Section 3406 (b)(1) 

Ramon Martin and Kim Webb

U.S. Fish and Wildlife Service 

and

Tom Kisanuki

Bureau of Reclamation

Habitat Restoration Fish Passage Habitat Assessments Collaboration
(b)(1) Program Goal

• “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(Section 3406(b)(1) of the CVPIA).”

• AFRP Chinook Salmon Natural Production Targets 

Central Valley 990,000 

Fall Run 750,000

Late-Fall Run 68,000

Spring Run 68,000

Winter Run 110,000

• See AFRP website for more information 

http://www.fws.gov/stockton/afrp/index.cfm Photo: EBMUD
(b)(1) Objectives

• Improve habitat for all life stages of anadromous fish through 

provisions 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 the implementation and evaluation of 

restoration actions.
Project Development

• Habitat Restoration Coordinators (HRCs) are assigned to 

geographic areas/watersheds where they work closely with 

watershed groups, river management teams, technical 

advisory committees, stakeholders, and agencies.

• HRCs focus on limiting factors (technical issues), 

habitat assessments, development of watershed 

management plans, and feasibility (other issues such as 

landowner/community support) to identify and propose 

projects with agency staff and partners.

• Collaboration and coordination with the State and other 

programs/efforts (i.e. ERP, Delta Science Program, BDCP). 

• Planning and Permitting
(b)(1) Project Prioritization

• Annually AFRP staff evaluate prioritization process and revise if 

needed

• HRCs receive input from watershed groups, agencies, NGOs, and 

other stakeholders

• AFRP discuss ongoing projects, current status and needs for the 

next year

• New projects/studies/monitoring are proposed, discussed, and 

prioritized by HRCs
(b)(1) Project Prioritization

• Each proposed project is scored by all HRCs following the AFRP 

prioritization criteria. 

• Ongoing projects receive highest priority for funding.

• Scores are assigned to projects if they are in a 1) CVP stream, 2) 

watershed priority in the FRP, 3) doubling goal status, 4) limiting 

factor, 5) benefit ESA listed species, 6) permits and 

environmental documents are in place, 7) cost match, and 8) 

addresses a CPAR or PART action.

• An AWP of ranked projects/studies/monitoring is created for the 

next year. 
Yuba River Hammon Bar Riparian 

Habitat Restoration

• Five acres were planted with cottonwood and willow pole cuttings to restore 

riparian habitat in the lower Yuba River (FRP Evaluation 4).

• Post-project monitoring (FY13 AWP Activity 2.8.2) to evaluate site inundation 

frequency and the survival and growth of the pole cuttings.

• Results will be used to inform the installation of future riparian restoration 

projects so as to provide the greatest value to juvenile salmonid rearing habitat.

• Project partners include SYRCL, Americorps, CDFW, YCWA, PG&E, BLM, and 

Western Aggregates.

Credit: CBEC

Photo: USFWS
Yuba River Narrows Channel 

Restoration Project

• The Yuba River Narrows Channel Restoration Project will restore up to 0.5 miles of in-channel 

habitat by restoring and replenishing gravel and removing shot rock debris from the Narrows 

Reach. This project will benefit Fall- and Spring-run Chinook salmon and Steelhead (FRP 

Evaluation 4).

• FY13 AWP Activity 2.6.4 funds pre-project surveys for the Yuba River Narrows Channel 

Restoration Project.

• Results will be used to develop design alternatives that will provide the greatest value to 

improve salmonid spawning habitat.

• Project partners include YCWA, PG&E, USACOE, and CDWR.

Photo: USFWS Photo: USFWS
Yuba River Daguerre Alley 

Floodplain Restoration Project

• Yuba River Daguerre Alley Floodplain Restoration Project will restore up 

to 180 acres of floodplain habitat and approximately 2.5 miles of side 

channel habitat. This project will benefit steelhead and Chinook salmon 

(FRP Evaluation 4).

• FY13 AWP Activity 2.6.5 funds pre-project surveys and the development 

of a River2D model for the Daguerre Alley Floodplain Restoration Project .

• Results will be used to inform the design and feasibility as to provide the 

greatest value to juvenile salmonid rearing habitat.

• This project is a cooperative effort between the USFWS, CDFW, NMFS, 

USACOE, Yuba River Management Team, and Yuba County Water Agency.
Photo: Cramer Fish Sciences

Merced River Ranch Floodplain 

Restoration 

• Once completed in 2013, the Merced River Ranch Floodplain Enhancement Project will 

restore up to 6 acres of riparian floodplain and 1.23 miles of spawning habitat (FRP 

Action 3 and Evaluation 2).

• FY13 Activity funds the Reclamation Plan, complete implementation, and post-project 

monitoring (FY13 AWP Activity 2.4.3, 2.7.2, and 2.8.3) to determine if the project was 

installed according to the design standards. Hydrology, topography/bathymetry, 

sediment budget, and vegetation will be assessed. 

• Complements the multi-phased restoration of the Merced River (ERP-02-P12-D).

• This project is a cooperative effort between the USFWS, CDFW, and ERP. 

Photo: USFWS
Merced River Snelling 

Channel and Floodplain Restoration 

• The Merced River Snelling Channel and Floodplain Restoration Project at Henderson Park will 

restore up to 80 acres of riparian floodplain and 2 miles of in-channel spawning habitat (FRP 

Action 3 and Evaluation 2).

• FY13 AWP Activity 2.7.3 and 2.7.4 funds the first stage of construction and implementation.

• Complements the multi-phased restoration of the Merced River described in the Merced 

River Restoration Corridor Plan (ERP-02-P12-D).

• This project is a cooperative effort between the USFWS, Merced County, CDFW, and ERP. 
• Continue ongoing restoration at six gravel augmentation sites and three side 

channels at Nimbus Basin, Upper Sailor Bar, Lower Sailor Bar, Upper Sunrise, and 

River Bend Park (FRP Action 5) (FY13 AWP Activity 2.7.5).

• Project monitoring and development of a Structured Decision Making Model to 

assess limiting factors and restoration actions.

• This project is being co-implemented with the CDFW, the Sacramento Area Water 

Forum, Sacramento County Parks, CSU-Sacramento, and the 3406 (b)(13) program 

which provided FY 2012 funding of $260,000 for ongoing gravel augmentation.

Lower American River 

Floodplain Restoration

Photo: USFWS Photo: USFWS
• The Floodplain Restoration Project at Knights Ferry (FRP Action 2) will restore 

up to 1 acre of side-channel and floodplain habitat to benefit Chinook salmon and 

steelhead. 

• FY13 AWP activities fund the environmental compliance, engineering designs, 

and pre-project monitoring (FY13 AWP Activity 2.4.1, 2.5.1 and 2.6.1).

• Addresses Action III.2.3 in NMFS OCAP BO

• This project is a cooperative effort between the USFWS, USBR, CDFW, and the 

USACOE.

Stanislaus River 

Floodplain Restoration 

Photos: Cramer Fish 

Sciences
• The Floodplain Restoration Project at Buttonbush (FRP Action 2) will restore up 

to 18 acres of floodplain habitat and approximately 2,800 feet of side-channel 

habitat to benefit Chinook salmon and steelhead. 

• FY13 AWP activities fund the engineering designs and pre-project monitoring 

(FY13 AWP Activity 2.5.2).

• Addresses Action III.2.3 in NMFS OCAP BO

• This project is a cooperative effort between the USFWS, USBR, CDFW, and the 

USACOE.

Stanislaus River 

Floodplain Restoration 

Photos: USFWS
• The Stanislaus River Floodplain and Side-channel Restoration Project at 

Lancaster Rd. (FRP Action 2) was completed in 2012 and restored 2 acres of 

floodplain habitat and approximately 640 feet of side-channel habitat to benefit 

Chinook salmon and steelhead. 

• FY13 AWP activities fund the post-project monitoring (FY13 AWP Activity 

2.8.1).

• Addresses Action III.2.3 in NMFS OCAP BO

• This project is a cooperative effort between the USFWS, USBR, and the 

USACOE.

Stanislaus River 

Floodplain Restoration 

Photos: USFWS
• South Fork Cottonwood Fish Passage Improvement Project will repair a fish passage 

barrier blocking five miles of high quality spawning and rearing habitat. Species to 

benefit include steelhead, Fall- and Spring-run Chinook salmon.

• This activity will fund pre-project monitoring and permitting at the Hammer Diversion 

hydropower dam (FY13 AWP Activity 2.4.2 and 2.6.2).

• This project is a cooperative effort between USFWS, CDFW, and NMFS. 

South Fork Cottonwood 

Fish Passage Improvement Project

Photo: CDFW Photo: CDFW
• Mill Creek Fish Passage Phase 2 funds environmental compliance and preproject monitoring to address fish passage at the Upper Dam and Ward Dam 

diversion structures in Mill Creek. This project will benefit Chinook salmon and 

steelhead and provide access to 44 miles of spawning habitat (FY13 AWP 

Activity 2.4.4 and 2.6.3).

• This project is a cooperative effort between USFWS, CDFW, and Los Molinos

Mutual Water Company.

Mill Creek Fish Passage

Upper Dam

Photo: CDFW Photo: USFWS

Ward Dam
• The juvenile fish passage improvement project will prevent out-migrating 

salmonids from becoming entrained in the two diversion canals in 

Antelope Creek. Although the diversions are screened, no bypass system 

was installed during construction due to site complexity (FRP Action 1). 

• FY13 activities fund environmental compliance and additional design 

alternatives (FY13 Activity 2.4.5 and 2.5.3).

• This project is a cooperative effort between the USFWS, CDFW, NMFS, 

TCRCD, Los Molinos Mutual Water Company, and the landowner.

Juvenile Fish Passage 

Improvement Project in Antelope Creek

Photos: CDFW
• Completed in 2012 and improved passage to 13 miles of 

spawning and holding habitat for spring run Chinook salmon 

in Antelope Creek (FRP Action 1).

• FY13 Activity 2.8.4 funds the post-project topographic 

surveys and monitoring.

• Addresses Action I.3.5 in NMFS OCAP BO

• This project is a cooperative effort between the USFWS, 

USBR, and the CDFW.

Tehama Wildlife Area 

Fish Passage Project

Photos: USFWS Photos: CDFG
Cosumnes River and Delta 

Cougar Wetland Restoration

Photo: CDFG

• This project will restore up to 85 acres of riparian and tidal shallow water 

habitat for Fall Chinook and Steelhead (FRP Delta Evaluations 4 and 6). 

• The interagency project team has developed conceptual plans to 

reconnect historic tidal sloughs to the mainstem Cosumnes River and return 

this site to a flooded tidal marsh/oak woodland complex.

• This project is a collaborative effort between the USFWS, BLM, USACOE, 

CDWR, and Ducks Unlimited. Total project costs are estimated at $800,000 

and CVPIA has funded $250,000 towards the implementation of this project.

Photo: Westervelt

Photo: UC Davis
• San Joaquin River Sturgeon Acoustic Study 

(FY13 AWP Activity 4.2.1)

• San Joaquin River Sturgeon Habitat 

Assessment (FY13 AWP Activity 4.2.2 and 4.2.3)

• Identify sturgeon spawning habitat and use in 

the San Joaquin River system (FRP Evaluation 4).

Research, Evaluations, Studies, 

Investigations

Photo: USFWS Photo: USFWS

Photo: USGS

Photo: USGS
• Mill and Deer Creek Wild Juvenile Chinook Acoustic Tagging Investigation 

(FY13 AWP Activity 4.2.4)

• Juvenile spring- and fall-run Chinook salmon will be implanted with acoustic 

transmitters to evaluate the effects of natural and anthropogenic changes in 

flow and related water project operations on their survival and movement 

patterns within the Sacramento River and Delta (FRP Upper Mainstem

Sacramento Evaluation 1).

• This activity provides funding for Year 2 of a 3 -year study with the NMFS 

Southwest Science Center. Cost share of $1.7 million from ERP and CVPIA is 

funding $450,000. Project partners include NMFS, CDFW, UC Davis, and UC 

Santa Cruz.

Research, Evaluations, Studies, 

Investigations

Photo: USFWS Photo: USFWS
Adaptive Management
Adaptive Management

0

50

100

150

200

250

300

350

400

450

500

550

8/1/2010

8/15/2010

8/29/2010

9/12/20109/26/2010

10/10/201010/24/2010

11/7/2010

11/21/2010

12/5/2010

12/19/2010

1/2/2011

1/16/20111/30/2011

Date

Number of Fish

0

500

1000

1500

2000

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Flow below WIDD (cfs)

Chinook salmon

DCC Closure

Golf Flow (cfs)

2010-2011 Mokelumne River fall-run Chinook salmon escapement
Stanislaus River 

Adaptive Management

Source: Cramer Fish Sciences

Post project assessment and Radio-tagged Chinook salmon

Photos: Cramer Fish Sciences

• Overall survival (for fish outmigrating

through entire study area):

• S0 = 0.07 (SE = 0.03; lower 95% CI = 0.03, 

upper 95% CI = 0.13)
Stanislaus River 

Adaptive Management

Floodplain Restoration

Photos: Cramer Fish Sciences

• Inundated Floodplain at 1500 cfs in the 

Stanislaus (red)

• Identify floodplain restoration areas Source: USFWS, unpublished data
Questions?

Photo: EBMUD