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NOAA National Marine Fisheries Service’s (NMFS) Biological and Conference Opinion on the Long-Term Operations of the Central Valley Project and State Water Project National Research Council Committee on Sustainable Water and Environmental Management in the California Bay-Delta

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NOAA National Marine Fisheries Service’s (NMFS)

Biological and Conference Opinion on the Long-Term Operations of the Central Valley Project and State Water Project

National Research Council

Committee on Sustainable Water and Environmental Management in the California Bay-Delta

January 25, 2010

salmon population viability









Salmon Population Viability
viability criteria for esus
Viability Criteria for ESUs
  • At least two viable populations per diversity group
  • If possible, the populations should not have highly correlated risks of catastrophic disturbance

Status of

CV Spring-




population anatomy
Population Anatomy

Historical fall-run habitat Current fall-run habitat

  • Central Valley Salmonid ESUs are threatened with extinction
  • Water project facilities and operations have negative effects on fish habitat, with cascading effects on spatial structure, diversity, productivity, and abundance of populations
  • Improving in-stream flows and curtailing exports is necessary to conserve salmon, but will not be sufficient for recovery
  • An ecosystem perspective is needed to understand how human activities impact salmon
  • Adaptive management is needed to reduce risks
scope of today s presentation
Scope of today’s presentation
  • Brief highlights of Opinion – not all topics presented due to time constraints
  • Opinion itself is a summary document of over four years of analytic work between 5 agencies
  • Biological assessment, NMFS technical memos, peer review reports are important
  • 700+ scientific citations
  • Administrative record is 150,000 pages - - documents full decision-making process
approach to biological opinion challenges
Approach to Biological Opinion:Challenges
  • Complexity - geographic scope
  • Multi-species
  • State and federal project – combined operations
  • Number of dams and diversions
  • Economic importance of project
    • Urban water supply, agricultural water supply, commercial salmon fishery
  • Long-term proposed operations (21 years)
  • Litigation history
  • Current events (recession, drought, fishery closure)
approach to biological opinion constraints
Approach to Biological Opinion: Constraints
  • Our task – Limited to analyzing the Federal action, as proposed
  • Uncertainty in science; risk is balanced in favor of the species
  • Reasonable and Prudent Alternative (RPA) –
    • Limited to actions within authority and discretion of USBR and DWR
    • Minimum to avoid jeopardy; NOT a recovery plan
    • Must avoid jeopardy in short-term and long-term
    • Not necessary to prove quantitatively
consultation process
Consultation Process
  • Used a team of experienced federal biologists and hydrologists.
  • Adhered closely to legal requirements, agency guidelines, and used the best available scientific and commercial information
  • Maintained close and meaningful collaboration with the U.S. Bureau of Reclamation, CA Department of Water Resources, U.S. Fish and Wildlife Service, and CA Department of Fish and Game
  • Draft opinion peer reviewed by CALFED Independent Science Panel and Center for Independent Experts (CIE)
scientific evidence
Scientific Evidence
  • Used best scientific and commercial information
  • Literature review - 700 citations
  • Information from previous listing decisions, critical habitat rules, etc.
  • USBR’s Biological Assessment, including model outputs
  • Draft recovery plan
  • Monitoring reports
consultation background
Consultation Background
  • NMFS OCAP biological opinions:
    • Feb. 14, 1992, limited to winter-run Chinook salmon
    • 1993-2002, interim opinions issued due to changes in operations and new species listed
    • October 22, 2004: In 2008, Federal court invalidated that Opinion, and ordered that NMFS prepare a new Opinion.
    • June 4, 2009: Six complaints filed to date.
  • Close coordination with the USFWS throughout the OCAP consultation process
peer reviews of the draft biological opinion
CALFED Science Panel:

James J. Anderson, University of Washington & Columbia Basin Research

Mike Deas, Watercourse Engineering, Inc.

Philip B. Duffy, Climate Central, Inc.; University of California, Merced

Daniel L. Erickson, Consultant

Reg Reisenbichler, Retired--U.S. Geological Survey (USGS)

Kenneth A. Rose, Louisiana State University

Peter E. Smith, Retired--USGS

CIE reviewers:

Richard A. Marston

Ian A. Fleming

E. Eric Knudsen

Peer Reviews of theDraft Biological Opinion

CALFED & CIE reviews supported NMFS overall conclusions

peer reviews of the draft biological opinion cont d
Peer Reviews of the Draft Biological Opinion (cont’d)
  • Significant changes made in response to peer review recommendations:
    • Editing for clarity and consistency between division analyses
    • Estimate ranges of loss from compilation of existing studies, even when we did not have complete data sets
    • Assessed risk based on weighting and key lines of evidence
    • Plan for drought sequence – not a single dry year
analytical overview
Analytical Overview
  • Evaluated each stressor by species, life stage, and location
    • Risk and uncertainty incorporated throughout
      • Weighted evidence by certainty and magnitude of effect
    • Stated assumptions, reviewed model constraints and applicability, used ranges
    • Identified all direct and indirect effects
  • Considered variability in the Bay-Delta ecosystem
  • Summed for individual, population, diversity group and species levels.
analytical approach









Analytical Approach
  • Viable Salmonid Populations
analytical approach cont d
Analytical Approach (cont’d)
  • Central Valley Technical Recovery Team products:
    • Historical population structure
    • Assessing viability of Central Valley salmon and steelhead populations
  • Life cycle approach
stressors on listed species
Stressors on Listed Species
  • Loss of habitat and degraded water quality due to:
    • Non-Federal dams and diversions
    • Land use activities
  • Invasive species
  • Hatcheries
  • Harvest activities
  • Environmental variations
    • Ocean conditions
    • Climate change
effects overview
Effects Overview
  • Shasta Reservoir: Future operations, including climate change:
    • 5 to 65% mortality of winter-run Chinook salmon eggs and fry
  • Red Bluff Diversion Dam (RBDD):
    • Delays adult passage of up to 15% of the winter-run and up to 70% of the spring-run that spawn above the RBDD
    • Blocks up to 35% of green sturgeon from its only known spawning ground
  • American River:
    • Mean water temperatures > 65°F, results in increased incidence of disease in juvenile steelhead
    • ~75% of time in June, 100% in July and August, >95% in September
effects overview cont d
Effects Overview (cont’d)
  • Juvenile survival at export facilities:
    • About 1 in 3 survive through the Federal facilities
    • About 1 in 6 survive through the State facilities
  • Overall mortality in the interior Delta:
    • 35-90% of those that enter interior Delta
    • 5-20% of each winter-run Chinook salmon population
  • Juvenile San Joaquin River steelhead:

90-99% mortality from project and non-project stressors

  • Reduction in approximately 13-15% fall- and late fall-run Chinook salmon, which is killer whale prey; effects from hatchery management.
findings of the biological opinion
Findings of the Biological Opinion
  • OCAP would likely jeopardize:
    • Sacramento winter-run Chinook salmon
    • Central Valley spring-run Chinook salmon
    • Central Valley steelhead
    • Southern DPS of North American green sturgeon
    • Southern Resident killer whales
  • Destruction or adverse modification of designated and proposed critical habitat
  • Central California Coast steelhead – not likely to adversely affect this species or its critical habitat
reasonable and prudent alternative rpa overview
Reasonable and Prudent Alternative (RPA) Overview
  • Identified actions to alleviate major stressors for each species and summed these for short-term and long-term
  • Included appropriate flexibilities in RPA where possible
  • Monitoring, reporting, research, adaptive management
rpa overview cont d
RPA Overview (cont’d)
  • Scope – minimum to avoid jeopardy
    • Over 50 individual actions grouped by division, plus a fish passage program
  • Themes:
    • Water quantity and quality
    • gravel augmentation
    • improve passage
    • decrease entrainment
    • engineered solutions
key elements of the rpa
Key Elements of the RPA
  • Clear Creek below Whiskeytown Dam - increased flows and reduced temperatures
  • Shasta Reservoir and the Upper Sacramento River - new temperature management program
  • Shasta Dam - long-term passage prescriptions to allow re-introduction of listed salmon
  • Red Bluff Diversion Dam - interim gate operations until 2012, then gates up all year.
  • Lower Sacramento River basin and Delta - improved juvenile rearing habitat
key elements of the rpa cont d
Key Elements of the RPA (cont’d)
  • American River - New flow and temperature plan; fish passage at Folsom Dam
    • Hatchery Genetics Management Plan for Nimbus Hatchery for steelhead and fall-run Chinook salmon.
  • Stanislaus River – new flow schedule, temperature criteria, and habitat improvements
  • Delta Cross Channel Gates - Additional gate closures during key times when listed fish are likely to be migrating through the area
key elements of the rpa cont d1
Key Elements of the RPA (cont’d)
  • Old and Middle Rivers - Flows will be modified to reduce the number of juveniles exposed to the Delta pumps, and fish salvage improvements to reduce mortality
  • San Joaquin Basin - Increased flows and pumping curtailments.
  • Studies – 6 year study of acoustic tagged fish in the San Joaquin Basin to evaluate the effectiveness of the RPA and refine it over the life-time of the project.
rpa flexibilities
RPA Flexibilities
  • Real-time operations
  • Phased-in implementation
  • Performance-based approaches
  • Take limits based on annual juvenile production estimates
  • Actions tiered to water year type/drought exception
  • Research and adaptive management
other alternative rpa actions
Other Alternative RPA Actions
  • Evaluated during consultation and rejected (ineffective, critical habitat concerns, smelt concerns, predation issues, etc):
    • Trap and haul of San Joaquin steelhead
    • New screens at the existing pumps
    • New screens in the Delta (e.g., Georgiana Slough)
    • Permanent operable barriers at Head of Old River
    • Non-physical barrier alone at the Head of Old River (without increased flows and export curtailments)
alternatives continued
Alternatives (continued)

Alternatives to water supply evaluated and included in RPA:

  • Gravel augmentation
  • Rearing habitat restoration
  • Engineered solutions, including:
    • New fish screen at Red Bluff
    • New temperature infrastructure at Whiskeytown and Folsom Dams
    • Retrofits to existing salvage facilities
    • Non-physical barrier (bubble curtain)
carry over storage in shasta
Carry over Storage in Shasta

Long-term Average Annual and End of September Storage Differences for Shasta Storage, Spring Creek Tunnel Flow, and Keswick Release

Study 6.0 = 2004 operations Study 7.1 = near future operations

Study 7.0 =current operationsStudy 8.0 = future operations

Calsim and Sacramento River Water Quality Modeling results for temperature exceedances at Balls Ferry under future conditions Study 8.0




















Mean Daily Temperature (F)






























Date (month/day)

egg and fry mortality by water year type at balls ferry
Study 7.1

(near future)

Study 6.0


Study 7.0


Study 8.0


Percent Mortality

Water Year Type

Egg and Fry Mortality by Water Year Type at Balls Ferry
Study 7.1

(near future)

Study 6.0


Study 7.0


Study 8.0


Percent Mortality

Water Year Type

Percent Mortality

Water Year Type

summary of significant effects on the mainstem sacramento river
Summary of Significant Effects on the Mainstem Sacramento River
  • Long-term average loss of 121 TAF September carry-over storage (including effects of climate change) will:
    • Eliminate spring-run spawning in the mainstem
    • Reduce winter-run spawning habitat in the mainstem
    • Increase egg mortality substantially in consideration of climate change [i.e., Critical years increases to 5 to 65% for winter-run, 40 to 95% for spring-run (Sac. R mainstem only), and 4% for steelhead (based on late fall-run Chinook salmon as a surrogate)].
    • Result in shorter emigration period and lower survival for juvenile salmonids
4 months closed

2 months closed

summary of the main effects from operating rbdd
Summary of the Main Effects from Operating RBDD
  • Adult upstream migration:
    • Delays passage of up to 15% of the winter-run and

up to 70% of the spring-run

    • Blocks up to 35% of green sturgeon from its main spawning ground.
  • Juvenile downstream migration:
    • Higher predation rates on juvenile winter-run, steelhead, and green sturgeon as they pass through Lake Red Bluff and the diversion gates (i.e., 45% to 50% during May).
  • Critical habitat: Adverse modification of 6 stream miles from inundation behind RBDD.
rpa actions to address key sacramento river division effects
RPA Actions to Address Key Sacramento River Division Effects
  • Clear Creek: New temperature curtain in Whiskeytown
    • Reduce temperatures in October
  • Shasta Reservoir: Higher Shasta storage required in Sept. & April
  • Shasta Dam: New temperature management program
  • Upper Sacramento River:
    • Long-term passage prescriptions at Shasta Dam to allow re-introduction of listed salmon
    • RBDD gates up, year round by 2012
  • Lower Sacramento River and Delta: Restore juvenile rearing habitat
Exposure to daily mean water temps. above 65°F are associated with anal vent inflammation in juvenile steelhead in the LAR





“VSP” = Viable Salmonid Population

Folsom and Nimbus Dams


Loss of natural river function

Flow fluctuations


Redd scour

Low flows

Nimbus hatchery

Warm water temps

Angling impacts

Baseline Stressors

Project Stressors

summary of main effects on the lower american river
Summary of Main Effects on the Lower American River
  • Mean water temperatures above 65°F ~75% in June, 100% in July and August, >95% in September, resulting in increased incidence of disease in juvenile steelhead.
  • Reduced genetic diversity from hatchery management program.
rpa actions to address key american river division effects
RPA Actions to Address Key American River Division Effects
  • New flow and temperature plan; fish passage at Folsom Dam
  • Structural modifications for
    • Improved water temperature control device at Folsom Dam
    • Temperature control curtains at Lake Natoma
    • Temperature control at El Dorado Irrigation District Diversion
  • Hatchery Genetics Management Plan for Nimbus Hatchery for steelhead and Fall-run Chinook salmon.
eastside division

Eastside Division

New Melones and Stanislaus River operations

Rhonda Reed

stanislaus river new melones dam
Stanislaus River – New Melones Dam
  • Listed Species: Central Valley steelhead
  • Southern Sierra Nevada diversity group
  • Current population numbers very low for all 4 populations




summary of the main effects on the stanislaus river
Summary of the Main Effects on the Stanislaus River
  • Temperature
    • Water temperatures too warm for CV steelhead, 3-20% of time , especially May-Sept.
summary of the main effects on the stanislaus river1
Summary of the Main Effects on the Stanislaus River
  • Temperature
  • Flow
    • Instream flow requirements for CV steelhead not addressed
summary of the main effects on the stanislaus river2
Summary of the Main Effects on the Stanislaus River
  • Temperature
  • Flow
  • Ongoing critical habitat degradation
    • Channel incision cuts off rearing habitat
    • Spawning gravel washed out
    • Channel encroachment.
Modeled Monthly Temperature Exceedance Probability:

July- Orange Blossom Bridge

Daily Temperature Variability

channel demobilization
Channel Demobilization

Kondolf, et al. 2001

rpa actions to address key east side division effects
RPA Actions to Address Key East Side Division Effects
  • Establish Stanislaus Operations Group
  • Set operational temperature criteria
  • Set minimum flows for steelhead survival
  • Channel maintaining flows in wet years
  • Habitat improvements for spawning and rearing habitat, building on Central Valley Project Improvement Act authorities
  • Assess fish passage past New Melones Dam
delta division

Delta Division

Jeff Stuart

key elements in delta division

Key Elements in Delta Division

Climate Change

DCC Gates

Proposed Export Changes

Direct Entrainment at Project Facilities

Indirect Mortality within Delta

San Joaquin River Inflow to Delta

climate change impacts to delta
Climate Change Impacts to Delta:

Fall and winter seasons have greatest sensitivity to climate change according to OCAP modeling.

Drier climates:

In wet years: > risk of pumping entrainment in winter compared to current climate.

In dry years: minimal change in OMR flows during winter and spring.

Wetter climates:

In wet years: < pumping entrainment risk in winter, more positive OMR flows

In dry years: > risks in the winter , slightly more negative OMR flows

dcc gate operations
DCC Gates

Sacramento River

DCC Gate Operations





dcc gates
DCC Gates
  • Manmade channel (early 1950s) to enhance water quality for CVP exports at Tracy
  • Can pass 6,000 cfs when gates are open, ≈ 20 to 25 percent of Sacramento River flow at Freeport can move into the Mokelumne River
  • Listed salmonids are diverted into the channel when the gates are open. Entrainment rate is related to river flow, time of day, and tidal cycle.
  • Survival of these fish is substantially lower than those fish that remain in the Sacramento River .
  • Early migrating salmon and steelhead (Nov – Jan) are at risk under current operations schedule.
Timing of Juvenile winter-run passage at Knights Landing

rotary screw trap sampling 1995-2006

(Low, White, and Chappell 2006)

rpa overview for dcc gates
RPA Overview for DCC Gates
  • Integrate current monitoring triggers with new gate operations in December and January.
  • Close DCC gates from December 15 to January 31.
  • Weekly evaluations of monitoring data by the Delta Operations for Salmonids and Sturgeon technical team (DOSS).
  • Flexibility of gate operations regarding water quality criteria and experimental studies.
  • Study alternative engineering solutions to control access to the Delta interior
modeled changes in export levels
Modeled Changes in Export Levels

CVP and SWP exports increase in both near future (Study 7.1) and future conditions (Study 8.0) compared to the current condition (Study 7.0).

Significant increases in exports during the late fall and winter time frames over current operations.

SWP exports increase in April and May due to decrease in “fish water” available for export curtailment.

effects to listed salmonids
Effects to Listed Salmonids

Elevated exports result in an increased potential for entrainment at the export facilities, as well as migrational delays for fish entering the Delta interior,

Increases in exports reflected in increased negative Old and Middle River flows

Diversion of listed fish into the interior of the Delta increases the risk of mortality (i.e., predation) as well as exposure to contaminants in the Delta interior. Overall mortality in the interior Delta:

35-90% of those that enter the interior Delta

5-20% of winter-run Chinook salmon population entering the Delta

San Joaquin River Basin fish have an increased vulnerability to entrainment with increased exports levels.



Flow Patterns in the Delta

particle entrainment at the export facilities under different omr flows
Particle Entrainment at the Export Facilities under different OMR flows

~ 40%

USFWS 2008

Initial Slope

SWP Loss vs. OMR flows

rpa overview for exports
RPA Overview for Exports
  • Integrate current monitoring triggers with new export operations January through June.
  • Limit OMR flows, no more negative than -5,000 cfs January through June.
  • Staged Reductions in exports when fish are present at the facilities, measured by OMR flow levels.
  • Weekly review of operations and fish salvage by the DOSS technical group.
  • Actions compatible with the FWS Delta smelt actions
direct entrainment at project facilities
Direct Entrainment at Project Facilities
  • Survival is low through the salvage facilities:
    • 1 out of 6 fish survive at the SWP
    • 1 out of 3 fish survive at the CVP
  • Screening Efficiency
  • Predation issues
  • CHTR operations (Collection, Handling, Trucking and Release)
rpa overview for direct export entrainment
RPA Overview for Direct Export Entrainment
  • Increase overall salvage efficiency to 75% for both facilities
  • Directed actions for both facilities include:
    • Improve screening efficiency/operations
    • Reduce predation losses
    • Improve reporting methodology
  • Improve survival of salvaged fish releases
    • Release fish from mobile barges, multiple release sites, or other methods
indirect mortality in delta interior
Indirect Mortality in Delta Interior

Assessed indirect mortality within delta interior utilizing applicable studies and literature.

Compared export and non-export related mortality within the interior delta utilizing DWR’s Delta Survival model and CalSim II output from Studies 7.0 (current operations),

7.1 (near future operations), and 8.0 (future operations).

Assessed recent survival studies utilizing acoustically tagged fish.

results from dwr survival model
Monthly export related mortality for Sacramento River fish ranged from <1% to 15% combining all studies and water year types for the period between December and June.

Monthly Indirect mortality (non-export) for Sacramento River fish ranged from 3% to 32% combining all studies and water year types for the period between December and June.

Higher E/I ratios had higher mortality levels.

Higher E/I ratios typically occurred in December and January in drier hydrological conditions.

Monthly total population mortality for Sacramento River basin fish migrating downstream in the Sacramento River ranged from 23% to 59% under same conditions as above.

Results from DWR Survival Model
rpa overview for indirect mortality
RPA Overview for Indirect Mortality
  • Indirect mortality is related to most of the project elements associated with the Delta
  • The suite of RPA actions that focus on the Delta elements act in concert to reduce indirect mortality by reducing exposure to the sources of mortality
san joaquin river inflow to the delta
San Joaquin River Inflow to the Delta
  • OCAP assumes that VAMP – like flows and exports will continue into the future.
  • BUT: No defined description of this operation has been presented to date and there is limited “fish water” available to offset VAMP water costs in the future.
  • Spring-time flows currently seen during the VAMP operations on the Tuolumne River and Merced River are likely to decline
  • Project and non-project stressors result in 90-99% mortality of Juvenile San Joaquin River steelhead.
  • Increased survival and subsequent adult returns are linked to increased river flows during the juvenile outmigration period
Total Escapement to the San Joaquin River Tributaries, 1951 through 1996,

And Spring Time flows 2.5 years Earlier

From Baker and Morhardt, 2001

Relationship between Adult Fall-run Chinook Salmon Escapement

and the Vernalis flow to export ratio 2.5 years earlier

From 2006 VAMP report

rpa overview for san joaquin river flows into the delta
RPA Overview for San Joaquin River Flows into the Delta
  • Flows are based on previous studies and historical gaged flows at Vernalis.
  • Numerous iterations of the proposed flow criteria were run to examine the effects of the action before deciding on a final action.
  • RPA is phased in over time
  • Flexibility in RPA pertaining to water year type and drought conditions
  • Continuing adaptive management
NMFS’ OCAP Opinion is located at