 

Operations Models 3406 (g)

FY 2014 Accomplishments 

The Modeling Program obligated $678,000 from the 

Restoration Fund and $290,000 from the Water and 

Related Fund in FY14.

CalSim II accomplishments for FY14 include: 

(1) Analyzing the impact of alternative streamflow 

standards (including the proposed New Melones 

Revised Plan of Operations) on Stanislaus River 

operations using the CalSim SJR model, (2) providing 

CalSim support for development of models for the 

Remanded Biological Opinions EIS, (3) reviewing 

CalSim baseline for the Folsom Water Control 

Manual Update, which led to some model updates, 

(4) reviewing software tools for improved visualization 

of CalSim results and submitted an S&T proposal on 

this topic, (5) collaborating with BDO to create a draft 

protocol for CalSim Model Maintenance Management 

(CM3) process, (6) completion of CalSim II codes 

to use with new WRIMS2 engine and to develop 

the study results for the 2013 Delivery Reliability 

Report, (7) completion of the CalSim II codes to 

incorporate the D1485, D1641, B2, and BO RPAs and 

then investigation of the effects of these regulations 

on water supply and Delta outflow, (8) development 

of several baseline CalSim II models for the COA 

negotiations and the COA Agreement re-evaluations, 

(9) development of a post processing tool to analyze the 

results for tracking water from CVP and SWP reservoirs 

to Delta, (10) development of a multi-step runner to run 

multi-regulation studies, (11) sensitivity of including 

different B2 actions in the model, and (12) development 

of more user-friendly automated data processing 

packages for input/output analysis and display. These 

developments and modifications facilitate the use of 

the model for numerous studies by Reclamation and 

others which ultimately lead to increased understanding 

referenced in §3406(g).

CalLite accomplishments for FY14 include: 

(1) reviewing and providing comments to DWR on 

CalLite Forecast Allocation Module (FAM), (2) using 

modified version of CalLite to analyze benefits of 

additional South-of-Delta storage in San Luis and Los 

Vaqueros, (3) provided support to DWR for testing and 

QA-QC of final version of CalLite 3.0 (expected release 

data is late Sept - Oct 2014), (4) implementation of 

North Delta Diversion option (a.k.a. Isolated Facility), 

(5) development of a dynamic San Joaquin, (6) addition 

of an enlarged Shasta Dam option, (7) addition of an 

enlarged Las Vaqueros option (5) implementation of 

the Forecast Allocation Model (FAM), (8) the addition 

of the D-1485 run basis, and of batch run, (9) position 

analysis script for CalLite, and (10) improved and more 

flexible CalLite GUI for post processing. 

CalSim 3.0 accomplishments for FY14 include: 

(1) Continued CalSim 3.0 QA/QC and improvement; 

(2) continued CalSimHydro model improvement; (3) 

initiated development of CalSimForecast; (4) initiated 

development of CalSim 3.0 water rights management 

feature; (5) incorporated expansion of CalSim 

3.0 model domain; (6) developed methodology to 

determine historical change of rice planting date 

and growing season based on Landsat imagery for 

CalSimHydro.

C2VSIM (California Central Valley GroundwaterSurface Water Simulation Model) accomplishments 

for FY14 include: (1) Held public workshops on the 

C2VSIM model, (2) held workshops on IWFM and 

IDC models, (3) released IWFM version 4.1 for public 

use in July 2014, (4) started a project in the application 

of a modified version of C2VSIM to estimate natural 

inflows into the Sacramento – San Joaquin Delta 

(ongoing).

ANN Model accomplishments for FY14 include 

studying the methodology used by the Metropolitan 

Water District (MWD) to predict turbidity in Delta 

channels.

DSM2 model accomplishments for FY14 include: 

(1) partial development of a new water Quality module 

for DSM2, (2) continued development of better Delta 

consumptive use estimates, (3) Delta drought real 

time support, (4) Improvement of visualization tools 

for Drought analysis, (5) continuation of adding fish 

behaviors to the PTM module of DSM2, (6) new 

calibration techniques using PEST (Model-Independent 

Parameter Estimation and Uncertainty Analysis) 

(7) partial completion of the replacement the DSM2 

cross section development program using GIS tools.

In FY14, the HydroGeoSphere San Joaquin Valley 

Model (HGSSJVM) was calibrated and presented to 

staff of the Tracy and Fresno offices. HGSSJVM is a 

groundwater model that can be used to simulate the 

land subsidence resulting from groundwater pumping. 

The model has been developed for analyzing possibility 

of incurring irreversible subsidence due to specific 

groundwater pumping plans such as the Warren Act 

pumping, as well as performing a more comprehensive 

sensitivity analysis of the relationship between pumping 

and subsidence.
CHAPTER 5 - INDEPENDENT PROGRAMS | Ecosystem and Water Systems Operations Model 3406 (g)

Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 53

The 3406 (g) program also prepared publications 

and provided support to model applications for 

stakeholders. 

All of the projects that were undertaken in FY2014 met 

or exceeded the performance targets.
54 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 5 - INDEPENDENT PROGRAMS | Land Retirement Program 3408 (h)

Land Retirement Program 3408 (h)

The Land Retirement Program (LRP) purchases land, 

water and other property interests from willing sellers 

who receive CVP water. By ceasing irrigation of these 

drainage impaired 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 Land Retirement Demonstration Project (LRDP) 

was implemented in 1999 at two sites—one in the 

western San Joaquin Valley (Tranquility, managed 

by Reclamation) and the other in Tulare Lake Basin 

(Atwell Island, managed by the Bureau of Land 

Management (BLM))--to study the environmental 

impacts of land retirement and to evaluate cost-effective 

restoration strategies for retired lands.

The LRP obligated $400,000 of FY14 funds towards 

an inter-agency agreement with BLM to complete 

land acquisition and restoration activities at the Atwell 

Island LRDP site. This site is managed by BLM to 

further the LRP goals of drainage source reduction and 

wildlife habitat enhancement. It is anticipated that the 

LRP will not receive additional CVP Restoration funds 

after FY 14.

FY2014 Accomplishments 

The program obligated $515,000 from the Restoration 

Fund, and $70,000 from the Water and Related 

Resources Fund during FY14. Table 23 lists the 

cumulative accomplishments of the Land Retirement 

Program (LRP). 

Retire Agricultural Land

Over 9,300 acres of drainage impaired land have been 

acquired to date from willing sellers for the Land 

Retirement Demonstration Project (LRDP). Contacts 

with the multiple land owners were made for the 

acquisition of the remaining 750 acres at the Atwell 

Island project during FY14. No additional land was 

acquired from willing sellers by the program during FY 

2014. 

Restore Habitat

Ecological restoration treatments have been perfomed 

on over 6,800 acres of drainage impaired farmland that 

has been retired as a result of the LRDP. BLM planted 

two-hundred fifty pounds of locally grown seed at the 

Atwell Island site in the winter of 2014. A fair response 

of annual flora was observed during spring 2014 at the 

two restoration sites planted in 2013 as well as the 10 

acres in the winter of 2014, contributing to the ongoing 

restoration of alkali sink habitat at the site. Twenty-five 

pounds of alkali Sacaton grass seed was harvested for 

grow out; grass plugs to be planting fall 2015. 

Reduce Agricultural Drainage Volume

The program reduced the amount of agricultural 

drainage water on LRDP lands by approximately 3,600 

acre-feet in FY 2014. Cumulative drainage reduction 

estimates were revised based on LRDP land use data 

provided by BLM.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 55

CHAPTER 5 - INDEPENDENT PROGRAMS | Land Retirement Program 3408 (h)

Overall Targets

------------------------

Acres Acquired

Overall Targets

------------------------

Acres Acquired

Annual Targets

------------------------

Acres Restored

Annual Targets

------------------------

Reduction in 

Agricultural Drainage 

(acre-feet)

Year

Atwell Island 

(8,000 acres)

Tranquillity*

(7,000 acres) 400 acres 6,000 acre-feet

1995 0 591 0 236

1996 0 0 0 236

1997 0 0 0 236

1998 0 995 1,220 634

1999 0 60 100 658

2000 2,645 0 777 1,716

2001 1,414 444 702 1,992

2002 1,510 0 373 2,672

2003 616 0 261 2,772

2004 155 0 308 2,962

2005 625 0 349 3,275

2006 38 0 416 3,275

2007 213 0 475 3,275

2008 0 0 390 3,275

2009 0 0 380 3,275

2010 50 0 400 3,320

2011 0 0 260 3,361

2012 0 0 260 3,465

2013 0 0 197 3,585

2014 0 0 10 3,585

Total 7,266 2,090 6,868 47,805** 

 * Land acquisition at the Tranquility site was deemed complete in 2001 with the retirement of approximately 100,000 acres of

 drainage problem lands by the Westlands Water District. Acreage shown reflect only USBR acquired lands. 

** Reduction in Agricultural Drainage Total is cumulative from 1995-2014.

Table 23: Land Acquired and Restored, and Drainage Reduction by Year, 1995-2014
56 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 5 - INDEPENDENT PROGRAMS | San Joaquin River Restoration Program Public Law 111-11

San Joaquin River Restoration 

Program Public Law 111-11

The San Joaquin River is a major tributary to 

the Sacramento-San Joaquin Delta, historically 

providing flows 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 

confluence with the Sacramento-San Joaquin Delta 

Estuary. 

Subsequent to the passage of CVPIA, a Stipulation 

of Settlement (Settlement) was reached in September 

2006 that resolved long-standing disputes related to 

Reclamation’s operation of Friant Dam. The Settlement 

ended an 18-year lawsuit between the U.S. Departments 

of the Interior and Commerce, the Natural Resources 

Defense Council (NRDC) and the Friant Water Users 

Authority (FWUA). 

Public Law 111-11 specifies that “...the Settlement 

satisfies and discharges all of the obligations of the 

Secretary contained in section 3406(c)(1)...” The 

San Joaquin River Restoration Program (SJRRP) 

implements the Settlement consistent with Public 

Law 111-11.

The agencies responsible for the management of 

the SJRRP include Reclamation (lead), the Service, 

National Marine Fisheries Service (NMFS), California 

Department of Water Resources (DWR), and California 

Department of Fish and Wildlife (CDFW). Actions to 

implement the Settlement are anticipated to be funded 

using four different funding sources in FY 2014. These 

include mandatory and appropriated funds in the San 

Joaquin River Restoration Fund, funds from the State 

of California, and funds from the CVP Restoration 

Fund. Actions to implement the Settlement will also be 

accomplished with in-kind services conducted by the 

State of California through the Department of Water 

Resources and Department of Fish and Wildlife. This 

description of program goals and objectives is intended 

to focus on those activities that are anticipated to be 

implemented using funds from the CVP Restoration 

Fund. See the Annual Report published by the San 

Joaquin River Restoration Program for a description 

of all of the Program’s activities (annual reports are 

available at http://www.restoresjr.net). 

Performance Measures

The Settlement includes two goals:

• Water Management. To reduce or avoid 

adverse water supply impacts to all of the Friant 

Division long-term contractors that may result 

from implementation of the Settlement. (The 

Settlement calls for interim flows and restoration 

flows, which are additional releases out of Friant 

Dam to support fish and wildlife habitat needs.) 

• Restoration. To restore and maintain fish 

populations in “good condition” in the main 

stem of the San Joaquin River below Friant Dam 

to the confluence of the Merced River, including 

naturally reproducing and self-sustaining 

populations of salmon and other fish.

FY 2014 Accomplishments 

The Program obligated $1,936,000 from the Restoration 

Fund to achieve the Reach 4B, Eastside Bypass and 

Mariposa Bypass Channel and Structural Improvements 

Projects. In FY 2014 and in support of the Restoration 

Goal, Reclamation funded a contract for ongoing work 

towards development of the Environmental Impact 

Statement/Environmental Impact Report for this 

project. The purpose of this project is to determine 

and implement a long-term solution to flow and fish 

routing in the Reach 4B / Eastside Bypass area of 

San Joaquin River and to provide for fish passage 

and juvenile rearing habitat in the selected route. The 

project is one of the high priority channel and structural 

improvements projects called for in Paragraph 11(a) 

and 11(b) of the Settlement. 

The above accomplishments were achieved with 

CVPIA funding. To see all SJRRP accomplishments, 

visit http://www.restoresjr.net.
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 57

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA ACCOMPLISHMENTS

CHAPTER 6 - PROGRESS TO DATE TOWARD 

CVPIA PERFORMANCE GOALS

The CVPIA Program tracks performance targets from 

several sources including CPAR (goals based upon 

CVPIA), Interior goals (Performance Assessment 

and Rating Tool or PART) and program-defined 

goals. Listed below are goals by program for ongoing 

programs. The 2014 Accomplishment status is based 

upon the specific FY 2014 actions, cumulative Program 

to Date accomplishments, or a yearly average over 

the life of the program. At the bottom of the listing 

are completed or inactive programs and their status. 

Detailed assessments of progress toward the Central 

Valley fish doubling goals are found in the CAMP 

Annual Report at: http://www.fws.gov/sacramento/

Fisheries/CAMP-Program/Documents-Reports/

Documents/2014_CAMP_Annual_Report.pdf.

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, or 

Average)

To Date

(Cumulative 

or Average)

% of 

Target

Accomplishments Comments

Fisheries

Anadromous Fish Restoration Program (AFRP), 3406 (b)(1)

Double the number of naturally 

produced, Central Valley wide, 

Fall-run Chinook

750,000 

fish

1992-2013 

average

359,613 48 404,269

Double the number of naturally 

produced, Central Valley wide, 

Late Fall-run Chinook

68,000 fish 1992-2013 

average

 16,869 25 8,838

Double the number of naturally 

produced, Central Valley wide, 

Winter-run Chinook

110,000 

fish

1992-2013 

average

 6,273 6 7,798

Double the number of naturally 

produced, Central Valley wide, 

Spring-run Chinook

68,000 fish 1992-2013 

average

 14,127 21 20,015

Double the number of Central 

Valley wide Green Sturgeon

2,000 fish 1992-2009 

average

 2,946 147 N/A

Double the number of Central 

Valley wide 15-year old, White 

Sturgeon

11,000 fish 1992-2009 

average

 6,237 57 N/A

Double the number of Central 

Valley wide Striped Bass

2,500,000 

fish

1992-2012 

average

952,705 38 N/A

Double the number of Central 

Valley wide American Shad

4,300 fish 1992-2013 

average

 2,206 51 309

Cubic Yards of Spawning 

gravel placed in the American, 

Merced, and/or Tuolumne 

rivers.

unspecified Annual N/A N/A 55,496 American was the only 

river with gravel placed 

this year

Complete 105 structural actions 105 actions Cumulative 73 68 0 Merced River Ranch 

Floodplain and Channel 

Restoration Project was 

completed in November 

2013
58 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA ACCOMPLISHMENTS

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, or 

Average)

To Date

(Cumulative 

or Average)

% of 

Target

Accomplishments Comments

Contribute towards completion 

of 128 High and Medium Priority 

Actions

128 actions Cumulative 46 36 0 Although no CPAR actions 

were completed in 2014, 

substantial progress was 

made on 38 individual 

projects in 20 separate 

watersheds.

Dedicated Project Yield, 3406 (b)(2)

Provide instream flow, specified 

based on Wet, Dry, or Critically 

Dry year.

Dry Year 

target is 

600,000 

acre-feet

Annual N/A 100 402,000 The total (b)(2) water 

allocation was 600 

thousand acre feet (TAF) 

during the 2014 water 

year. However, due to 

these historically dry 

hydrological conditions, 

Interior was only able 

to make approximately 

400,000 AF of the 600,000 

AF of CVPIA (b)(2) water 

available.

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

Provide supplemental (b)(2) 

instream flow water

200,000 

acre-feet

Average from 

1994-2013

71,091 0 0

Tracy Pumping Plant/Tracy Fish Test Facility, 3406 (b)(4)

Complete 23 actions to mitigate 

for fishery impacts

23 

mitigation 

actions

Cumulative 17 74 0 Secondary Louver 

Replacement project, 

Action #18 completed

Clear Creek Restoration, 3406 (b)(12)

Restore stream channel 2 miles Cumulative 1.5 75 0

Place spawning gravel annually 25,000 

tons (1)

Annual N/A N/A 7,700 7,700 tons (30.8%) 

projected

Meet variable flow target Variable 

(cfs)

Annual N/A 100 200 Ongoing operation

Maintain water temperature 

for optimum anadromous fish 

production

Maintain 

proper 

temperature 

100% of the 

time

Annual N/A 100

96

100% for 60°F 1-Jun to 

14-Sep

96% for 56°F 15-Sep to 

31-Oct

2013 data

Spawning Gravel, 3406 (b)(13)

Place 10,000 tons of spawning 

gravel annually in the 

Sacramento River

10,000 

tons

Annual N/A 0 0

Place 3,000 tons of spawning 

gravel annually in the Stanislaus 

River

3,000 tons Annual N/A 0 0

Place 7,000 tons of spawning 

gravel annually in the American 

River

7,000 tons Annual N/A 143 10,000

Increase the percentage of 

spawning salmonids using 

placed gravel in the Sacramento 

River

25% usage Annual N/A 304 76%
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 59

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA ACCOMPLISHMENTS

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, or 

Average)

To Date

(Cumulative 

or Average)

% of 

Target

Accomplishments Comments

Increase the percentage of 

spawning salmonids using 

placed gravel in the Stanislaus 

River

10% usage Annual N/A 280 28%

Increase the density of redds 

on emplaced gravel in the 

American River

0.03 redds/

sq. meter

Annual N/A 33 0.01

Comprehensive Assessment and Monitoring Program, 3406 (b)(16)

Create an Annual Report 1 Annual 

Report

Annual 1 100 1

Management of CVPIA data Unspecified Annual N/A N/A N/A

Anadromous Fish Screens Program (AFSP), 3406 (b)(21)

Screen all high priority 

diversions on prescribed 

streams

Unspecified Cumulative 44 Undefined 3

Trinity River Restoration Program (TRRP), 3406 (b)(23)

Increase the escapment of 

Hatchery produced Fall-run 

Chinook Salmon

9,000 fish 1992-2013 

Average

21,223 142 12,785

Increase the escapment of 

Naturally produced Fall-run 

Chinook Salmon

62,000 fish 1992-2013 

Average

21,025 27 16,689

Increase the escapment of 

Hatchery produced Spring-run 

Chinook Salmon

3,000 fish 1992-2013 

Average

 7,493 195 5,835

Increase the escapment of 

Naturally produced Spring-run 

Chinook Salmon

6,00 fish 1992-2013 

Average

 6,147 52 3,144

Increase the escapment of 

Hatchery produced Coho 

Salmon

2,100 fish 1992-2013 

Average

 9,560 704 14,782

Increase the escapment of 

Naturally produced Coho 

Salmon

1,400 fish 1992-2013 

Average

 2,025 308 4,305

Increase the escapment of 

Hatchery produced Steelhead

10,000 fish 1992-2013 

Average

 9,268 68 6,816

Increase the escapment of 

Naturally produced Steelhead

40,000 fish 1992-2013 

Average

 7,018 23 9,119

Improve Infrastructure to allow 

ROD flows (369 TAF - 815 TAF)

Unspecified Annual Within 

target

 100

Provide minimum annual flows. 

The program releases between 

369,000 and 815,000 AF each 

year, in accordance with the 

ROD

369,000 Annual N/A 100 369,000 Based on 2014 as a 

critically dry water year

Trinity River Restoration Program (TRRP), 3406 (b)(1) Other

Complete 47 channel 

rehabilitation projects in the 

Trinity mainstem and 3 side 

channels

47 projects Cumulative 31 66 1

Place 10,000 cubic yards of 

coarse sediment annually

10,000 

cubic yards

Annual N/A 36 3,620
60 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA ACCOMPLISHMENTS

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, or 

Average)

To Date

(Cumulative 

or Average)

% of 

Target

Accomplishments Comments

Reduce fine sediment delivery 

from tributary watersheds

10,000 to 

20,000 

cubic yards

Annual N/A 78-155 15,500

San Joaquin River Restoration Plan (SJRRP), 3406 (c)(1)

Reduce or avoid water supply 

impacts to Friant Division longterm contractors

Unspecified Annual 0 Undefined 0

Restore and maintain fish 

populations in good condition

“Good” 

condition

Annual

Ecological and Water Systems Models, 3406 (g)

Develop readily usable and 

broadly available hydrologic and 

ecologic models and supporting 

data to evaluate existing and 

alternative water management 

strategies

9 

hydrologic/

ecologic 

modeltypes

Cumulative 8 89 0 (2)

CVP Water Operations

Reservoir Storage, 3406 (b)(19)

Maintain minimum reservoir 

storage in Shasta Reservoir

1.9 MAF Cumulative 14 of 16 88 1.16 MAF

Maintain minimum reservoir 

storage in Trinity Reservoir

600 TAF Cumulative 16 of 16 100 606 TAF

Refuges

Refuge Water Supply Program - Acquisition (INC L4), 3406 (b)(3) and 3406(d)(2)

Acquire 133,264 acre-feet 

for Incremental Level 4 water 

acquisition

133,264 

acre-feet

Annual 63,854 48 45,398

Refuge Water Supply Program - Conveyance, 3406 (d)(1) & (d) (2)

Provide Level 2 water supplies 

(Contract Year 2013)

422,251 

acre-feet

Annual N/A 64 387,611

Provide Incremental Level 4 

water supplies (Contract Year 

2013)

133,264 

acre-feet

Annual N/A 32 42,243 Full L4 delivery = 296,467 

(53% goal)

Refuge Water Supply Program - Construction (FULL L4 CAPACITY), 3406 (d)(5)

Provide external conveyance 

capacity to 19 refuges to receive 

Full Level 4 Water annually

555,515 

acre-feet

Cumulative 491,145 88

Refuge Water Supply Program - Construction (Planning, Design & Construction), 3406 (d)(5)

Planning, design & construction 

to provide conveyance capacity 

to deliver Full Level 4 water to 

19 Refuges

19 refuges 

with 

adequate 

conveyance

Cumulative 15 79 0

Other

Habitat Restoration, 3406 (b)(1) Other

Protect and/or restore habitat 

impacted by the CVP

Unspecified Cumulative 118,765 N/A 3,042

Protect and/or restore habitat 

areas specified by the SWRCB 

Decision 1641

45,391 

acres

Cumulative 9,847 20 795
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 61

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA ACCOMPLISHMENTS

Performance Goal Description Target

Reporting 

Period 

(Annual, 

Cumulative, or 

Average)

To Date

(Cumulative 

or Average)

% of 

Target

Accomplishments Comments

Land Retirement, 3408(h)

Retire 8,000 acres of Atwell 

Island land

8,000 

acres

Cumulative, 

1995–2014

 7,266 91 0

Retire 7,000 acres of Tranquility 

land

Complete Cumulative, 

1995–2014

7,000 100 N/A

Restore 400 acres of retired 

land annually

400 acres Cumulative, 

1995–2014

6,868 86 10

Reduce the production of 

agricultural drainage water by 

6,000 AF through the removal of 

irrigation water from the parcels 

within the Land Retirement 

Demonstration Project

6,000 acrefeetCumulative, 

1995–2014

47,805 60 0

(1) Clear Creek spawning gravel replenishment goal was erroneously reported in the Final CPAR, 2009 as 17,000 tons annually. 

This unit of measure for this goal should have been cubic yards. Applying a conversion factor, 17,000 cubic yards of spawning 

gravel equates to approximately 25,000 tons. This correction first occurred in the 2012 Accomplishment Report and therefore, the 

percentage of annual goal for this year forward will appear smaller than past years of the same amounts of gravel.

(2) The Modeling Program is reviewing procedures to provide a more comprehensive reporting metric. 

Complete and Inactive Programs

Program Name Status

Modify CVP Operations, 3406 (b)(1)(B) Incorporated into various programs

Contra Costa Canal Pumping Plant, 3406 (b)

(5)

Complete

Shasta Temperature Control Device, 3406 (b)

(6)

Complete

Meet Flow Standards and Objectives, 3406 

(b)(7)

Complete

Short Pulse Flows, 3406 (b)(8) Incorporated into various programs

Coleman National Fish Hatchery, 3406 (b)(11) Complete

Delta Cross Channel and Georgiana Slough, 

3406 (b)(14)

Inactive

Head of Old River Barrier, 3406 (b)(15) Inactive

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

Glenn-Colusa Irrigation District Program, 3406 

(b)(20)

Complete

Waterfowl Incentive Program, 3406 (b)(22) Complete

Trinity River Restoration Program, 3406 (b)

(23)

Complete

San Joaquin River Restoration Program, 3406 

(c)(1) 

Complete. Currently funded through Public Law 111-11

Stanislaus River Basin Water Needs Program, 

3406 (c)(2)

Complete

Central Valley Wetlands Supply, 3406 (d)(6) Complete

Supporting Investigations, 3406 (e) Complete

Project Fisheries Impact Report, 3406 (f) Complete

Water Conservation Program, 3408 (i) Complete

Water Augmentation (Yield Study), 3408 (j) Complete

Red Bluff Diversion Dam, 3406(b)(10) Complete
62 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

CHAPTER 6 - PROGRESS TO DATE TOWARD CVPIA ACCOMPLISHMENTS

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Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 63

APPENDICES

APPENDICES

Appendix A: Acronyms

AF acre-feet 

AFRP Anadromous Fish Restoration Program

AFSP Anadromous Fish Screen Program

ARRA American Recovery and Reinvestment Act

ATR Annual Technical Report

BDCP Bay Delta Conservation Plan

BLM Bureau of Land Management 

BMP Best Management Practices

BO Biological Opinion

CAMP Comprehensive Assessment Monitoring 

Program

CALFED CALFED Bay-Delta Program 

CCWD Contra Costa Water District

CDFW California Department of Fish and Wildlife 

cfs cubic feet per second

CPAR CVPIA Program Activity Review Report

CVP Central Valley Project

CVPIA Central Valley Project Improvement Act

CY Contract year

DHCCP Delta Habitat Conservation and

Conveyance Program

DOI Department of the Interior

DWR Department of Water Resources

ECOSIM Ecology Cogent Operations Suite 

of Integrated Models

EDT Ecosystem Diagnostic and Treatment

EIR Environmental Impact Report

EIS Environmental Impact Statement

ESA Endangered Species Act

EWSOMP Ecosystem and Water Systems 

Operations Models Program

FWS US Fish and Wildlife Service 

FWA Friant Water Authority

FY Fiscal year

GCID Glenn-Colusa Irrigation District

GWD Grassland Water District

HGS HydroGeoSphere

HRP Habitat Restoration Program

IFIM Instream Flow Incremental Methodology

Interior Department of the Interior

IP Implementation Plan

IRWMT Interagency Refuge Water Management

Team

LRP Land Retirement Program

NMFS National Marine Fisheries Service 

NOAA National Oceanic & Atmospheric

Administration

NRDC Natural Resources Defense Council

NWR National Wildlife Refuge 

OCAP Operations Criteria and Plan

OMB Office of Management and Budget 

PART Program Assessment Rating Tool

PEIS Programmatic Environmental Impact

Statement

POD Pelagic Organism Decline

RBDD Red Bluff Diversion Dam

RHEM Riparian Habitat Establishment Model

ROD Record of Decision

RPA Reasonable and Prudent Alternative

RST Rotary Screw Trap

RWSP Refuge Water Supply Program

SDM structured decision making

SJBAPL San Joaquin Basin Action Plan Lands

SJBAP San Joaquin Basin Action Plan 

SJRA San Joaquin River Agreement 

SJRGA San Joaquin River Group Authority

SJRR San Joaquin River Restoration

SMUD Sacramento Municipal Utility District

SNWR Sacramento National Wildlife Refuge

SWP State Water Project

TFCF Tracy Fish Collection Facility 

TRRP Trinity River Restoration Program

USBR Bureau of Reclamation
64 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

APPENDICES

Appendix B: 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 fish

Those stocks of salmon (including other species, 

e.g., 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 San 

Francisco Bay or the Pacific Ocean; fish 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 fish resource issues in Central 

Valley streams that are tributary to the Delta 

• Biota

Total collection of organisms of a geographic 

region or a time period

• CALFED Bay-Delta Program

A unique collaboration among 25 state and 

federal agencies that came together to improve 

California’s water supply and the ecological 

health of the San Francisco Bay/Sacramento-San 

Joaquin River Delta 

• 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 defined 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 defined 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: 

○ Protect, restore, and enhance fish, wildlife, 

and associated habitats in the Central Valley 

and Trinity River basins of California 

○ Address impacts of the Central Valley 

Project on fish, wildlife and associated 

habitats 

○ Improve the operational flexibility of the 

Central Valley Project 

○ Increase water-related benefits provided 

by the Central Valley Project to the State 

of California through expanded use of 

voluntary water transfers and improved 

water conservation 

○ Contribute to the State of California’s 

interim and long-term efforts to protect the 

San Francisco Bay/Sacramento-San Joaquin 

Delta Estuary 

○ Achieve a reasonable balance among 

competing demands for use of Central 

Valley Project water, including the 

requirements of fish and wildlife, 

agricultural, municipal and industrial and 

power contractors

• 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

• Central Valley Rivers and Streams

The 22 Central Valley main rivers and streams 

were defined in the January 9, 2001, Final 

Restoration Plan, Appendix B as: Sacramento 

River, Clear Creek, Cow Creek, Cottonwood 

Creek, Battle Creek, Paynes Creek, Antelope 

Creek, Mill Creek, Deer Creek, Miscellaneous 

creeks, Butte Creek, Big Chico Creek, Feather 

River, Yuba River, Bear River, American River, 

Mokelumne River, Cosumnes River, Calaveras 

River, Stanislaus River, Tuolumne River, and 

Merced River.

• Constant fractional marking program (CFM)

When fish are counted for CVPIA monitoring, 

program managers differentiate between wild 

and hatchery fish; hatcheries mark a percentage 

of juveniles before they are released and when 

fish come back to spawn, the mark will indicate 

which were hatchery-born
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 65

APPENDICES

• Diversion

Area where river water is rerouted in a direction 

other than its natural course

• Entrainment

When fish are diverted from their natural 

occurring water course (e.g., caught in a water 

pump or diverted from the river into an irrigation 

channel)

• 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 

fish (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 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 define 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 

defined 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 defined by the 

provisions of CVPIA that includes specific 

physical or structural actions

• Metric

The defined quantifiable 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 defined by Section 3403(h) of the CVPIA, 

“fish 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 specific 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 defined 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 SacramantoSan Joaquin Delta; pelagic organisms include, 

most notably, the delta smelt and longfin smelt, 

federally-listed endangered species of fish

• 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 

oversee implementation of the CVPIA program 

activities; each active program activity has a 

program manager from its respective agency

• Redd Dewatering

Occurs when redds (fish egg “nests”) are left 

exposed by receding water levels

• Replacement Water

CVP Water that was provided to five refuges 

prior to CVPIA. It is to be replaced to the Project 

when available and acquired from willing sellers. 

Replacement water is delivered in addition to the 

Level 2 amounts specified in the CVPIA

• Restoration Fund

The fund established by Section 3407 of 

the CVPIA to contribute resources for the 

environmental restoration provisions of the Act; 
66 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

APPENDICES

• Target

The quantifiable 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 fish ladder that utilizes a series of small 

dams and pools to create a long channel and 

allow spawning fish to get around an obstruction, 

like a dam

• WY

Water year runs from October 1-September 30

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 Central Valley Project Improvement 

Act (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 of Delta

The area that includes the State Water Project 

authorized place of use downstream of Harvey 

O. Banks Pumping Plant and the Central Valley 

Project authorized place of use downstream of 

Jones Pumping Plant

• Stranding

Stranding is a term used to describe fish that 

are trapped in pools of water that have no 

connectivity to the larger stream because of 

insufficient flow
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 67

APPENDICES

Appendix C: CVPIA Title 34 of 

Public Law 102-575

Sections

Anadromous Fish Restoration Program – 

Section 3406 (b)(1)

“The Secretary ... is authorized and directed to ... 

develop within three years of enactment and implement 

a program which makes all reasonable efforts to 

ensure that, by the year 2002, natural production of 

anadromous fish in Central Valley rivers and streams 

will be sustainable, on a long-term basis, at levels not 

less than twice the average levels, attained during the 

period of 1967-1991.” The section also states, “this 

goal shall not apply to the San Joaquin River between 

Friant Dam and the Mendota Pool, for which a separate 

program is authorized under subsection 3406(c) of 

this title; Provided further, That the programs and 

activities authorized by this section shall, when fully 

implemented, be deemed to meet the mitigation, 

protection, restoration, and enhancement purposes 

established by subsection 3406(a) of this title; And 

provided further, That in the course of developing and 

implementing this program the Secretary shall make 

all reasonable efforts consistent with the requirements 

of this section to address other identified adverse 

environmental impacts of the Central Valley Project not 

specifically enumerated in this section.”

Habitat Restoration Program – 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.”

Trinity River Restoration Program – 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 identified adverse environmental 

impacts of the Central Valley Project not specifically 

enumerated in this section”; and 

“In order to meet Federal trust responsibilities to protect 

the fishery resources of the Hoopa Valley Tribe, and to 

meet the fishery 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 

fishery restoration, propagation, and maintenance...”

Dedicated 800,000 acre-feet Project Yield – 

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...”

Water Acquisition Program - Instream Water – 

Sections 3406 (b)(3) 

“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.”

Tracy (Jones) Pumping Plant Program – 

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.”

Flow Fluctuations and Reservoir Storage – 

Section 3406 (b)(9) and (b)(19)

“(9) Develop and implement a program to eliminate, 

to the extent possible, losses of anadromous fish due 

to flow fluctuations caused by the operation of 

any Central Valley Project storage or re-regulating 

facility...”

 “(19) Reevaluate existing operational criteria in order 

to maintain minimum carryover storage at Sacramento 

and Trinity River reservoirs to protect and restore the 

anadromous fish of the Sacramento and Trinity Rivers 

in accordance with the mandates and requirements 

of this subsection and subject to the Secretary’s 

responsibility to fulfill all project purposes, including 

agricultural water delivery.”
68 Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575

APPENDICES

Clear Creek Restoration Program – Section 

3406 (b)(12)

“Develop and implement a comprehensive program to 

provide flows to allow sufficient spawning, incubation, 

rearing, and outmigration for salmon and steelhead 

from Whiskeytown Dam as determined by instream 

flow studies conducted by the California Department 

of Fish and Game after Clear Creek has been restored 

and a new fish ladder has been constructed at the 

McCormick-Saeltzer Dam...”

Spawning and Rearing Habitat Restoration 

Program – Section 3406 (b)(13) 

“Develop and implement a continuing program ... to 

restore and replenish spawning gravel...and rearing 

habitat ... on the American, Stanislaus and Sacramento 

Rivers ... shall include preventive measures...”

Comprehensive Assessment and Monitoring 

Program – Section 3406 (b)(16)

“...Establish, in cooperation with independent entities 

and the State of California, a comprehensive assessment 

program to monitor fish and wildlife resources in the 

Central Valley to assess the biological results and 

effectiveness of actions implemented pursuant to this 

subsection....”

Anadromous Fish Screen Program – Section 

3406 (b)(21)

“Assist the State of California in efforts to develop 

and implement measures to avoid losses of juvenile 

anadromous fish ... 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 fishery-sensitive areas.”

San Joaquin River Restoration Program – 

Section 3406 (c)(1)

“The Secretary shall ” ... develop a comprehensive 

plan which is reasonable, prudent, and feasible to 

address fish, wildlife, and habitat concerns on the 

San Joaquin River, including but not limited to the 

streamflow, channel, riparian habitat, and water quality 

improvements that would be needed to reestablish 

where necessary and to sustain naturally reproducing 

anadromous fisheries from Friant Dam to its confluence 

with the San Francisco Bay/Sacramento-San Joaquin 

Delta Estuary.”

Refuge Water Supply Program – Section 3406 

(d)(1), 3406 (d)(2), 3406 (d)(5)

“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 two-thirds of the water supply 

needed for full habitat development for those habitat 

areas identified in the “San Joaquin Basin Action Plan/

Kesterson Mitigation Action Plan Report...”

“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 

identified in the “San Joaquin Basin Action Plan/

Kesterson Mitigation Action Plan Report...”

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

construct or to acquire from non-Federal entities such 

water conveyance facilities, conveyance capacity, and 

wells as are necessary to implement the requirements of 

this subsection; provided, that such authorization shall 

not extend to conveyance facilities in or around the 

Sacramento-San Joaquin Delta Estuary...”

Ecosystem and Water Systems Operations 

Models – Section 3406 (g)

“The Secretary, in cooperation with the State of 

California and other relevant interests and experts, 

shall develop readily usable and broadly available 

models and supporting data to evaluate the ecologic and 

hydrologic effects of existing and alternative operations 

of public and private water facilities and systems in the 

Sacramento, San Joaquin, and Trinity River watersheds. 

The primary purpose of this effort shall be to support 

the Secretary’s efforts in fulfilling the requirements 

of this title through improved scientific understanding 

concerning, but not limited to, the following:

(1) a comprehensive water budget of surface and 

groundwater supplies, considering all sources of 

inflow and outflow 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 fisheries 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 flows and channel 

maintenance flows to protect and restore natural 

channel and riparian habitat values;
Fiscal Year 2014 Annual Report, Central Valley Project Improvement Act, Public Law 102-575 69

APPENDICES

(6) implementation of operational regimes at State 

and Federal facilities to increase springtime flow 

releases, retain additional floodwaters, and assist 

in restoring both upriver and downriver riparian 

habitats;

(7) measures designed to reach sustainable harvest 

levels of resident and anadromous fish, 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 firm yield of existing 

Central Valley Project facilities, including improved 

management and operations, conjunctive use 

opportunities, development of offstream storage, 

levee setbacks, and riparian restoration.”

Land Retirement – 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 beneficial to the overall purchase program, 

including the purposes of this title.”