Source: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-ca9-12-15289/USCOURTS-ca9-12-15289-0/pdf.json

Nature of Suit Code: 893
Nature of Suit: Environmental Matters
Cause of Action: 

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FOR PUBLICATION

UNITED STATES COURT OF APPEALS

FOR THE NINTH CIRCUIT

SAN LUIS & DELTA-MENDOTA

WATER AUTHORITY; WESTLANDS

WATER DISTRICT; STOCKTON EAST

WATER DISTRICT; METROPOLITAN

WATER DISTRICT OF SOUTHERN

CALIFORNIA; OAKDALE IRRIGATION

DISTRICT; SOUTH SAN JOAQUIN

IRRIGATION DISTRICT; KERN

COUNTY WATER AGENCY;

COALITION FOR A SUSTAINABLE

DELTA; STATE WATER

CONTRACTORS,

Plaintiffs-Appellees,

CALIFORNIA DEPARTMENT OF

WATER RESOURCES,

Intervenor-Plaintiff–Appellee,

v.

GARY LOCKE; UNITED STATES

DEPARTMENT OF COMMERCE;

NATIONAL OCEANIC AND

ATMOSPHERIC ADMINISTRATION;

NATIONAL MARINE FISHERIES

SERVICE; JAMES W. BALSIGER;

RODNEY R. MCINNIS; U.S.

DEPARTMENT OF THE INTERIOR;

UNITED STATES BUREAU OF

No. 12-15144

D.C. No.

1:09-cv-01053-

LJO-DLB

 Case: 12-15289, 12/22/2014, ID: 9357518, DktEntry: 150-1, Page 1 of 80
2 SAN LUIS V. LOCKE

RECLAMATION; MICHAEL L.

CONNOR; DONALD R. GLASER; JANE

LUBCHENCO; SALLY JEWELL,

*

Defendants,

and

THE BAY INSTITUTE; CALIFORNIA

TROUT; FRIENDS OF THE RIVER;

NATURAL RESOURCES DEFENSE

COUNCIL; NORTHERN CALIFORNIA

COUNCIL OF THE FEDERATION OF

FLY FISHERS; SAN FRANCISCO

BAYKEEPER; SACRAMENTO RIVER

PRESERVATION TRUST; WINNEMEM

WINTU TRIBE; PACIFIC COAST

FEDERATION OF FISHERMEN’S

ASSOCIATIONS, INC., Institute for

Fisheries Research,

Intervenor-Defendants–Appellants.

SAN LUIS & DELTA-MENDOTA

WATER AUTHORITY; WESTLANDS

WATER DISTRICT,

Plaintiffs-Appellants,

and

No. 12-15289

D.C. No.

1:09-cv-01053-

LJO-DLB

*

 Sally Jewell is substituted for her predecessor, Kenneth Lee Salazar,

as Secretary of the Interior. Fed. R. App. P. 43(c)(2).

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SAN LUIS V. LOCKE 3

STOCKTON EAST WATER DISTRICT;

METROPOLITAN WATER DISTRICT OF

SOUTHERN CALIFORNIA; OAKDALE

IRRIGATION DISTRICT; SOUTH SAN

JOAQUIN IRRIGATION DISTRICT;

KERN COUNTY WATER AGENCY;

COALITION FOR A SUSTAINABLE

DELTA; STATE WATER

CONTRACTORS,

Plaintiffs,

CALIFORNIA DEPARTMENT OF

WATER RESOURCES,

Intervenor-Plaintiff,

v.

GARY LOCKE; UNITED STATES

DEPARTMENT OF COMMERCE;

NATIONAL OCEANIC AND

ATMOSPHERIC ADMINISTRATION;

NATIONAL MARINE FISHERIES

SERVICE; JAMES W. BALSIGER;

RODNEY R. MCINNIS; U.S.

DEPARTMENT OF THE INTERIOR;

UNITED STATES BUREAU OF

RECLAMATION; MICHAEL L.

CONNOR; DONALD R. GLASER; JANE

LUBCHENCO; SALLY JEWELL,

Defendants-Appellees,

THE BAY INSTITUTE; CALIFORNIA

TROUT; FRIENDS OF THE RIVER;

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4 SAN LUIS V. LOCKE

NATURAL RESOURCES DEFENSE

COUNCIL; NORTHERN CALIFORNIA

COUNCIL OF THE FEDERATION OF

FLY FISHERS; SAN FRANCISCO

BAYKEEPER; SACRAMENTO RIVER

PRESERVATION TRUST; WINNEMEM

WINTU TRIBE; PACIFIC COAST

FEDERATION OF FISHERMEN’S

ASSOCIATIONS, INC., Institute for

Fisheries Research,

Intervenor-Defendants–Appellees.

SAN LUIS & DELTA-MENDOTA

WATER AUTHORITY; WESTLANDS

WATER DISTRICT; STOCKTON EAST

WATER DISTRICT; METROPOLITAN

WATER DISTRICT OF SOUTHERN

CALIFORNIA; OAKDALE IRRIGATION

DISTRICT; SOUTH SAN JOAQUIN

IRRIGATION DISTRICT; KERN

COUNTY WATER AGENCY;

COALITION FOR A SUSTAINABLE

DELTA,

Plaintiffs,

CALIFORNIA DEPARTMENT OF

WATER RESOURCES,

Intervenor-Plaintiff,

and

No. 12-15290

D.C. No.

1:09-cv-01053-

LJO-DLB

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SAN LUIS V. LOCKE 5

STATE WATER CONTRACTORS,

Plaintiff-Appellant,

v.

GARY LOCKE; UNITED STATES

DEPARTMENT OF COMMERCE;

NATIONAL OCEANIC AND

ATMOSPHERIC ADMINISTRATION;

NATIONAL MARINE FISHERIES

SERVICE; JAMES W. BALSIGER;

RODNEY R. MCINNIS; U.S.

DEPARTMENT OF THE INTERIOR;

UNITED STATES BUREAU OF

RECLAMATION; MICHAEL L.

CONNOR; DONALD R. GLASER; JANE

LUBCHENCO; SALLY JEWELL,

Defendants-Appellees,

THE BAY INSTITUTE; CALIFORNIA

TROUT; FRIENDS OF THE RIVER;

NATURAL RESOURCES DEFENSE

COUNCIL; NORTHERN CALIFORNIA

COUNCIL OF THE FEDERATION OF

FLY FISHERS; SAN FRANCISCO

BAYKEEPER; SACRAMENTO RIVER

PRESERVATION TRUST; WINNEMEM

WINTU TRIBE; PACIFIC COAST

FEDERATION OF FISHERMEN’S

ASSOCIATIONS, INC., Institute for

Fisheries Research,

Intervenor-Defendants–Appellees.

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6 SAN LUIS V. LOCKE

SAN LUIS & DELTA-MENDOTA

WATER AUTHORITY; WESTLANDS

WATER DISTRICT; STOCKTON EAST

WATER DISTRICT; METROPOLITAN

WATER DISTRICT OF SOUTHERN

CALIFORNIA; OAKDALE IRRIGATION

DISTRICT; SOUTH SAN JOAQUIN

IRRIGATION DISTRICT; STATE

WATER CONTRACTORS,

Plaintiffs,

CALIFORNIA DEPARTMENT OF

WATER RESOURCES,

Intervenor-Plaintiff,

and

KERN COUNTY WATER AGENCY;

COALITION FOR A SUSTAINABLE

DELTA,

Plaintiffs-Appellants,

v.

GARY LOCKE; UNITED STATES

DEPARTMENT OF COMMERCE;

NATIONAL OCEANIC AND

ATMOSPHERIC ADMINISTRATION;

NATIONAL MARINE FISHERIES

SERVICE; JAMES W. BALSIGER;

RODNEY R. MCINNIS; U.S.

DEPARTMENT OF THE INTERIOR;

UNITED STATES BUREAU OF

No. 12-15291

D.C. No.

1:09-cv-01053-

LJO-DLB

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SAN LUIS V. LOCKE 7

RECLAMATION; MICHAEL L.

CONNOR; DONALD R. GLASER; JANE

LUBCHENCO; SALLY JEWELL,

Defendants-Appellees,

THE BAY INSTITUTE; CALIFORNIA

TROUT; FRIENDS OF THE RIVER;

NATURAL RESOURCES DEFENSE

COUNCIL; NORTHERN CALIFORNIA

COUNCIL OF THE FEDERATION OF

FLY FISHERS; SAN FRANCISCO

BAYKEEPER; SACRAMENTO RIVER

PRESERVATION TRUST; WINNEMEM

WINTU TRIBE; PACIFIC COAST

FEDERATION OF FISHERMEN’S

ASSOCIATIONS, INC., Institute for

Fisheries Research,

Intervenor-Defendants–Appellees.

SAN LUIS & DELTA-MENDOTA

WATER AUTHORITY; WESTLANDS

WATER DISTRICT; STOCKTON EAST

WATER DISTRICT; OAKDALE

IRRIGATION DISTRICT; SOUTH SAN

JOAQUIN IRRIGATION DISTRICT;

STATE WATER CONTRACTORS; KERN

COUNTY WATER AGENCY;

COALITION FOR A SUSTAINABLE

DELTA,

Plaintiffs,

No. 12-15293

D.C. No.

1:09-cv-01053-

LJO-DLB

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8 SAN LUIS V. LOCKE

CALIFORNIA DEPARTMENT OF

WATER RESOURCES,

Intervenor-Plaintiff,

and

METROPOLITAN WATER DISTRICT OF

SOUTHERN CALIFORNIA,

Plaintiff-Appellant,

v.

GARY LOCKE; UNITED STATES

DEPARTMENT OF COMMERCE;

NATIONAL OCEANIC AND

ATMOSPHERIC ADMINISTRATION;

NATIONAL MARINE FISHERIES

SERVICE; JAMES W. BALSIGER;

RODNEY R. MCINNIS; U.S.

DEPARTMENT OF THE INTERIOR;

UNITED STATES BUREAU OF

RECLAMATION; MICHAEL L.

CONNOR; DONALD R. GLASER; JANE

LUBCHENCO; SALLY JEWELL,

Defendants-Appellees,

THE BAY INSTITUTE; CALIFORNIA

TROUT; FRIENDS OF THE RIVER;

NATURAL RESOURCES DEFENSE

COUNCIL; NORTHERN CALIFORNIA

COUNCIL OF THE FEDERATION OF

FLY FISHERS; SAN FRANCISCO

BAYKEEPER; SACRAMENTO RIVER

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SAN LUIS V. LOCKE 9

PRESERVATION TRUST; WINNEMEM

WINTU TRIBE; PACIFIC COAST

FEDERATION OF FISHERMEN’S

ASSOCIATIONS, INC., Institute for

Fisheries Research,

Intervenor-Defendants–Appellees.

SAN LUIS & DELTA-MENDOTA

WATER AUTHORITY; WESTLANDS

WATER DISTRICT; STOCKTON EAST

WATER DISTRICT; METROPOLITAN

WATER DISTRICT OF SOUTHERN

CALIFORNIA; OAKDALE IRRIGATION

DISTRICT; SOUTH SAN JOAQUIN

IRRIGATION DISTRICT; KERN

COUNTY WATER AGENCY;

COALITION FOR A SUSTAINABLE

DELTA; STATE WATER

CONTRACTORS,

Plaintiffs-Appellees,

CALIFORNIA DEPARTMENT OF

WATER RESOURCES,

Intervenor-Plaintiff–Appellee,

v.

GARY LOCKE; UNITED STATES

DEPARTMENT OF COMMERCE;

NATIONAL OCEANIC AND

ATMOSPHERIC ADMINISTRATION;

NATIONAL MARINE FISHERIES

No. 12-15296

D.C. No.

1:09-cv-01053-

LJO-DLB

OPINION

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10 SAN LUIS V. LOCKE

SERVICE; JAMES W. BALSIGER;

RODNEY R. MCINNIS; U.S.

DEPARTMENT OF THE INTERIOR;

UNITED STATES BUREAU OF

RECLAMATION; MICHAEL L.

CONNOR; DONALD R. GLASER; JANE

LUBCHENCO; SALLY JEWELL,

Defendants-Appellants,

and

THE BAY INSTITUTE; CALIFORNIA

TROUT; FRIENDS OF THE RIVER;

NATURAL RESOURCES DEFENSE

COUNCIL; NORTHERN CALIFORNIA

COUNCIL OF THE FEDERATION OF

FLY FISHERS; SAN FRANCISCO

BAYKEEPER; SACRAMENTO RIVER

PRESERVATION TRUST; WINNEMEM

WINTU TRIBE; PACIFIC COAST

FEDERATION OF FISHERMEN’S

ASSOCIATIONS, INC., Institute for

Fisheries Research,

Intervenor-Defendants.

Appeal from the United States District Court

for the Eastern District of California

Oliver W. Wanger, District Judge, Presiding

Argued and Submitted

September 15, 2014—San Francisco, California

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SAN LUIS V. LOCKE 11

Filed December 22, 2014

Before: Richard C. Tallman and Johnnie B. Rawlinson,

Circuit Judges, and Thomas O. Rice, District Judge.**

Opinion by Judge Tallman

SUMMARY***

Endangered Species Act

The panel affirmed in part and reversed in part the district

court’s summary judgment and remanded for entry of

summary judgment in favor of defendants, federal agencies

and intervenor-environmental groups, in an action pertaining

to a formal Biological Opinion developed by the Commerce

Department’s National Marine Fisheries Service pursuant to

the Endangered Species Act regarding the impact of

continuing water extraction in the California Central Valley

on certain threatened and endangered Salmonid species.

The Marine Fisheries Service in its 2009 Biological

Opinion determined that the Department of Interior Bureau of

Reclamation’s proposed water project in the Central Valley

would jeopardize some of the Delta’s endangered Salmonids. 

To remedy this problem, the Marine Fisheries Service

**

 The Honorable Thomas O. Rice, United States District Judge for the

Eastern District of Washington, sitting by designation.

 

*** This summary constitutes no part of the opinion of the court. It has

been prepared by court staff for the convenience of the reader.

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12 SAN LUIS V. LOCKE

required the Bureau to change the way it pumps water out of

the Central Valley’s rivers. A number of groups that depend

on the Central Valley’s water sued to halt this change. On

summary judgment, the district court found, in part, that the

Marine Fisheries Service violated the Administrative

Procedure Act’s arbitrary or capricious standard when

developing much of the Biological Opinion.

On an initial evidentiary question, the panel held that the

district court went beyond the exceptions, set forth in Lands

Council v. Powell, 395 F.3d 1019 (9th Cir. 2004), when it

admitted extra-record declarations and substituted the

analysis in those declarations for that provided by the Marine

Fisheries Service.

The panel held that the district court did not give the

Service the substantial deference it was due under the

Administrative Procedure Act. The panel found that the

components of the Biological Opinion invalidated by the

district court were reasonable and supported by the record

and therefore the panel upheld the Biological Opinion in its

entirety. 

Specifically, the panel found that: (1) the Service acted

within its substantial discretion when it used raw salvage data

instead of data scaled to fish population to set flows in the

Old and Middle Rivers; (2) the Service’s jeopardy opinion

components were not arbitrary and capricious as they

pertained to the winter-run Chinook, the Southern Resident

orca, the steelhead critical habitat, and the impact of indirect

mortality factors on the listed species; and (3) the Biological

Opinion’s challenged reasonable and prudent alternative

actions were not arbitrary and capricious. 

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SAN LUIS V. LOCKE 13

Affirming, on cross-appeal, several components of the

district court’s opinion, the panel held that the Marine

Fisheries Service did not need to distinguish between

discretionary and non-discretionary actions; that the

Biological Opinion’s indirect mortality factors were direct

effects under the Endangered Species Act; and that Bureau of

Reclamation was not independently liable under the

Endangered Species Act. 

COUNSEL

Rebecca Rose Akroyd, Daniel J. O’Hanlon, Hanspeter

Walter, Kronick, Moskovitz, Tiedemann, & Girard, PC,

Sacramento, California, for Plaintiffs-Appellees/CrossAppellants San Luis & Delta-Mendota Water Authority and

Westlands Water District.

David A. Diepenbrock, Eileen Diepenbrock, Jonathan Marz,

and Jon D. Rubin, Diepenbrock Elkin LLP, Sacramento,

California, for Plaintiffs-Appellees San Luis & DeltaMendota Water Authority.

Robert D. Thornton and Paul S. Weiland, Nossaman LLP,

Irvine, California, for Plaintiff-Appellee/Cross-Appellant

Kern County Water Agency and Plaintiff-Appellee Coalition

for a Sustainable Delta.

Amelia T. Minaberrigarai, General Counsel, Bakersfield,

California, for Plaintiff-Appellee/Cross-Appellant Kern

County Water Agency.

Martha F. Bauer, Mark J. Mathews, Brownstein Hyatt Farber

Schreck, LLP, Denver, Colorado; Steve Sims, Brownstein

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14 SAN LUIS V. LOCKE

Hyatt Farber Schreck, LLP, Albuquerque, New Mexico;

David Longly Bernhardt (argued), Brownstein Hyatt Farber

Schreck, LLP, Washington, D.C.; Harold Craig Manson,

General Counsel, Fresno, California, for PlaintiffAppellee/Cross-Appellant Westlands Water District.

Tim O’Laughlin and William C. Paris, III, O’Laughlin &

Paris LLP,forPlaintiffs-Appellees Oakdale Irrigation District

and South San Joaquin Irrigation District.

Steven M. Anderson, Melissa R. Cushman, Steven G. Martin,

and Gregory K. Wilkinson, Best Best & Krieger, LLP,

Riverside, California; Paeter E. Garcia, Best Best & Krieger

LLP, Los Angeles, California, for Plaintiffs-Appellees State

Water Contractors.

Alexis K. Galbraith, Karna Elizabeth Harrigfeld, Jennifer

Lynn Spaletta, and Jeanne M. Zolezzi, Herum Crabtree,

Stockton, California, for Plaintiff-Appellee Stockton East

Water District.

Christopher J.Carr and William M. Sloan (argued), Morrison

& Foerster LLP, San Francisco, California; Linus

Masouredis, Chief Deputy General Counsel, Sacramento,

California,forPlaintiff-Appellee Metropolitan Water District

of Southern California.

Michael M. Edson, Allison Goldsmith, Daniel S. Harris,

Clifford T. Lee (argued), Deputy Attorneys General—Office

of the California AttorneyGeneral, San Francisco, California,

for Intervenor-Plaintiff–Appellee California Department of

Water Resources.

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SAN LUIS V. LOCKE 15

Ellen J. Durkee (argued) and Bridget McNeil, United States

Department of Justice, Washington, D.C., for DefendantsAppellants/Cross-Appellees United States Department of

Commerce, National Oceanic and Atmospheric

Administration, National Marine Fisheries Service, United

States Department of the Interior, and United States Bureau

of Reclamation.

Trent W. Orr and George Matthew Torgun, Earthjustice, San

Francisco, California, for Intervenor-Defendants–Appellants/

Cross-Appellees Pacific Coast Federation of Fisherman’s

Associations, Institute for Fisheries Research, The Bay

Institute, California Trout, Friends of the River, Northern

California Counsel of the Federation of Fly Fishers, San

Francisco Baykeeper, Sacramento River Preservation Trust,

Winnemem Wintu Tribe.

Katherine S. Poole (argued) and Douglas A. Obegi, San

Francisco, California, for Intervenor-Defendant/Appellant

Natural Resources Defense Counsel.

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16 SAN LUIS V. LOCKE

TABLE OF CONTENTS

I. FACTS AND PROCEEDINGS BELOW. . . . . . . . . . 23

A. Background. . . . . . . . . . . . . . . . . . . . . . . . . . . 23

1. Factual Background—The SacramentoSan Joaquin Delta. . . . . . . . . . . . . . . . 23

a. The Central Valley and the River

Systems. . . . . . . . . . . . . . . . . . 23

b. The State Water Project and the

Central Valley Project. . . . . . . 25

c. Threatened and Endangered

Species in the Delta. . . . . . . . . 28

2. Legal Background—The Endangered

Species Act.. . . . . . . . . . . . . . . . . . . . . 30

B. Proceedings Leading to the Current Controversy

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

1. The 2009 Salmonid Biological Opinion

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

a. The Consultation Request. . . . 32

b. The Jeopardy Opinion. . . . . . . 33

c. The Reasonable and Prudent

Alternatives. . . . . . . . . . . . . . . 34

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SAN LUIS V. LOCKE 17

2. The Present Case. . . . . . . . . . . . . . . . . 35

II. STANDARDS OF REVIEW. . . . . . . . . . . . . . . . . . . . 39

III. THE RECORD ON REVIEW. . . . . . . . . . . . . . . . 40

IV. THE LEGAL FRAMEWORK.. . . . . . . . . . . . . . . 44

A. The APA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

B. The ESA.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

V. THE MERITS OF THE BIOLOGICAL OPINION. . . 47

A. We Defer To the Agency’s Choice To Use Raw

Salvage Figures. . . . . . . . . . . . . . . . . . . . . . . . 49

B. The Challenged Jeopardy Opinion Components

Are Not Arbitrary or Capricious. . . . . . . . . . . 52

1. Winter-Run Chinook. . . . . . . . . . . . . . 52

2. Southern Resident Orca. . . . . . . . . . . . 53

3. Steelhead Critical Habitat. . . . . . . . . . 55

4. Indirect Mortality Factors. . . . . . . . . . 57

C. The Challenged RPA Actions Are Not Arbitrary

or Capricious. . . . . . . . . . . . . . . . . . . . . . . . . . 60

1. The Legal Requirements for an RPA

Action.. . . . . . . . . . . . . . . . . . . . . . . . . 60

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18 SAN LUIS V. LOCKE

a. The ESA Does Not Require

NMFS To Explain How Each

RPA Action Is Essential To Avoid

Jeopardy. . . . . . . . . . . . . . . . . . 62

b. The ESA Does Not Require

NMFS To Articulate Compliance

with the Non-Jeopardy Factors

. . . . . . . . . . . . . . . . . . . . . . . . . 63

2. Challenged RPA Actions. . . . . . . . . . . 64

a. Action IV.2.1. . . . . . . . . . . . . . 64

b. Action IV.2.3 and Action IV.3

. . . . . . . . . . . . . . . . . . . . . . . . . 66

c. Action IV.4.2. . . . . . . . . . . . . . 68

d. Action III.1.2. . . . . . . . . . . . . . 69

e. Action III.1.3. . . . . . . . . . . . . . 71

f. Action III.2.2. . . . . . . . . . . . . . 73

VI. CROSS-APPEAL. . . . . . . . . . . . . . . . . . . . . . . . . 74

A. NMFS Need Not Distinguish Discretionary and

Non-Discretionary Actions. . . . . . . . . . . . . . . 74

B. The Biological Opinion’s Indirect Mortality

Factors Are Direct Effects Under the ESA. . . 75

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SAN LUIS V. LOCKE 19

C. Reclamation Is Not Independently Liable Under

the ESA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

VII. CONCLUSIONS. . . . . . . . . . . . . . . . . . . . . . . . . . 77

GLOSSARY OF TERMS. . . . . . . . . . . . . . . . . . . . . . . . . 79

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20 SAN LUIS V. LOCKE

OPINION

TALLMAN, Circuit Judge:

And then the dry years would come, and

sometimes there would be only seven or eight

inches of rain. The land dried up and the

grasses headed out miserably a few inches

high and great bare scabby places appeared in

the valley. The live oaks got a crusty look

and the sage-brush was gray. The land

cracked and the sprigs dried up and the cattle

listlessly nibbled dry twigs. Then the farmers

and the ranchers would be filled with disgust

for the Salinas Valley. The cows would grow

thin and sometimes starve to death. People

would have to haul water in barrels to their

farms just for drinking.

John Steinbeck, East of Eden 5 (Penguin Books 2002) (1952).

Although John Steinbeck wrote about California’sSalinas

Valley, the same can be said for California’s Central Valley. 

Like the Salinas Valley, the Central Valley is rich and fertile. 

It is home to some of California’s most productive

agriculture, and food grown in the Valley sits on the tables in

most American homes. But the Central Valley is also

naturally dry. The Valley floor receives an average of five to

sixteen inches of rainfall per year; the United States

Geological Service considers it to be arid or semi-arid. In its

natural state, the Valley could not sustain the level of

agriculture that the country demands from it.

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SAN LUIS V. LOCKE 21

To remedy this problem, the federal and state

governments have invested enormous sums of money

developing infrastructure to pump water out of the rivers that

crisscross the Valley’s floor, store it, and deliver it to

agricultural and domestic consumers in California. This

water is essential to the continuing vitality of agriculture in

the Central Valley, and some 25 million Californians depend

on it for daily living. But that water is also an important

habitat for thousands of river and anadromous fish, many of

which are endangered.

And therein lies the conflict: If the governments did not

extract water from the Central Valley’s rivers, the Valley

could not support the farms that feed, the dams that power,

and the canals that hydrate millions of Americans. But by

extracting the water, people dramatically alter the rivers’

natural state and threaten the viability of the species that

depend on them. People need water, but so do fish.

This case is about the competing demands for these

limited water resources. In 2006 the Department of Interior’s

Bureau of Reclamation (“Reclamation”), the federal agency

that oversees water resources in the West, asked the

Commerce Department’s National Marine Fisheries Service

(“NMFS”) to evaluate under the Endangered Species Act

(“ESA”) the impact of continuing water extraction in the

Central Valley on certain threatened and endangered

Salmonid species that live there. In response, NMFS

developed a Biological Opinion (“BiOp”) in which it

determined that Reclamation’s proposed project would

jeopardize some of the Delta’s endangered Salmonids. See

generally 2009 Salmonid BiOp at 574–75. To remedy this

problem, NMFS required Reclamation to change the way it

pumps water out of the Valley’s rivers. See id. at ch. 11. A

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22 SAN LUIS V. LOCKE

number of groups that depend on the Central Valley’s water

sued to halt this change. On summary judgment, the district

court found that NMFS had violated the Administrative

Procedure Act’s (“APA”) arbitrary or capricious standard

when developing much of the BiOp. See generally In re

Consolidated Salmonid Cases, 791 F. Supp. 2d 802, 955–59

(E.D. Cal. 2011); 5 U.S.C. § 706(2)(a) (2012). Defendants—

joined by environmental groups—appealed, and once again

we enter the fray.

1

We hold that the district court did not give NMFS the

substantial deference it is due under the APA. On

independent record review, we find that the components of

the BiOp invalidated by the district court are reasonable and

supported by the record. As a result, we uphold the BiOp in

its entirety. We, therefore, REVERSE and REMAND for

entry of summary judgment in favor of Defendants.

1 This is not the first time we have addressed this conflict, nor is it likely

to be the last. We recently addressed the conflict between Delta irrigation

and a small threatened fish known as the Delta Smelt. See San Luis &

Delta Mendota Water Auth. v. Jewell (Delta Smelt), 747 F.3d 581 (9thCir.

2014). In Delta Smelt we reversed the district court and upheld a 2008

BiOp in which the Fish and Wildlife Service (“FWS”) concludes that

continued water extraction from the Central Valley’s rivers would

jeopardize the Delta Smelt and offers reasonable and prudent alternatives

that Reclamation should take to ameliorate this impact. See id. at 593–92. 

Our opinion in Delta Smelt informs much of our analysis here.

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I. FACTS AND PROCEEDINGS BELOW

A. Background

1. Factual Background—The Sacramento-San

Joaquin Delta

a. The Central Valley and the River Systems

The Central Valley is a flat-bottom basin covering 22,500

square miles in inland California. The walls of the basin are

created by several mountain ranges: the Sierra Nevada and

Cascade Mountains to the east, the Klamath Mountains to the

north, the Coast Range to the west, and the Tehachapi

Mountains to the south. See infra, Fig. A. The Valley is long

and narrow. It stretches from Bakersfield in the south to

Redding in the north (about 450 miles) and is between 40 and

60 miles wide from east to west.

The Central Valley contains several major river systems. 

Those systems are comprised of the San Joaquin River

(which flows west from the Cathedral Range of the Sierra

Nevada Mountains, turns north around Fresno, and enters the

San Francisco Bay north of Berkeley), the Sacramento River

(which flows south from the Salmon and Trinity Mountains

around Redding and passes through Sacramento before

joining the San Joaquin River), and their tributaries. The

Sacramento and San Joaquin Rivers converge around

Antioch, about thirty miles northeast of Oakland, where they

form the San Joaquin River Delta. The water from the Delta

flows past Chipps Island, into the Suisun Bay, through Bulls

Head Channel, and into the San Francisco Bay. The water

passes the city of San Francisco and flows under the Golden

Gate Bridge where it finally enters the Pacific Ocean. See

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24 SAN LUIS V. LOCKE

infra, Fig. A. The brackish body of water through which the

rivers flow on their way to the Pacific Ocean is called the

“Bay-Delta.” The river delta is called simply “the Delta.”

Fig. A. Delta Map.2

2 California Water Science Center, U.S. Geological Survey,

http://ca.water.usgs.gov/gama/Provs/CenVly.htm (last visited Oct. 21,

2014, 9:09 a.m.).

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b. The State Water Project and the Central

Valley Project

Since the early part of the twentieth century, land owners,

local irrigation districts, and the federal and California state

governments have pumped fresh water out of the San Joaquin

and Sacramento Rivers (and their tributaries) to irrigate the

agricultural lands of the Central Valley and to provide

drinking water to the people of California. See Cent. Delta

Water Agency v. United States, 306 F.3d 938, 943 (9th Cir.

2002). California governs this pumping through the State

Water Project (“SWP”) and the federal government does so

through the Central Valley Project (“CVP”) (collectively,

“the Projects”).

The SWP is the largest state-built water project in the

United States. Delta Smelt, 747 F.3d at 594. It consists of

“21 dams and reservoirs, . . . five power plants, 16 pumping

plants, and 662 miles of aqueduct.” Id. (internal citations

omitted). The California Department of Water Resources

(“DWR”)—Plaintiff-in-Intervention here—oversees

operations of the SWP. Id.

The CVP is “the largest federal water management project

in the United States.” Cent. Delta Water Agency, 306 F.3d at

943. Congress initially authorized it in the Rivers and

Harbors Act of 1935. Id. It comprises a series of dams, “21

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

aqueducts.” Delta Smelt, 747 F.3d at 594. Reclamation

oversees operations of the CVP. The CVP is partially

governed by the Central Valley Project Improvement Act

(“CVPIA”), id. at 594, which Congress passed in 1992 to

“achieve a reasonable balance among competing demands for

use of Central Valley Project water, including the

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requirements of fish and wildlife, agricultural, municipal and

industrial and power contractors.” Central Valley Project

Improvement Act, Pub L. No. 102–575, 106 Stat. 4706

(1992).

Together, the Projects provide water to more than 25

million agricultural and domestic consumers in central and

southern California. They do so, in part, by pumping fresh

water out of the Delta using the Harvey O. Banks Pumping

Plant (“Banks pumping plant”) and the C.W. “Bill” Jones

Pumping Plant (“Jones pumping plant”), both of which are

located near Tracy, California.3 The Banks pumping plant is

capable of pumping water at the rate of 10,300 cubic feet per

second (“cfs”), but it generally operates closer to 6,680 cfs. 

See OCAP BA at 2-2. The Jones pumping plant has a

maximum pumping capability of 4,600 cfs. See id. The

plants operate by lifting water from the Delta using motorgenerated pumps.4 They pump the water into pipes that

deliver it into the California Aqueduct or the Delta-Mendota

Canal, respectively. See Jones & Banks Pumping Facilities. 

From there, the Projects deliver the water to agricultural users

in the Central Valley and domestic users in central and

southern California. See id.; see also Fig. B.

3

See Biological Assessment on the Continued Long-term Operations of

the Central Valley Project and the State Water Project, U.S. Bureau of

Reclamation, http://www.usbr.gov/mp/cvo/ocapBA_051608.html 2-1 (last

visited Oct. 20, 2014) [hereinafter “OCAP BA”]; see also Fig. A.

4 Central Valley Project’s C.W. “Bill” Jones Pumping Plant and Tracy

Fish Collection Facility, U.S. Bureau of Reclamation (July 2012),

http://www.usbr.gov/mp/PA/docs/fact_sheets/Jones_Pumping_Plant.pdf

[hereinafter “Jones and Banks Pumping Facilities”].

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The Projects also control the volume of water flowing

through the Central Valley’s rivers by prescribing releases

from upstream reservoirs, which operate as water storage

facilities. Releases from CVP/SWP reservoirs cool water

temperatures, reduce the salinity of the Delta, provide flood

control, improve volume for fish habitat and migration, and

supply additional water for agricultural use. See OCAP BA

at 2-5.

Fig. B. CVP and SWP Map.5

5 Central Valley Project, U.S. Bureau of Reclamation,

http://www.usbr.gov/projects/Project.jsp?proj_Name=Central+Valley+

Project (last visited Oct. 21, 2014 8:55 a.m.); James Nickles et al.,

California’s BAY-DELTA: USGS Science Supports Decision Making,

http://pubs.usgs.gov/fs/2010/3032/ (last visited Oct. 21, 2014, 9:00 a.m.).

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c. Threatened and Endangered Species in the Delta

Although the Projects provide substantial benefits to

people and to state agriculture, they arguably harm species

native to the Delta by modifying those species’ natural

habitats. Five such species are at issue in this case: (1) the

endangered Sacramento River winter-run Chinook salmon

(“winter-run Chinook”); (2) the threatened Central Valley

spring-run Chinook salmon (“spring-run Chinook”); (3) the

threatened Central Valley steelhead (“CV steelhead”); (4) the

threatened Southern Distinct Population Segment of North

American green sturgeon (“green sturgeon”); and the

endangered Southern Resident orca whale (“Southern

Resident orca”). See 2009 Salmonid BiOp at 30.

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The four Salmonid species (the first four listed) are

anadromous fish, and Southern Resident orca are marine

mammals. Anadromous fish live most of their lives in salt

water.6 Nevertheless, they are born, mature, lay eggs, and

often die in inland freshwater lakes and rivers. After they

grow from fry (baby fish) to smolts (juvenile fish) in fresh

water, anadromous salmon outmigrate through rivers and

deltas into the oceans and seas where they will spend most of

their adult lives. When it is time to reproduce, these salmon

migrate back through the deltas to the rivers and lakes in

which they were born to lay eggs. During this migration,

salmon must pass impediments in inland rivers such as locks,

dams, channels, and pumps.

The San Francisco Bay-Delta is an essential conduit for

anadromous fish that return to California’s inland rivers and

lakes to reproduce. Nevertheless, human interactions with the

Delta and California’s inland rivers over the past century

have significantly altered them, threatening their ability to

serve as salmonid habitats. SWP and CVP operations

increase pollution, encourage the growth of non-native

species, and create water shortages in the Delta that harm

salmon by exposing them to unnatural stressors. See 2009

Salmonid BiOp at 374–82. Migrating salmon can also be

caught in, and killed by, the large water pumps that serve the

Projects. Finally, CVP/SWP operations that limit cold water

releases from dams upstream of traditional spawning sites

potentially impact critical spawning habitat by making the

rivers less conducive to reproduction.

6

See, e.g., Chinook Salmon (Oncorhynchus tshawytscha), NOAA

Fisheries Office of Protected Resources, http://www.nmfs.noaa.gov/

pr/species/fish/chinooksalmon.htm (last updated May 15, 2014).

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2. Legal Background—The Endangered Species Act

We must review NMFS’s formal opinion as to how

Reclamation and DWR should operate the Projects to avoid

jeopardizing endangered Salmonid species. Before further

discussing the relationship between the Projects and the

species, we briefly review the legal framework for that

opinion.

The federal government protects listed and threatened

species, such as the five at issue here, primarily through the

ESA. See Endangered Species Act, 16 U.S.C. §§ 1531–1544

(2012). When Congress passed the ESA in 1973, it sought to

bring about the “better safeguarding, for the benefit of all

citizens, [of] the Nation’s heritage in fish, wildlife, and

plants.” Id. § 1531(a)(5).

Section 7 of the ESA “addresses the obligations of federal

agencies with respect to conservation and protection of

species listed as either endangered or threatened under the

ESA.” Lawrence R. Liebesman & Rafe Petersen,

Endangered Species Deskbook 39 (2d ed. 2010). ESA section

7 prohibits a federal agency from taking any action that is

“likely to jeopardize the continued existence” of any listed or

threatened species or “result in the destruction or adverse

modification” of those species’ critical habitat. 16 U.S.C.

§ 1536(a)(2).

Section 7 requires an agency proposing a project that

might harm listed or threatened species to consult with either

NMFS or the Interior Department’s Fish and Wildlife Service

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(“FWS”)7about the proposed action. 16 U.S.C. § 1536(a)(2). 

As part of this consultation, the action agency prepares an

initial assessment of the project in which it evaluates the

project’s impact on any listed or endangered species. This is

called a Biological Assessment (“BA”). 50 C.F.R. § 402.02

(2009). The appropriate consultation agency reviews the

action agency’s BA and uses it to prepare a Biological

Opinion (“BiOp”) in which it ultimately determines whether

the proposed agency action is likely to adversely impact

endangered or listed species, or negatively modify their

critical habitats. See 16 U.S.C. § 1536(a)(2).8

If the agency concludes that the proposed action will

jeopardize species or critical habitats, “the Biological

Opinion must outline any ‘reasonable and prudent

alternatives’ that the [agency] . . . believes will avoid that

consequence.” Bennett v. Spear, 520 U.S. 154, 158, 117 S.

Ct. 1154, 1159 (1997) (quoting 16 U.S.C. § 1536(b)(3)(A)). 

Reasonable and prudent alternatives (“RPAs”) are

alternative actions identified during formal

consultation that can be implemented in a

manner consistent with the intended purpose

of the action, that can be implemented

consistent with the scope of the Federal

7 Whether an agency consults with NMFS or FWS depends on the

species for which it is seeking consultation. NMFS consults on marine

and anadromous species. See Liebesman & Petersen, supra, at 40.

8 The consultation agency’s determination with regard to whether the

proposed project is likely to jeopardize listed species is called the

“jeopardy opinion” component of the BiOp. See U.S. Fish & Wildlife

Serv. & Nat’ l Marine Fisheries Serv., ESA Section 7 Consultation

Handbook 4-37 (Mar. 1998) [hereinafter “Handbook”].

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agency’s legal authority and jurisdiction, that

is [sic] economically and technologically

feasible, and that the Director believes would

avoid the likelihood of jeopardizing the

continued existence of listed species or

resulting in the destruction or adverse

modification of critical habitat.

50 C.F.R. § 402.02. The consulting agency may also

issue—with the BiOp—an incidental take statement (“ITS”)

that permits the action agency to harm listed species when

implementing the RPAs without violating the ESA. See id.

B. Proceedings Leading to the Current Controversy

1. The 2009 Salmonid Biological Opinion

a. The Consultation Request

In 2006, Reclamation asked NMFS to prepare a BiOp

assessing the impact of continued and future CVP/SWP

operations on Delta Salmonid species.9 This request was

motivated by the listing of new endangered species and the

designation of new critical habitats. 2009 Salmonid BiOp at

31. In it, Reclamation asked NMFS to evaluate the effect of

Reclamation and DWR’s proposal to continue to operate the

Projects “to divert, store, and convey Project water . . . ,”

OCAP BA at 2-1, on winter-run Chinook, spring-run

Chinook, CV steelhead, CCC steelhead (a fish not at issue

9 Although the SWP is a state project, it is subject to federal consultation

along with the CVP because of a 1986 agreement between the federal

government and DWR. 2009 Salmonid BiOp at 31.

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here), green sturgeon, and Southern Resident orca, see 2009

Salmonid BiOp at 30.

Reclamation developed a BA that could provide the basis

for such a consultation in the fall of 2008. Id. at 32. Using

the data Reclamation provided in the BA, supplementing it

with its own research, NMFS developed a draft Salmonid

BiOp that it released to Reclamation and DWR for comment

in the winter of 2008. Id. at 33. Reclamation and DWR

reviewed and commented on the document. NMFS also

requested and received peer review from the CALFED BayDelta Program and the Center for Independent Experts. See

id. Based on the comments received, NMFS published a final

560-page BiOp on June 4, 2009. Reclamation provisionally

accepted the BiOp that same day.

Plaintiffs contest the legality of the 2009 BiOp here,

arguing—for various reasons—that parts of it are arbitrary or

capricious in violation of the APA. Before discussing

Plaintiffs’ specific challenges and the issues on appeal, we

briefly review the portions of the BiOp that are relevant.

b. The Jeopardy Opinion

In the first part of the BiOp, NMFS concludes that “the

long-term operations of the CVP and SWP are likely to

jeopardize the continued existence of the” winter-run

Chinook, the spring-run Chinook, the CV steelhead, the green

sturgeon, and the Southern Resident orca. Id. at 575. 

Similarly, “[t]he long-term operations of the CVP and SWP

are likely to destroy or adversely modify critical habitat for”

winter-run Chinook, spring-run Chinook, CV steelhead, and

green sturgeon. Id.

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c. The Reasonable and Prudent Alternatives

Because NMFS concludes that ongoing CVP/SWP

operations would threaten listed species, it issued over

seventy RPAs that Reclamation is supposed to implement to

avoid jeopardy. See generally id. at 574–724. The proposed

RPAs fall into five operational categories—(I) Sacramento

River Division, (II) American River Division, (III) East Side

Division, (IV) Delta Division, and (V) Fish Passage Program. 

See id. at 19. On appeal, the parties challenge provisions of

the RPAs falling into categories III and IV.

Actions in category III relate to CVP/SWP operations on

the Stanislaus River, which provides critical spawning and

smolting grounds for the CV steelhead. See id. at 619–20. 

Prior to the construction of the New Melones Dam on the

Stanislaus River, CV steelhead spawned in the cold

tributaries upstream of where the New Melones Reservoir is

now located. See id. at 107–08, 619. Now, “[t]he steelhead

population on the Stanislaus River is precariously small and

limited to habitat areas below the [Goodwin and New

Melones] Dams that historically were unsuitable owing to

high summer temperatures.” Id. at 619. In RPA category III,

NMFS prescribes certain volumes of releases from the

Goodwin and New Melones Dams that, according to NMFS,

will cool the rivers enough to facilitate steelhead spawning. 

See id. at 620. The flows will also rejuvenate the gravel that

is essential to steelhead spawning habitat and provide

migratory cues to adult and juvenile fish.

Actions in category IV relate to operations in the Delta. 

See id. at 628–30 (describing Delta division action). NMFS

concludes that the proposed actions for the Projects, which

“include continued diversion of water from the Delta at the

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project’s export facilities, with increased export levels,” “will

increase the level of stressors in the Delta,” further degrading

it as a habitat. Id. at 629. The category IV RPA Actions

address this jeopardy finding by imposing flow-to-export

ratios for the Old and Middle Rivers, see id. at 643–44,

prescribing maximum negative flow rates for the Old and

Middle Rivers, id. at 648, and requiring a certain salvage

efficiency at major fish salvage stations, id. at 655.

2. The Present Case

On June 15, 2009, Plaintiffs San Luis & Delta-Mendota

Water Authority and Westlands Water District challenged the

legality of the 2009 BiOp by filing suit against the

Department of Commerce, the National Oceanic and

Atmospheric Administration, and NMFS (collectively

“Federal Defendants”)10in the Eastern District of California. 

See Compl. at 1, ECF No. 1. The district court consolidated

that case with several other cases in which state water

districts challenged the 2009 BiOp.11 DWR intervened as a

plaintiff. See Joinder by Calif. Dep’t of Water Res., ECF No.

137. And several environmental and fishing groups

10 Reclamation and the United States Department of the Interior were

later joined. They are included under the umbrella of “Federal

Defendants.” See In re Consolidated Salmonid Cases, 791 F. Supp. 2d at

813.

 

11 The plaintiffs fall into three separate groups. The Export Plaintiffs

are San Luis & Delta Mendota Water Authority and Westlands Water

District; State Water Contractors; Kern County Water Agency and

Coalition for a Sustainable Delta; and Metropolitan Water District of

Southern California. The Stanislaus River Plaintiffs (or “SR Plaintiffs”)

are Stockton East Water District, Oakdale Irrigation District, and South

San Joaquin Irrigation District. The DWR Plaintiff in Intervention is the

California Department of Water Resources.

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intervened as defendants.12See In re Consolidated Salmonid

Cases, 791 F. Supp. 2d at 813.

On August 6, 2010, several Plaintiffs moved for summary

judgment on their claim that the 2009 BiOp violates the ESA

and the APA. Id. The Stanislaus River Plaintiffs and DWR

filed separate motions for summary judgment. Id. The

Federal Defendants and Defendant-Intervenors responded

with cross-motions for summary judgment. Id. “These crossmotions, which included over 700 pages of briefing and

thousands of pages of supporting declarations and exhibits,

came on for hearing on December 16 and 17, 2010.” Id. On

September 20, 2011, the district court filed a 157-page

opinion granting in part and denying in part Plaintiffs’ claims,

and granting in part and denying in part Defendants’ claims. 

Id. at 955–59.

The district court made dozens of conclusions relating to

almost every component of the BiOp when rendering this

complex and lengthy opinion. We briefly review the

conclusions at issue in this appeal.

The Defendants ask us to overturn the following of the

district court’s holdings in which it struck down components

of the BiOp:

• NMFS acted unlawfully by relying on raw salvage data to

set negative flow thresholds for the Old and Middle

12 Those Defendant-Intervenors are The Bay Institute; California Trout;

Friends of the River; Natural Resources Defense Council; Northern

California Council of the Federation of Fly Fishers; San Francisco

Baykeeper; Sacramento River Preservation Trust; Winnemem Wintu

Tribe; and Pacific Coast Federation of Fishermen’s Associations, Inc.

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Rivers. Basic scientific principles require the agency to

use data scaled to population to determine the impact of

exports on fish survival. Id. at 827.

• NMFS erred by failing to provide sufficient support for

its classification of the winter-run Chinook as “high risk”

rather than the less serious classification of “not viable.” 

Id. at 864.

• NMFS erred by failing to reconcile the 2009 Salmonid

BiOp’s jeopardy determination relating to the Southern

Resident orcawith an apparentlycontradictoryconclusion

in a different 2009 BiOp (“2009 Orca BiOp”). Id. at 866.

• NMFS failed to adequately explain how continued

operation of the Projects will adversely modify the CV

steelhead’s critical habitat by reducing spawnable area

and degrading gravel quality and quantity. Id. at 936.

• Although NMFS sufficiently established that delta

hydrologic conditions—as altered in part by the

Projects—are favorable to invasive species, the BiOp

does not support the conclusion that continued CVP/SWP

operations promote invasive species, which in turn

threaten listed species. Id. at 870. Nor does the BiOp

sufficiently explain “how the projects influence

contaminants or cause food limitations.” Id.

• NMFS provided no support for its decision to use

“maximum steelhead habitat” as a benchmark for

evaluating the effect of East Side Division operations on

listed species in the Stanislaus River. Because the

modeling related to the New Melones Dam flows are

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based on the “maximum habitat” benchmark, the New

Melones Dam flow limits violate the APA. Id. at 938.

• NMFS’s modeling assumptions relating to the Stanislaus

River are flawed because NMFS set its goal as

“doubling” CV steelhead habitat. Id. at 950.

• NMFS failed to establish how each RPA Action complies

with 50 C.F.R. § 402.02’s non-jeopardy factors. 

Specifically, NMFS did not establish how each RPA

Action complies with the many purposes of the CVPIA,

id. at 918, nor did it consider how each Action is feasible,

id. at 919. NMFS erred particularly by failing to show

how Delta Action IV.4.2 is feasible.

• NMFS erred by failing to explain how certain RPA

Actions are “essential” to avoid jeopardy of the listed

species or adverse modification of their habitats. Id. at

897 & n.26. Those actions are Delta Division RPAs

IV.2.1, IV.2.3, and IV.3 and East Side Division RPAs

III.1.2, III.1.3, and III.2.2.

Plaintiffs ask us to overturn the following of the district

court’s holdings that were favorable to the BiOp:

• Reclamation did not violate its obligations under section

7 of the ESA when it accepted the 2009 Salmonid BiOp. 

Id. at 955.

• NMFS did not need to segregate discretionary and nondiscretionary agency activities when constituting the

environmental baseline. Id. at 852.

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• NMFS did not err by classifying indirect mortality factors

as a direct effect of the continuing Projects. Id. at

870–71.

The district court entered its final judgment on December

12, 2011. See Final Judgment, ECF No. 655. The parties

timely cross-appealed. This court has jurisdiction under

28 U.S.C. § 1291 (2012).

II. STANDARDS OF REVIEW

We review the district court’s summary judgment rulings

de novo. McFarland v. Kempthorne, 545 F.3d 1106, 1110

(9th Cir. 2008) (internal citations omitted). Summary

judgment is appropriate when the pleadings and record

demonstrate that “there is no genuine dispute as to any

material fact and the movant is entitled to judgment as a

matter of law.” Fed. R. Civ. P. 56(a). This court also reviews

de novo the district court’s evaluations of an agency’s

actions. Sierra Club v. Babbit, 65 F.3d 1502, 1507 (9th Cir.

1995) (“De novo review of a district court judgment

concerning a decision of an administrative agency means we

view the case from the same position as the district court.”). 

We evaluate a district court’s decision to admit extra-record

evidence for abuse of discretion. Lands Council v. Powell,

395 F.3d 1019, 1030 n.11 (9th Cir. 2004).

This is a record review case, so we will conduct our own

review of the administrative record and, if necessary, “direct

that summary judgment be granted to either party . . . .” Id.

at 1026.

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III. THE RECORD ON REVIEW

Before reviewing the merits of the 2009 Salmonid BiOp,

we must resolve an initial evidentiary question: Did the

district court err in its own record review by supplementing

the administrative record with dozens of extra-record

declarations? The district court relied on extra-record

declarations comprising thousands of pages of scientific

opinion, to evaluate and—in some circumstances—call into

question the BiOp. See In re Consolidated Salmonid Cases,

791 F. Supp. 2d at 813 (describing how the parties’ cross

motions for summary judgment “included . . . thousands of

pages of supporting declarations and exhibits”). It did so

under our holding in Lands Council, 395 F.3d at 1030, which

permits district courts to supplement an administrative record

in a few limited circumstances. Id.; see Tr. of Proceeding

Mot. to Admit Expert Test. vol. 1, at 12, ECF No. 695

[hereinafter Expert Tr. vol. 1]; id. at 14–15 (describing the

Lands Council exceptions). The question here is whether the

district court properly applied Lands Council, or whether it

went beyond Lands Council to improperly question NMFS’s

scientific determinations. We hold, based in part on our

opinion in Delta Smelt, 747 F.3d at 602–04, that the district

court went beyond the Lands Council exceptions when it

admitted extra-record declarations and substituted the

analysis in those declarations for that provided by NMFS.

In general, a court reviewing agency action under the

APA must limit its review to the administrative record. See

Camp v. Pitts, 411 U.S. 138, 142, 93 S. Ct. 1231, 1244

(1973). We have applied this rule many times, in many

different contexts. See, e.g., Delta Smelt, 747 F.3d at 602–04

(stating the rule and applying it to strike extra-record

declarations admitted by the district court); Fence Creek

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Cattle Co. v. U.S.F.S., 602 F.3d 1125, 1131 (9th Cir. 2010)

(“Generally, judicial review of an agency decision is limited

to the administrative record on which the agency based the

challenged decision.”); Sw. Ctr. for Biological Diversity v.

U.S.F.S., 100 F.3d 1443, 1450 (9th Cir. 1996) (“Judicial

review of an agency decision typically focuses on the

administrative record in existence at the time of the decision

and does not encompass any part of the record that is made

initially in the reviewing court.”); Asarco, Inc. v. E.P.A.,

616 F.2d 1153, 1159 (9th Cir. 1980) (“[A]gency action must

be examined by scrutinizing the administrative record at the

time the agency made its decision.”).

This rule ensures that the reviewing court affords

sufficient deference to the agency’s action. The APA gives

an agency substantial discretion “to rely on the reasonable

opinions of its own qualified experts even if, as an original

matter, a court might find contrary views more persuasive.” 

Marsh v. Or. Natural Res. Def. Council, 490 U.S. 360, 378,

109 S. Ct. 1851, 1861 (1989). “When a reviewing court

considers evidence that was not before the agency, it

inevitably leads the reviewing court to substitute its judgment

for that of the agency.” Asarco, 616 F.2d at 1160. In so

imposing its judgment, the reviewing court effectively

conducts a de novo review of the agency’s action rather than

limiting itself to the deferential procedural review that the

APA’s arbitrary or capricious standard permits. See River

Runners for Wilderness v. Martin, 593 F.3d 1064, 1070 (9th

Cir. 2010) (per curiam).

But we have also recognized several exceptions to this

rule. Under Lands Council, a reviewing court may consider

extra-record evidence where admission of that evidence (1) is

necessary to determine “‘whether the agency has considered

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all relevant factors and has explained its decision,’” (2) is

necessary to determine whether “‘the agency has relied on

documents not in the record,’ (3) ‘when supplementing the

record is necessary to explain technical terms or complex

subject matter,’ or (4) ‘when plaintiffs make a showing of

agency bad faith.’” 395 F.3d at 1030 (quoting Sw. Ctr. for

Biological Diversity v. U.S.F.S., 100 F.3d at 1450). These

exceptions are to be narrowly construed, and the party

seeking to admit extra-record evidence initially bears the

burden of demonstrating that a relevant exception applies. 

See Fence Creek, 602 F.3d at 1131.

The first Lands Council exception—the “relevant factors”

exception—is the most difficult to apply, so we pause here to

further examine it. Although the relevant factors exception

permits a district court to consider extra-record evidence to

develop a background against which it can evaluate the

integrity of the agency’s analysis, the exception does not

permit district courts to use extra-record evidence to judge the

wisdom of the agency’s action. Asarco, 616 F.2d at 1160. 

This distinction is a fine, but important, one. Reviewing

courts may admit evidence under this exception only to help

the court understand whether the agency complied with the

APA’s requirement that the agency’s decision be neither

arbitrary nor capricious. See id. at 1159; see also Motor

Vehicle Mfrs. Ass’n of U.S., Inc. v. State Farm Mut. Auto Ins.

Co., 463 U.S. 29, 103 S. Ct. 2856 (1983) (further describing

the APA’s standards). But reviewing courts may not look to

this evidence as a basis for questioning the agency’s scientific

analyses or conclusions. Asarco, 616 F.2d at 1160–61.

We most recently considered the scope of the Lands

Council exceptions in Delta Smelt. See Delta Smelt, 747 F.3d

at 602–04. There, like here, the district court admitted

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“multiple declarations from multiple experts” to augment the

administrative record. Id. at 603. We held that, in doing so,

the district court violated the APA for two reasons. First, the

court admitted more than forty expert declarations under

Lands Council in addition to certifying four expert

declarations under Federal Rule of Evidence 706. Id. at 599

n.13 (citing Fed. R. Evid. 706), 603. We questioned whether

the district court needed the extra-record declarations to

explain the technical language in the BiOp or provide

background material because the Rule 706 court-appointed

experts served those purposes. See id. at 603. Thus, we were

critical of the district court opening the administrative record

as a forum for the experts to debate the merits of the BiOp. 

Id. at 603–04.

Second, we held in Delta Smelt that the district court

erred when it used the extra-record declarations as a basis for

judging the wisdom of the agency’s scientific analysis. 

747 F.3d at 604. Even if a reviewing court properly admits

extra-record evidence under Lands Council, it may not use

the admitted extra-record evidence “to determine the

correctness or wisdom of the agency’s decision.” Asarco,

616 F.2d at 1160. Such use is never permitted.

Here too, the district court violated Delta Smelt’s holding

when it used several extra-record declarations to question

NMFS’s scientific judgments. As in Delta Smelt, the district

court here “relied . . . on the declarations of the parties’

experts-as-advocates as the basis for rejecting the BiOp.” 

747 F.3d at 604. In this way, the district court overstepped

the bounds of Lands Council by opening the administrative

record as a forum for the experts to debate the merits of the

BiOp. The district court employed extra-record declarations

at the following points for this impermissible purpose: In re

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Consolidated Salmonid Cases, 791 F. Supp. 2d at 827, 852

(Deriso Decl., ECF No. 440); id. at 829, 832, 834, 841

(Burnham Decl., ECF No. 439); id. at 840, 841 (Hilborn

Reply Decl., ECF No. 493); id. at 863 (Cramer Decl., ECF

No. 448); id. at 880 (Cummings Decl., ECF No. 445); id. at

884, 889–90, 893 (Cavallo Decl., ECF No. 446–1); id. at

942–43 (Dotan Decl., ECF No. 442). By admitting these

declarations and relying on them to question the wisdom of

NMFS’s judgments, the district court abused its discretion

under Lands Council.

IV. THE LEGAL FRAMEWORK

A. The APA

The ESA does not provide its own standard of judicial

review, so we evaluate the BiOp under the APA’s arbitrary or

capricious standard. See Bennett, 520 U.S. at 174–77; Delta

Smelt, 747 F.3d at 601. Section 706(2)(A) of the APA

requires a reviewing court to uphold agency action unless it

is “arbitrary, capricious, an abuse of discretion, or otherwise

not in accordance with law.” 5 U.S.C. § 706(2)(A). Under

this standard, we will “sustain an agency action if the agency

has articulated a rational connection between the facts found

and the conclusions made.” Pac. Coast Fed’n of Fishermen’s

Ass’ns v. U.S. Bureau of Reclamation, 426 F.3d 1082, 1090

(9th Cir. 2005).

The arbitrary or capricious standard is a deferential

standard of review under which the agency’s action carries a

presumption of regularity. See Citizens to Preserve Overton

Park, Inc. v. Volpe, 401 U.S. 402, 415–16, 91 S. Ct. 814

(1971), abrogated in part on other grounds as recognized in

Califano v. Sanders, 430 U.S. 99, 97 S. Ct. 980 (1977); Kern

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Cnty. Farm Bureau v. Allen, 450 F.3d 1072, 1076 (9th Cir.

2006). Although the court’s inquiry must be “searching and

careful, . . . the ultimate standard of review is a narrow one.” 

Marsh, 490 U.S. at 378 (internal citations omitted). Thus,

“[e]ven when an agency explains its decision with ‘less than

ideal clarity,’ a reviewing court will not upset the decision on

that account ‘if the agency’s path may be reasonably

discerned.’” Ala. Dep’t of Envt’l Conservation v. E.P.A.,

540 U.S. 461, 497, 124 S. Ct. 983 (2004) (quoting Bowman

Transp. v. Ark.—Best Freight Sys., Inc., 419 U.S. 281, 286,

95 S. Ct. 438 (1974)). It is not the reviewing court’s task to

“make its own judgment about” the appropriate outcome. 

River Runners for Wilderness, 593 F.3d at 1070. “Congress

has delegated that responsibility to” the agency. Id. “The

court’s responsibility is narrower: to determine whether the”

agency complied with the procedural requirements of the

APA. Id.

This traditional deference to the agency is at its highest

where a court is reviewing an agency action that required a

high level of technical expertise. Marsh, 490 U.S. at 377; see

also Baltimore Gas &Elec. Co. v. Natural Res. Def. Council,

Inc., 462 U.S. 87, 103, 103 S. Ct. 2246 (1983) (“When

examining this kind of scientific determination . . . a

reviewing court must generally be at its most deferential.”). 

As part of this deference, we afford the agency discretion to

choose among scientific models; we “reject an agency’s

choice of a scientific model only when the model bears no

rational relationship to the characteristics of the data to which

it is applied.” Delta Smelt, 747 F.3d at 621 (internal citations

omitted).

Nevertheless, the deference we owe an agency is not

unlimited. We may not automatically defer to an agency’s

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conclusions, even when those conclusions are scientific. See

Marsh, 490 U.S. at 378. Rather, our review must be

sufficiently probing to ensure that the agency has not

relied on factors which Congress has not

intended it to consider, entirely failed to

consider an important aspect of the problem,

offered an explanation for its decision that

runs counter to the evidence before the

agency, or is so implausible that it could not

be ascribed to a difference in view or the

product of agency expertise.

State Farm, 463 U.S. at 43. A different approach “would not

simply render judicial review generally meaningless, but

would be contrary to the demand that courts ensure that

agency decisions are founded on a reasoned evaluation of the

relevant factors.” Marsh, 490 U.S. at 378 (internal citations

omitted).

B. The ESA

The ESA requires an agency to use “the best scientific

and commercial data available” when formulating a BiOp. 

16 U.S.C. § 1536(a)(2); 50 C.F.R. § 402.14(g)(8). An

agency’s failure to do so violates the APA. See 5 U.S.C.

§ 706(2)(A); Pac. Coast Fed’n v. Gutierrez, 606 F. Supp. 2d

1195, 1244 (E.D. Cal. 2008).

The purpose of the best available science standard is to

prevent an agency from basing its action on speculation and

surmise. Bennett, 520 U.S. at 176. Under this standard, an

agency must not “‘disregard[] available scientific evidence

that is in some way better than the evidence [it] relies on.’” 

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Kern Cnty., 450 F.3d at 1080 (quoting Sw. Ctr. for Biological

Diversity v. Babbitt, 215 F.3d 58, 60 (D.C. Cir. 2000)). The

standard does not, however, require an agency to conduct

new tests or make decisions on data that does not yet exist. 

See Am. Wildlands v. Kempthorne, 530 F.3d 991, 998–99

(D.C. Cir. 2008) (holding that an agency’s use of available

data and test methods was reasonable even though better test

methods existed because those test methods had not yet been

used on the species in question). Moreover, if the only

available data is “‘weak,’ and thus not dispositive,” an

agency’s reliance on such data “does not render the agency’s

determination ‘arbitraryand capricious.’” GreenpeaceAction

v. Franklin, 14 F.3d 1324, 1336 (9th Cir. 1992) (quoting Stop

H-3 Ass’n v. Dole, 740 F.2d 1442, 1460 (9th Cir. 1984)). An

agency complies with the best available science standard so

long as it does not ignore available studies, even if it

disagrees with or discredits them. See Kern Cnty., 450 F.3d

at 1081 (rejecting Kern’s argument that FWS violated the

best available science standard when it cited but allegedly

misinterpreted three studies).

Finally, what constitutes the best scientific and

commercial data available is itself a scientific determination

deserving of deference. Miccosukee Tribe of Indians of Fla.

v. United States, 566 F.3d 1257, 1265 (11th Cir. 2009) (citing

Marsh, 490 U.S. at 377–78). For that reason “[a] court

should be especially wary of overturning such a

determination on review.” In re Consolidated Salmonid

Cases, 791 F. Supp. 2d at 821.

V. THE MERITS OF THE BIOLOGICAL OPINION

With these standards in mind, we evaluate each BiOp

component that is challenged on appeal.

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Plaintiffs originally challenged dozens of specific

components of the 2009 Salmonid BiOp. At summary

judgment, the district court upheld as valid many of them, and

determined that several others were arbitrary or capricious. 

See id. at 955–59. Defendants appeal each part of the district

court opinion in which the court found the BiOp unlawful. 

Plaintiffs cross-appeal several portions of the opinion in

which the district court upheld the BiOp.

We discuss each challenge to the BiOp in turn. First, we

address the district court’s objections to NMFS’s use of raw

salvage data. Second, we discuss the challenges to NMFS’s

jeopardy opinions, including the portion of the BiOp dealing

with indirect mortality factors. Third, we review the

challenges to NMFS’s RPAs, clarifying what the ESA and its

implementing regulations require from the agency when it is

developing and defining RPAs. We then evaluate the

challenged Actions in light of those requirements. Finally,

we discuss the three cross-appeal issues.

As our record review will show, the district court—in

many instances—did not afford the agency proper deference

under the APA. Rather than evaluating the agency’s

decision-making process and deferring to the agency’s

scientific conclusions when those conclusions are fairly

traceable to the record, the district court engaged in an indepth substantive review of the science supporting the BiOp

and substituted its own opinions, and those of the parties’

experts, for the opinions of NMFS. As a result, the district

court invalidated much of the BiOp under a quasi de novo

review. But the APA does not permit such an in-depth

review, particularly where, like here, the conclusions

implicate agency expertise. See Marsh, 490 U.S. at 375–77.

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We correct the district court’s errors in our own review;

and as a result, we uphold the BiOp in its entirety. After

reviewing the record as a whole, we are satisfied that, when

developing each component of the BiOp, NMFS relied on the

factors that Congress intended it to consider, considered all

important aspects of the problem, and offered explanations

for its decisions that are in line with the evidence. See State

Farm, 463 U.S. at 43. We are also satisfied that, in doing so,

NMFS used the best scientific data available, even if that

science was not always perfect. Cf. Greenpeace Action,

14 F.3d at 1336.

A. We Defer To the Agency’s Choice To Use Raw

Salvage Figures

The Projects pump fresh water out of the Old and Middle

Rivers in volumes sufficient to reverse the rivers’ traditional

flow. Delta Smelt, 747 F.3d at 606. Absent pumping, the

rivers would flow north into the Delta. Under pumping

operations, the rivers flow south to the Jones and Banks

pumping plants. Listed species—particularly juveniles—are

caught in the negative current and drawn towards the

pumping facilities. See 2009 Salmonid BiOp at 651. Some

of these fish are salvaged at the pumps, meaning they are

diverted from the fatal pumping plants to fish salvage

facilities and into tanks where they are counted, measured,

loaded into trucks, driven north, and dumped back into the

Delta.13 But even if salvaged, fish that are drawn towards the

pumps in the Rivers’ negative flow have a lower likelihood

13 See Fish Facilities Unit Monitoring and Operations Projects, Cal.

Dep’t of Wildlife, http://www.dfg.ca.gov/delta/data/salvage/

salvageoverview.asp (last visited Oct. 20, 2014, 4:02 p.m.).

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of surviving outmigration than their counterpoints that are

lucky enough to avoid entrainment.14

NMFS concluded in the BiOp that as negative flow of the

Old and Middle Rivers increases, fish are more likely to be

diverted out of the main Delta and towards the pumping

facilities. 2009 Salmonid BiOp at 651. To counter this effect

and enhance the likelihood of salmonids successfully exiting

the Delta, several of the RPA Actions regulate negative flows

and limit exports when fish numbers are high or are likely to

be high. NMFS developed these RPA Actions, in part, by

considering the raw number of fish salvaged at certain

volumes of negative flow. See id. at 361–62 (Figs. 65 & 66).

Plaintiffs argue that NMFS violated the ESA by using raw

salvage data instead of data scaled to fish population. They

assert that the number of fish salvaged every month could be

related to the number of fish in the Delta rather than to the

volume of negative flows in the Old and Middle Rivers. The

district court agreed, concluding that it goes against the grain

of traditional science to use raw instead of scaled salvage

numbers. In re Consolidated Salmonid Cases, 791 F. Supp.

2d at 827. And because “[t]he agency is required to apply

generally recognized and accepted biostatistical principles,

which constitute the best available science, in reaching its

decisions,” NMFS’s use of raw salvage data was arbitrary or

capricious. Id. Defendants appeal that holding here.

14 A fish is “entrained” when it follows diverted water rather than the

natural course of a river, stream, pond, or lake. The danger with

entrainment is that fish can become stranded in irrigation canals or killed

when they are trapped in pumps.

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This issue is almost entirely controlled by our holding in

Delta Smelt. There, the consulting agency—FWS—also used

raw salvage data to set maximum negative flows for the Old

and Middle Rivers. See Delta Smelt, 747 F.3d at 606–07;

2009 Delta Smelt BiOp at 349–50. We determined that the

choice to use raw salvage data was appropriate for three

reasons. First, the agency has substantial discretion to choose

between available scientific models, provided that it explains

its choice. See Delta Smelt, 747 F.3d at 610 (citing Nw. Coal.

for Alts. to Pesticides v. E.P.A., 544 F.3d 1043, 1050 (9th Cir.

2008)). Second, other studies helped inform the specific flow

requirements imposed. Finally, the flow limits “work in

tandem with the incidental take statement (“ITS”), which

accounts for population-level impacts.” Id. at 608.

All three factors are present here. First, the agency

adequately explained why the loss data, although un-scaled

to population, usefully assisted NMFS in identifying whether

and how fish loss relates to negative flow velocity. See 2009

Salmonid BiOp at 360–62; OCAP BA at 13-43–45.

Second, NMFS—like FWS—did not base its maximum

negative flow prescriptions on raw salvage data alone. 

Rather, it used the same particle tracking models FWS used

in the Delta Smelt BiOp to evaluate the effect of heightened

exports on naturally buoyant particles. 2009 Salmonid BiOp

at 362–63. It also relied on studies, such as a 2008 study by

Wim J. Kimmerer, to support its conclusion that there exists

a positive relationship between the volume of water exported

from project pumping plants and juvenile salmonid

entrainment at those plants. See, e.g., id. at 361; Delta Smelt,

747 F.3d at 612 (describing how FWS used the same study).

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Finally, here—like in the Delta Smelt BiOp—the ITS

uses population data to scale incidental take, and the RPA

uses data generated from incidental take to introduce more

restrictive flows in the Old and Middle Rivers. Like the Delta

Smelt BiOp, the Salmonid BiOp sets a range of acceptable

negative flow in the Old and Middle Rivers and requires the

action agency to use population-based data generated from

incidental take to scale in more permissive or restrictive

flows, with a minimum flow of -5,000 cfs. 2009 Salmonid

BiOp at 650.

For these three reasons, the agency acted within its

substantial discretion when it used a non-scaled data model

to set flows in the Old and Middle Rivers.

B. The Challenged Jeopardy Opinion Components Are

Not Arbitrary or Capricious

NMFS determined that the proposed continuing

operations of the Projects are likely to jeopardize the viability

and essential habitat of the listed species. Id. at 575. The

district court invalidated several specific components of this

provision as arbitrary or capricious. See In re Consolidated

Salmonid Cases, 791 F. Supp. 2d at 955–59. Defendants

appeal the district court’s holdings, so we review them here.

1. Winter-Run Chinook

According to the district court, NMFS based its finding

that ongoing CVP/SWP operations jeopardize winter-run

Chinook in part on its determination that winter-run Chinook

is at a “high risk” of extinction. Id. at 864. The court

concluded that NMFS’s “high risk” designation was

“completely unsupported by the record.” Id. As a result, the

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district court determined that this aspect of the BiOp must be

remanded and fixed.

The district court was incorrect in so concluding. NMFS

did not characterize winter-run Chinook as being at “high risk

of extinction” instead of characterizing the species as being

“not viable.” See id. at 864. Rather, NMFS informed its

designation of winter-run Chinook as “not viable” by

considering Dr. Lindley’s 2007 study, in which he suggests

that winter-run Chinook is at a “high risk” of extinction in

several categories. See 2009 Salmonid BiOp at 85–88. 

NMFS discussed the limitations of Lindley’s categories and

explained how it made up for these limitations by relying on

other studies. See id. (citing McElhany et al. (2000),

Liermann and Hilborn (2001), and others). In doing so,

NMFS adequately explained how its various descriptions of

winter-run Chinook as “high risk” influenced its ultimate

jeopardy opinion. Such an explanation is sufficient to satisfy

State Farm’s requirement that the agency consider all

relevant factors and offer an explanation for its conclusion

that is grounded in the evidence. See 463 U.S. at 43. Thus,

this part of the BiOp need not be remanded and fixed.

2. Southern Resident Orca

NMFS concludes in the BiOp that continued CVP/SWP

operations are likely to jeopardize the viability of the

Southern Resident orca. 2009 Salmonid BiOp at 573–74. 

The logic supporting this conclusion is relatively simple. The

orca population at issue has fewer than ninety members, and

so NMFS felt compelled to scrutinize “even small effects on

the fitness of individuals that increase the risk of mortality or

decrease the chances of successful reproduction.” Id. at 573. 

Winter-run and spring-run Chinook are a critical prey base

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for the Southern Resident orca. Id. According to NMFS,

reduction in populations of this prey-base jeopardize the

Southern Resident orca because, for example, less food

requires whales to spend too much energy foraging and

“insufficient prey could cause whales to rely upon their fat

stores, which contain high contaminant levels.” Id. NMFS

concluded that continued CVP/SWP operations threaten the

viability of winter-run and spring-run Chinook. Id. at

574–75. This determination led it to also conclude that these

operations jeopardize the Southern Resident orca. Id.

The district court reversed and remanded this conclusion. 

It held that NMFS did not consider all relevant factors of the

problem because it failed to discuss a seemingly contrary

finding it made, in a BiOp issued on May 5, 2009, that

commercial ocean “harvest of salmon would not jeopardize

the Southern Resident Killer Whales.” See In re

Consolidated Salmonid Cases, 791 F. Supp. 2d at 864–65.

The district court’s conclusion is incorrect because NMFS

did discuss the 2009 Orca BiOp in the Salmonid BiOp,

showing that it did not “entirely fail[] to consider” an aspect

of the problem. See State Farm, 463 U.S. at 43. NMFS

discussed the 2009 Orca BiOp as part of its baseline analysis. 

See 2009 Salmonid BiOp at 218–21. NMFS clarified that the

2009 Orca BiOp—unlike the 2009 Salmonid BiOp—does not

consider the long-term health of Chinook on the continued

viability of the Southern Resident orca, but rather analyzes

the year-to-year impact of commercial harvest on the whales’

short-term food supply. Id. at 218. In this way, NMFS

distinguished the two BiOps as dealing with different time

frames. NMFS’s discussion of how findings in the 2009 Orca

BiOp relate to findings in the 2009 Salmonid BiOp, although

brief, is sufficient to show that NMFS considered the 2009

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Orca BiOp when developing the 2009 Salmonid BiOp. This

consideration satisfiesNMFS’s obligations under State Farm. 

See 463 U.S. at 43.

3. Steelhead Critical Habitat

The BiOp makes two relevant conclusions regarding how

the proposed action will adversely modify CV steelhead

critical habitat in the Stanislaus River. First, NMFS

concludes that CV steelhead prefer to spawn when water is

flowing at 200 cfs; proposed deviations from that flow could

reduce spawnable habitat as much as ninety-five percent in

some years. 2009 Salmonid BiOp at 306, 311. Second,

NMFS concludes that continued CVP/SWP operations,

specifically those that dictate flows from the New Melones

and Goodwin Dams, will degrade spawning gravel below the

Goodwin Dam, thereby undermining replenishment efforts. 

Id.

The district court found these conclusions to be arbitrary

or capricious. Specifically, with regard to spawnable area,

the district court found that NMFS used “maximum habitat”

as a benchmark for evaluating the Projects’ impacts. That

benchmark was improper because “maximizing” habitat is

not a goal of the ESA. In re Consolidated Salmonid Cases,

791 F. Supp. 2d at 935. The district court also found that no

record evidence supported NMFS’s conclusion that the

CVP/SWP operations cause the recorded gravel loss. Id. at

936.

We side with the agency on both issues. First, NMFS did

not misapply the ESA by relying on a study that sets a goal of

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“maximizing” habitat.15 The record shows that NMFS looked

to Aceituno (1993) and other studies to determine the point at

which the Projects’ restriction of flows in the Stanislaus River

would “appreciabl[y] reduce[]” habitat, see 2009 Salmonid

BiOp at 42 (citing 50 C.F.R. § 402.02). The record does not

show that NMFS abandoned the ESA’s prescription to “avoid

jeopardy” in favor of Aceiunto’s goal of “maximizing

habitat,” see id. (discussing jeopardy requirement). Rather,

NMFS explained why Aceiunto’s 1993 study provided an

adequate baseline for developing minimum and pulse flows

in the Stanislaus River.16

In providing this explanation,

NMFS satisfied its obligations under the ESA and State

Farm. 463 U.S. at 43.

Second, the record provides adequate support (grounded

in best available science) for NMFS’s conclusion that

CVP/SWP operations negatively impact spawning gravel

quantity and quality. Before construction of dams, channel

forming flows of 8,000 cfs and mobilizing flows of 5,000 to

8,000 cfs created channels—outside of traditional gravel

spawning grounds—in which the river deposited fine

sediment. 2009 Salmonid BiOp at 308 (citing Mesick (2001);

15 It is to be expected that the language of the studies on which an

agency relies will not alwaystrack the statutory language of the ESA. Not

all studies are conducted to serve as a basis for section 7 consultation. 

Thus, the mere fact that Aceituno’s study seeks to “maximize” CV

steelhead habitat does not require NMFS to disregard it.

16 See Memorandum from Rhonda Reed, Section 7 Biologist, on The

Development ofthe Reasonable and Prudent Alternatives (RPA) to Avoid

Jeopardy to CV Steelhead in the Stanislaus River, Specifically as it

Relates to Flow and Temperature 2–9 (May 31, 2009) (NMFS biologist

Rhonda Reed describes how NMFS used Aceituno’s suggested minimum

flows as a starting point but altered those flows based on discussions with

agency and stakeholder scientists).

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Kondolf et al.(2001)). But CVP/SWP operations have all but

halted these flows in recent years. Id. Thus, fine sediment

collects in CV steelhead gravel spawning ground, degrading

the quality of spawning areas. Id. According to Dr.

Kondolf’s 2001 study (upon which NMFS bases much of this

part of the jeopardy opinion), “poor quality of spawning

gravels due to deposition of sand and fine sediment” is one of

four primary factors limiting salmon survival in the

Stanislaus River.17 The specific component of the BiOp

challenged here essentially adopts this conclusion. See 2009

Salmonid BiOp at 308 (citing Kondolf et al. (2001)). 

Although NMFS could have done a better job making the

connection between CVP/SWP operations and the quantityof

gravel suitable for CV steelhead rearing, that connection is

fairly discernable from a review of the “whole record.” See

5 U.S.C. § 706; Bowman Transp., 419 U.S. at 286. The

conclusion is, thus, not arbitrary or capricious.

4. Indirect Mortality Factors

The BiOp evaluates the impact of both direct and indirect

mortality factors on listed species. Direct mortality factors,

such as entrainment, are those project components that

directly harm or kill listed species. See 50 C.F.R. § 402.02. 

Indirect mortality factors are those caused by continued

operations that do not directly cause the death of listed

species, but lead to it. Those indirect mortality factors

include predation, harm inflicted on native species by

non-native species, pollution, and food limitations. See 2009

Salmonid BiOp at 374. NMFS concludes that CVP/SWP

17 G.M. Kondolf, et al., Reconnaissance-Level Assessment of Channel

Change and Spawning Habitat on the Stanislaus River Below Goodwin

Dam, Rpt. to the U.S. Fish and Wildlife Service 1 (Mar. 22, 2001).

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operations cause indirect mortality for listed species by

creating conditions in the Delta that favor non-native species,

species that prey on listed Salmonids. CVP/SWP operations

also negatively influence the listed species by lengthening the

time members remain in the interior delta—where they are

exposed to pollution and other indirect mortality

factors—before outmigrating to the ocean. See id.

Plaintiffs challenged this finding at summary judgment. 

See In re Consolidated Salmonid Cases, 791 F. Supp. 2d at

869–71. The district court mostly agreed with them, holding

that although NMFS sufficiently established that Delta

hydrologic conditions—as altered in part bythe Projects—are

favorable to invasive species, NMFS failed to articulate the

connection among continuing Projects operations, invasive

species, and harm to listed species. See id. at 870 (posing the

following questions: “What effect do these exotics have on

the Listed Species? To what extent does the contribution of

the Projects to the continued presence of these exotics

contribute to the jeopardy finding?”). That failure, according

to the district court, rendered the indirect mortality analysis

arbitrary and capricious. Id. at 870–71.

We disagree. NMFS adequately connected indirect

mortality factors to CVP/SWP operations, thus satisfying its

obligations under the APA and ESA. NMFS’s conclusion

that the Projects’ operations exacerbate Salmonid indirect

mortality proceeds in three steps. First, NMFS explains how,

over the past half century, the Projects’ operations have

worked to degrade the environment in the interior delta,

converting a thriving river system into an unnatural inland

lake-like habitat ill-suited to many native species. This

statement is uncontested. See id. at 870 (“Plaintiffs do not

directly contest the conclusion that the altered hydrologic

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conditions are favorable for invasive species. Nor do

Plaintiffs challenge the BiOp’s conclusion that CVP and SWP

operations contribute to this ecosystem alteration.”). Second,

NMFS concludes that continued CVP/SWP operations

(specifically pumping from the Jones and Banks facilities)

cause fish outmigrating through the main channels of the

Delta to divert into intersecting channels that split off from

the main rivers and lead towards the inner delta. 2009

Salmonid BiOp at 374. The Projects’ operations cause this

diversion by, among other things, reversing the flows of the

Old and Middle Rivers. Id. at 651 (citing Vogel (2004) to

support the conclusion that “fish chose channels leading south

more frequently when exports were elevated, than when

exports were lower”). Third, fish that are drawn through

intersecting channels and into the inner Delta have a lower

survival rate than fish that remain in the main Delta. Id. at

375. Not all of these fish are killed in pumping plants; many

are eaten by non-native predators, trapped by non-native

plants, or fall prey to pollution in the inner Delta. Id. at

374–81.

The second step provides the critical causal link between

the Projects’ operations and indirect mortality factors that the

district court found lacking. We find that NMFS cited

enough scientific evidence to support its conclusions that high

levels of pumping from the Jones and Banks facilities

influence fish to swim towards the inner Delta where they fall

prey to indirect mortality factors. See id. at 651 (citing Vogel

(2004), SJRGA (2006), SJRGA (2007), SJRGA (2008)). 

Although the agency’s analysis is not perfect, it may

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reasonably be discerned, see Bowman Transp., 419 U.S. at

286, and is thus not arbitrary or capricious.18

C. The Challenged RPA Actions Are Not Arbitrary or

Capricious

We now consider the RPA Actions invalidated by the

district court. Before wading into the specific Actions, we

clarifywhat the ESA and its implementing regulations require

from an agency when the agency is developing RPAs as part

of a BiOp.

1. The Legal Requirements for an RPA Action

ESA section 7 provides that “[i]f jeopardy or adverse

modification is found [during consultation], the Secretary

shall suggest those reasonable and prudent alternatives which

he believes would not . . . ,” 16 U.S.C. § 1536(b)(3)(A), 

18 Nevertheless, we can see where the district court got derailed into

thinking that NMFS blamed continuing CVP/SWP operations for exotics

in the Delta. See In re Consolidated Salmonid Cases, 791 F. Supp. 2d at

870. NMFS essentially makes this statement, without any record support,

in its summary of the indirect mortality component of the BiOp. 2009

Salmonid BiOp at 382. The district court properly questioned this

conclusion: NMFS did not support the assertion that continuing

CVP/SWP operations cause that level of environmental decline. Although

NMFS seemed to say as much on page 382 of the BiOp, the crux of its

indirect mortality argument is in the pages preceding the summary on page

382. NMFS makes clear that the question is not whether “altered project

operations reduce [or exacerbate] the presence of exotics?” but rather

“whether altered project operations could keep more fish in the main delta

where they are less likely to come into contact with exotic species and

die?” As explained, NMFS believes the answer to this question is yes,

and it supported its conclusion by relying on the best available science. 

See, e.g., id. at 651.

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“jeopardize the continued existence of any endangered [or

threatened] species . . .” or result in adverse modification of

critical habitat, id. § 1536 (a)(2). Reasonable and prudent

alternatives are alternative actions identified during formal

consultation that (1) “can be implemented in a manner

consistent with the intended purpose of the action,” (2) “can

be implemented consistent with the scope of the Federal

agency’s legal authority and jurisdiction,” (3) are

“economically and technologically feasible,” and (4) “the

Director believes would avoid the likelihood of jeopardizing

the continued existence of listed species or resulting in the

destruction or adverse modification of critical habitat.” 50

C.F.R. § 402.02. The first three of these factors are the

non-jeopardy factors developed by the agency. The final is

the jeopardy factor, and it is taken from ESA section 7. See

Delta Smelt, 747 F.3d at 634.

Under these provisions, the district court reversed and

remanded several RPA Actions because the agency did not

(1) explain how each RPA Action is “essential to avoid

jeopardy,” In re Consolidated Salmonid Cases, 791 F. Supp.

2d at 922; see also id. at 897 n.26, or (2) explain how each

RPA Action complies with § 402.02’s three non-jeopardy

factors. We recently held in Delta Smelt that these are not the

correct legal standards under which to evaluate an RPA

Action. As we further clarify below, neither section 7 nor

§ 402.02 require NMFS to explain why each Action is

“essential” or to fully elucidate the non-jeopardy factors.

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a. The ESA Does Not Require NMFS To

Explain How Each RPA Action Is Essential

To Avoid Jeopardy

The district court held that § 402.02 requires NMFS to

show how each RPA Action is essential to avoid jeopardy.

19

The effect of this holding was to impose an onerous, highly

precise standard on NMFS under which the district court

invalidated RPA Actions anytime NMFS did not explain why

the Action was necessary, over all others, to preserve the

species. See, e.g., In re Consolidated Salmonid Cases, 791 F.

Supp. 2d at 898.

As we explained in Delta Smelt, neither the ESA nor its

implementing regulations require this level of precision from

the agency. The ESA requires only that the agency impose

RPAs that are “not likely to jeopardize” the species or its

habitat. See 16 U.S.C. § 1536(a)(2), (b)(3)(B). The

regulations interpret this section as requiring the agency to

develop RPAs “that the Director believes” would avoid

jeopardy. 50 C.F.R. § 402.02. This moderate and deferential

language is a far cry from that which would impose a strictly

essential requirement. Rather, this language imposes a

“flexible standard for the consulting agency” that does not

require the Secretary “to explain why he chose one RPA over

another . . . .” Delta Smelt, 747 F.3d at 624 (citing Sw. Ctr.

for Biological Diversity v. U.S. Bureau of Reclamation,

19 The district court articulated its holding as requiring NMFS to explain

how each RPA Action is an “essential component of an overall RPA

designed to avoid jeopardy.” In re Consolidated Salmonid Cases, 791 F.

Supp. 2d at 897 n.26. But in practice, the district court invalidated BiOp

provisions when NMFS failed to explain how they were “essential to

avoid jeopardy . . . .” Id. at 922. That is the holding we review.

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143 F.3d 515, 523 (9th Cir. 1998)). Under this deferential

standard, the agency need not pick the best RPA or the one

most likely to avoid jeopardy. Id. Rather, we give the

agency flexibility to choose among several appropriate

alternatives. We will uphold that choice so long as it is

reasonably supported based on a review of the record as a

whole. See Sw. Ctr. for Biological Diversity v. U.S. Bureau

of Reclamation, 143 F.3d at 523.

b. The ESA Does Not Require NMFS To

Articulate Compliance with the Non-Jeopardy

Factors

The district court also held that Agency regulations

require NMFS to describe how each RPA Action meets

§ 402.02’s non-jeopardy factors. See In re Consolidated

Salmonid Cases, 791 F. Supp. 2d at 917. It invalidated

several RPA Actions, including Action IV.4.2, for failing to

establish compliance with these factors. We hold that the

district court erred in interpreting § 402.02.

Again, this issue is largely controlled by Delta Smelt. We

said in Delta Smelt that, “[n]othing in § 402.02 obligates the

[consultation agency] . . . to address the non jeopardy factors

when it proposes RPAs. Section 402.02 is a definitional

section; it is defining what constitutes an RPA, not setting out

hoops that the [consultation agency] . . . must jump through.” 

747 F.3d at 635. Thus, while “a ‘thorough’ documentation of

jeopardy/adverse modification in the BiOp is always

required, . . . documentation of the non jeopardy factors is

only required when the RPA fails to meet a non jeopardy

factor.” Id. at 635–36. Based on this conclusion, we rejected

the district court’s finding that the agency acted arbitrarily or

capriciously by failing to include “some exposition in the

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record of why the agency concluded (if it did so at all) that all

four regulatory requirements for a valid RPA were satisfied.” 

San Luis & Delta-Mendota Water Auth. v. Salazar, 760 F.

Supp. 2d 855, 957 (E.D. Cal. 2010), aff’d in part rev’d in part

by Delta Smelt, 747 F.3d 581.

This holding applies with equal force here. NMFS is not

required to document its compliance with § 402.02’s nonjeopardy factors. Rather, it needed only to fairly conclude—

based on the record—that the proposed RPAs do not further

jeopardize the listed species or adversely affect critical

habitats. See Delta Smelt, 747 F.3d at 635. We evaluate

whether it did so below.

2. Challenged RPA Actions

a. Action IV.2.1

The district court invalidated several RPA Actions related

to the San Joaquin Delta. The first, Action IV.2.1, prescribes

San Joaquin River inflow to export ratios between April 1 and

May 31. 2009 Salmonid BiOp at 641. After a brief

adjustment period, Action IV.2.1 requires Reclamation and

DWR to implement specific flow to combined export ratios

on the San Joaquin River (measured at Vernalis, California). 

Id. at 643. Those ratios are:

San Joaquin Valley

Classification

Vernalis flow (cfs): CVP/SWP

combined export ratio

Critically dry 1:1

Dry 2:1

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Below normal 3:1

Above normal 4:1

Wet 4:1

2009 Salmonid BiOp at 643–44.

The district court invalidated the 4:1 flow-to-export ratio

as arbitraryand capricious. Although it concluded that record

evidence provided support for some flow-to-export ratio, the

district court determined that the agency did not provide

sufficient support for the specific 4:1 flow-to-export ratio. 

See generally In re Consolidated Salmonid Cases, 791 F.

Supp. 2d at 894–98.

We disagree with the district court and hold that the

record supports NMFS’s decision to impose the 4:1 ratio. 

NMFS bases its decision to impose a 4:1 flow-to-export ratio

primarilyon Vernalis Adaptive Management Plan (“VAMP”)

studies of Chinook salmon smolts. 2009 Salmonid BiOp at

644–45. VAMP has tested Salmonid survival based on a 2:1

ratio, but not a 4:1 ratio. Drawing on VAMP and other data

showing a positive correlation between a high-flow-to-lowexport ratio and successful salmonid outmigration,20 NMFS

concluded that “flow to export ratios should be at least 2:1

and preferably higher to increase survival and abundance.” 

Stuart 4:1 Memo., supra, at 22. NMFS settled on the 4:1

20 Memorandum from Jeffrey Stuart, NMFS Fisheries Biologist, on The

San Joaquin River “4:1 Flow to Export ratio” Reasonable and Prudent

Alternative (RPA) for the formal section 7 consultation regarding the

Long-Term Operations of the Central Valley Project and State Water

Project 20–21 (June 2, 2009) [hereinafter Stuart 4:1 Memo.].

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ratio as a high ratio (appropriate in above-normal

precipitation years) by studying historic monthly average

flows at Vernalis. Id. at 16. “This data shows that

approximately 6,000 cfs of flow is available at Vernalis in 50

percent of the wet and above normal water years.” Id. at 17.

Being that the minimum export level to maintain health and

safety is 1,500 cfs, id. at 22, a 4:1 export ratio in wet and

above normal years—although maximally protective of

fish—is traceable to the record. It is within the agency’s

discretion to choose a conservative threshold that will afford

maximum protection to the species so long as that threshold

is fairly supported, which it is. Tenn. Valley Auth. v. Hill,

437 U.S. 153, 184–85, 98 S. Ct. 2279 (1978).

b. Action IV.2.3 and Action IV.3

Actions IV.2.3 and IV.3 specify river flow management

strategies for the Old and Middle Rivers. Although the Old

and Middle Rivers typically flow north, CVP and SWP

pumping reverses that flow, drawing the water south to the

Jones and Banks pumping plants. See Delta Smelt, 747 F.3d

at 606. According to Particle Tracking Model (“PTM”) and

fish tagging studies cited by NMFS, listed fish outmigrating

through the San Joaquin River are vulnerable to diversion

into the channels that lead to the export facilities when

pumping is high and the flow of the Old and Middle Rivers

is very negative. 2009 Salmonid BiOp at 651. These

diverted fish have a lower rate of survival than their

counterparts that bypass the inner Delta and migrate directly

through the outer Delta to the San Francisco Bay.

Actions IV.2.3 and IV.3 seek to mitigate these effects by

imposing negative flow restrictions on the Old and Middle

Rivers. Action IV.2.3 requires the Projects to reduce exports

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from the Jones and Banks pumping plants between January 1

and June 15 such that the negative flow of the Old and

Middle Rivers is limited to -2,500 to -5,000 cfs, depending on

the presence of salmonids. Id. at 648–52. Action IV.3

requires the Projects to reduce exports between November 1

and December 31 when fish salvage numbers (the numbers of

fish caught at the pumps) meet certain triggers. Id. at 652–53.

The district court invalidated both Actions. It held, with

regard to Action IV.2.3, that the agency did not adequately

explain how imposition of the specific flow requirements in

the Action are “essential to avoid jeopardy.” In re

Consolidated Salmonid Cases, 791 F. Supp. 2d at 909

(citation omitted). It invalidated Action IV.3 because NMFS

based the specific triggers on raw salvage data and “failed to

provide any record explanation for why the specific triggers

were chosen.” Id. at 911.

We again reverse the district court and find that the record

supports NMFS’s decision to impose both Actions. The

record fairly supports NMFS’s imposition of the particular

flow restrictions in Action IV.2.3. PTM modeling cited by

NMFS supports the conclusion that risk of fish entrainment

at pumping facilities increases substantially between -2,500

and -5,000 cfs. 2009 Salmonid BiOp at 652. That same data

shows that the risk of entrainment increases at an even greater

rate with flow restrictions more negative than -5,000 cfs. Id. 

Thus, it is reasonable for NMFS to impose the -2,500 to

-5,000 cfs range as a minimum negative flow during times

when salmonids are likely to pass channel openings. The raw

data salvage numbers bolster this conclusion. According to

that data, “[l]oss of older juveniles at the CVP and SWP fish

collection facilities increases sharply at Old and Middle River

flows of approximately -5,000 cfs . . . .” Id. at 361. NMFS

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explained its rationale for imposing the specific flow

restrictions in Action IV.2.3, and supports that rationale with

what it has determined is the best available science—PTM

studies and raw salvage data.21It has, thus, satisfied its

procedural and substantive obligations under the APA and

ESA.

Action IV.3 is also fairly traceable to the 2009 Salmonid

BiOp and accompanying studies. NMFS explains that the

triggers imposed by Action IV.3 are developed from previous

work done by DWR, Reclamation, NMFS, and FWS.22

 The

specific triggers in Action IV.3 (eight fish/thousand acre feet

or fifteen fish/thousand acre feet) come from data compiled

by NMFS tending to show that when salvage exceeds those

levels, there is a pulse of fish in the system. See Stuart PTM

Memo., supra, at 28 (Fig. 15). The agency’s decision to set

these as particular triggers is based on its own data generated

over nine years, data that is well documented in the BiOp and

supporting memoranda. See id. For that reason, these

particular triggers are not arbitrary or capricious.

c. Action IV.4.2

Action IV.4.2 requires DWR to implement specific

measures to (1) reduce pre-salvage fish loss and (2) improve

21 We have already held, consistent with our opinion in Delta Smelt, that

NMFS acted within its considerable discretion when it elected to use raw

salvage data as a guide for setting certain RPA Actions.

22 Memorandum from Jeffrey Stuart, NMFS Fisheries Biologist, on

Particle Tracking Model results for Old and Middle River flow

manipulation (June 3, 2009) [hereinafter Stuart PTM Memo.] (describing

how the agencies have used a salmon “decision tree” based on salvage

data).

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salvage efficiency. 2009 Salmonid BiOp at 655. To reduce

pre-salvage loss, the Action requires DWR to “commence

studies to develop predator control methods for Clifton Court

Forebay,” the body of water the fish cross before reaching the

Tracy and Skinner Fish Collection Facilities. Id. at 656. The

Action also sets a specific benchmark for salvage efficiency

at the facilities, requiring DWR to “achieve a minimum 75

percent salvage efficiency for CV salmon, steelhead, . . . and

green sturgeon” at the Skinner Fish Collection Facility. Id. at

655.

Plaintiffs argued that this Action is not technologically or

economically feasible and that the agency thus violated

§ 402.02 by requiring it. The district court agreed. It

concluded that NMFS failed to “cite any record evidence

indicating that the efficiency improvement, albeit a minor

one, is economically or technologically feasible.” In re

Consolidated Salmonid Cases, 791 F. Supp. 2d at 926.

Delta Smelt made clear that the ESA does not require

NMFS to cite record evidence showing that each RPA Action

is economically and technologically feasible. Delta Smelt,

747 F.3d at 635. Thus, NMFS’s failure to cite such evidence

here was not arbitrary or capricious.

d. Action III.1.2

The remaining actions challenged by Plaintiffs,

invalidated by the district court, and challenged here, relate

to CVP/SWP operations on the Stanislaus River, in the east

side of the Central Valley.

Action III.1.2 pertains to the temperature of the Stanislaus

River. According to NMFS, increased temperature in the

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Stanislaus River threatens the critical habitat of the CV

steelhead. 2009 Salmonid BiOp at 619–20. To remedy this

problem and achieve desired temperatures, Action III.1.2

requires Reclamation to “make cold water releases from New

Melones Reservoir to provide suitable temperatures for CV

steelhead rearing, spawning, egg incubation smoltification,

and adult migration in the Stanislaus River downstream of

Goodwin Dam . . . .” Id. at 620–21. Action III.1.2 includes

an exception to this requirement when the projected

temperatures cannot be achieved. Id. at 621 (describing the

process that Reclamation should use to apply for an exception

to the temperature requirements).

The district court remanded this action to the agency after

determining that the agency did not sufficiently document

“the extent to which this RPA is ‘essential’ to avoiding

jeopardy . . . .” In re Consolidated Salmonid Cases, 791 F.

Supp. 2d at 947–49. More specifically, the court determined

that because the Action includes an exception with “no

limitations” it necessarily does not avoid jeopardy. Id. at 947.

The record does not support the district court’s conclusion

that the “Federal Defendants describe an exception that ‘has

no limitations.’” Id. at 947. NMFS will consider granting an

exception to the temperature requirements only when

Reclamation demonstrates that “after taking all actions within

its authorities, it is unlikely to meet” the temperature

requirements. 2009 Salmonid BiOp at 621. If that happens,

Reclamation must convene the Stanislaus Operations Group

(“SOG”)23to obtain recommendations on how to proceed. 

23

“Reclamation created a Stanislaus Operations Group (SOG) to provide

a forum for real-time operational flexibility and implementation of the

alternative actions defined in the RPA.” NOAA Fisheries, Stanislaus

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See id. at 621. If the SOG cannot come to a consensus,

NMFS will make recommendations. Reclamation must

satisfy several procedural requirements before NMFS will

grant an exception under Action III.1.2, leading us to

conclude that application of the exception is limited. For this

reason, the record supports NMFS’s conclusion that

imposition of Action III.1.2, notwithstanding its exception, is

likely to avoid jeopardy.

e. Action III.1.3

Action III.1.3 also relates to how CVP/SWP operations on

the Stanislaus River impact the CV steelhead. CV steelhead

adults respond to certain flows in the Stanislaus River as a

natural cue for fall migration. Juveniles depend on a

particular volume of spring flows to assist them in migrating

out of the River to the Delta and eventually to the Pacific

Ocean. Id. at 625. Pulse flows in the Stanislaus River also

benefit CV steelhead habitat by maintaining gravel quality,

promoting channel formation, and enhancing access to varied

rearing habitats. Id. at 624. To better provide these essential

cues and to sustain CV steelhead habitat, Action III.1.3

requires Reclamation to “operate releases from the East Side

Division reservoir to achieve a minimum flow schedule as

prescribed” in the RPA. Id. at 623. The minimum flow

schedule incorporates short periods of high volume flows in

October (fall attraction flows), several times in March and

April (outmigration cue flows), and in May (outmigration

flows). Id.

Operations Group, http://www.westcoast.fisheries.noaa.gov/

central_valley/water_operations/sog.html (last visited Oct. 20, 2014,

4:58 p.m.).

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The district court invalidated this Action because NMFS

failed to explain why the pulse flows would maintain gravel

quality in the Stanislaus River. In re Consolidated Salmonid

Cases, 791 F. Supp. 2d at 950. It remanded for further

explanation on this point, noting that “[p]articularly in light

of the potentially high water costs of these pulse flows, the

rationale for Action III.1.3 must be lawfully explained and

justified on remand.” Id.

We hold that the district court erred by failing to defer to

the Agency’s interpretation of a scientific study. NMFS

based Action III.1.3’s flow numbers on a 2001 study

conducted by Dr. Kondolf, et al. In that study, Dr. Kondolf,

et al. conclude that “flows around 5,000 to 8,000 cfs are

necessary” to mobilize the channel bed material. Kondolf et

al., supra, at 36. NMFS determined, after weighing the

relevant interests, that implementing pulse flows at the lowend of Kondolf’s flow range would achieve the appropriate

balance between habitat protection and maintaining water

reserves in the East Side Division Reservoir. See Reed,

supra, at 7–8. In doing so, NMFS balanced Kondolf’s pulse

flow suggestions against Reclamation’s conclusion that

prolonged flows exceeding 1,500 cfs would cause flooding. 

See id. Congress delegated this type of balancing to

administrative agencies when it passed the APA and ESA. 

See River Runners for Wilderness, 593 F.3d at 1070. As long

as the agency’s decision is properly documented, as it is here,

we will not overturn it. See State Farm, 463 U.S. at 43.24

 

24 Nor do we overturn NMFS’s choice to use the SJR salmon model to

help prescribe pulse flows on the Stanislaus River. Although it is true that

the SJR model determines flows needed to double salmon population,

NMFS explains why this model was a helpful guide for developing this

RPA. Also, NMFS did not rely exclusively on this model to prescribe

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f. Action III.2.2

Finally, the district court invalidated RPA Action III.2.2,

which relates to floodplain restoration and innundation flows

in the Stanislaus River. Prior to the construction of the New

Melones Dam in the late 1970s, snow melt from the Sierra

Nevada Mountains created pulse flows in the Stanislaus River

that formed new and scoured existing channels in the riverbed

and surrounding floodplains. 2009 Salmonid BiOp at 627. 

CV steelhead juveniles used (and continue to use) these

channels as a rearing habitat. Id. However, the floodplain

habitats that were “inundated before operation of the New

Melones Dam have become fossilized with fine material and

thick riparian vegetation that is never rejuvenated by

scouring,” id., because pulse flows from New Melones Dam

are infrequent. Thus “[f]loodplain juvenile rearing habitat

and connectivity will continue to be degraded by New

Melones operations, as proposed.” Id. To remedy this

impact, Action III.2.2 requires Reclamation to “seek advice

from SOG to develop an operational strategy to achieve

floodplain innundation flows that inundate CV steelhead

juvenile rearing habitat on a one- to three-year return

schedule.” Id. The district court found this action arbitrary

or capricious, holding that because it defines no action per se,

NMFS did not—and in fact could not—perform a feasibility

analysis as required by 50 C.F.R. § 402.02. In re

Consolidated Salmonid Cases, 791 F. Supp. 2d at 952.

Stanislaus River flows. See Reed, supra, at 5–7 (citing, in addition to the

SJR salmon model, Aceituno (1993) and Cramer Fish Sciences (2009)). 

Thus, the record does not support the district court’s conclusion that

“[n]othing in the record explains why it is appropriate to use a model

designed to double the existing salmon population to set numeric flow

targets to avoid jeopardy to the CV steelhead.” In re Consolidated

Salmonid Cases, 791 F. Supp. 2d at 950.

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The district court erred in invaliding this action. We held

in Delta Smelt that § 402.02 does not require the consultation

agency to explain how each Action is feasible. And neither

Plaintiffs nor the district court provide any reason why the

SOG would recommend an action that Reclamation and

DWR could not adopt. See Sw. Ctr. for Biological Diversity

v. U.S. Bureau of Reclamation, 143 F.3d at 523–24 (noting

that feasibility is examined from the perspective of the

agency). Thus, this court has no reason to declare that Action

III.2.2 violates § 402.02’s feasibility factor.

VI. CROSS-APPEAL

Plaintiffs cross-appeal several components of the district

court opinion in which the district court upheld the BiOp. We

affirm the district court on all three cross-appeal issues.

A. NMFS Need Not Distinguish Discretionary and NonDiscretionary Actions

ESA section 7 provides that, after an agency seeks

consultation on a potential project, the agency providing

consultation shall write a BiOp “detailing how the agency

action affects the species or its critical habitat.” 16 U.S.C.

§ 1536(b)(3)(A). To determine how agency action affects

listed species, the consulting agency must analyze the action

in relation to the “environmental baseline.” 50 C.F.R.

§ 402.02. “This baseline is intended to form a basic

‘snapshot’ of the status of the species at a particular moment

in time before the action is taken.” Liebesman & Petersen,

supra, at 46.

Plaintiffs argue that NMFS must separate discretionary

aspects of the Projects from non-discretionary aspects of the

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Projects to define the environmental baseline. The district

court disagreed, holding that “[n]othing in the law requires

NMFS to segregate discretionary aspects of coordinated

Project operations from non-discretionary ones in the manner

Export Plaintiffs demand.” In re Consolidated Salmonid

Cases, 791 F. Supp. 2d at 852.

Plaintiffs’ discretionary/non-discretionaryargument is the

same argument that we entertained and rejected in Delta

Smelt. See 747 F.3d at 638–40. We again reject these

arguments and affirm the district court on this point.

B. The Biological Opinion’s Indirect Mortality Factors

Are Direct Effects Under the ESA

For the purposes of ESA section 7 consultation, the

“effect” of a proposed action includes both direct and indirect

effects. 50 C.F.R. § 402.02. To show that something is an

indirect effect of the proposed action, an agency must

demonstrate (1) that it is caused by the action, (2) that it is

later in time than the action, and (3) that it is reasonably

likely to occur. Handbook, supra, at 4-27 (citing 50 C.F.R.

§ 402.02). Whether NMFS needed to make these findings

with regard to “indirect mortality factors” identified in the

BiOp, see 2009 Salmonid BiOp at 374, is a key issue on

cross-appeal.

NMFS concludes in the BiOp that CVP/SWP operations

subject listed species to indirect mortality factors—such as

predation and exposure to toxins—in the inner Delta. See

generally id. at 374–82. The district court determined that

“the indirect mortality findings challenged by Plaintiffs do

not constitute ‘indirect effects’” within the meaning of 50

C.F.R. § 402.02 because they are “caused by the action

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subject to consultation, not by some other action . . . .” In re

Consolidated Salmonid Cases, 791 F. Supp. 3d at 868 (citing

Handbook, supra).

We agree with the district court. Indirect effects are

typically more attenuated than those described in the 2009

BiOp. National Wildlife Federation v. Coleman provides a

clear, oft-cited example of an “indirect effect.” 529 F.2d 359,

373 (5th Cir. 1976). There, the Fifth Circuit held that the

Department of Transportation must consider the residential

and commercial development “that can be expected to result

from the construction of the highway” as an indirect effect of

highway construction. Id. NMFS and FWS provide another

example of an indirect effect in the consultation handbook. 

See Handbook, supra, at 4-29. This example is a little bit

closer to home:

A very complex example of indirect effects

arose in determining effects of renewingwater

services contracts . . . in the San Joaquin

Basin . . . . Upon checking with other Federal

and State agencies, the FWS determined that

the distribution of water for agricultural use

on the higher east side of the Valley provided

a hydrologic head maintaining the

groundwater table on the west side of the

Valley at a level making it economical to

pump.

Id. As a result, residents could use the pumped water to

convert the land to agriculture. But the conversion of the land

to agriculture destroyed the habitat of several listed species. 

Id. FWS considered this an indirect effect of renewing the

water services contracts. Id. These two examples show that

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an indirect effect—as envisioned by 50 C.F.R. § 402.02—is

one that the action makes possible (or indeed, more

probable), but does not directly cause.

The indirect mortality factors described in the BiOp are

direct effects. According to NMFS, CVP/SWP operations

draw listed fish into the inner Delta by reversing the flows of

the Old and Middle Rivers. See 2009 Salmonid BiOp at

361–62. NMFS concludes that the interior Delta is a

dangerous place for migrating salmonids partially because of

Project operations. See id. at 374–75, 433. These effects

occur concurrently with the Projects; they are not future

“indirect” actions “reasonably certain” to occur. See

50 C.F.R. § 402.02.

C. Reclamation Is Not Independently Liable Under the

ESA

Plaintiffs’ argument that Reclamation is independently

liable under the ESA is predicated on a finding that the BiOp

is legally flawed. See Pyramid Lake Paiute Tribe of Indians

v. U.S. Dep’t of the Navy, 898 F.2d 1410, 1415 (9th Cir.

1990) (compliance with a BiOp satisfies an action agency’s

procedural obligations under the ESA, but it does not satisfy

the agency’s substantive obligation to complywith section 7). 

Because we hold that the BiOp is legally sound, we dismiss

Plaintiffs’ argument.

VII. CONCLUSIONS

Based on the foregoing, we REVERSE the components of

the district court’s opinion in which it invalidated the BiOp

and AFFIRM the district court with regard to the three issues

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on cross-appeal. We REMAND for entry of summary

judgment in favor of defendants.

Each party shall bear its own costs.

REVERSED IN PART, AFFIRMED IN PART, AND

REMANDED.

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GLOSSARY OF TERMS

anadromous fish fish that ascend rivers from the sea

for breeding

APA Administrative Procedure Act

BA Biological Assessment

Bay-Delta San Francisco Bay and SacramentoSan Joaquin Delta

BiOp 2009 Salmonid Biological Opinion 

cfs cubic feet per second

CVP Central Valley Project

CVPIA Central Valley Project Improvement

Act

DWR California Department of Water

Resources

ESA Environmental Species Act

IFIM incremental flow instream

methodology

ITS Incidental Take Statement 

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listed species (1) the Sacramento River winter-run

Chinook salmon (“winter-run

Chinook”); (2) the Central Valley

spring-run Chinook salmon (“springrun Chinook”); (3) the Central

Valley steelhead (“CV steelhead”);

(4) the threatened Southern Distinct

Population Segment of North

American green sturgeon (“green

sturgeon”); and the Southern

Resident killer whales (“Southern

Resident orcas”).

NMFS National Marine Fisheries Service

the Projects Central Valley Project and State

Water Project

PTM Particle Tracking Model 

RPA reasonable and prudent alternatives

Reclamation U.S. Bureau of Reclamation

SOG Stanislaus Operations Group

SWP State Water Project

VAMP Vernalis Adaptive Management Plan

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