FOR PUBLICATION

UNITED STATES COURT OF APPEALS

FOR THE NINTH CIRCUIT

NATIONAL WILDLIFE FEDERATION; 

IDAHO WILDLIFE FEDERATION;

WASHINGTON WILDLIFE FEDERATION;

SIERRA CLUB; TROUT UNLIMITED;

PACIFIC COAST FEDERATION OF

FISHERMEN’S ASSOCIATIONS;

INSTITUTE FOR FISHERIES RESOURCES;

IDAHO RIVERS UNITED; IDAHO

STEELHEAD AND SALMON UNITED;

NORTHWEST SPORT FISHING

INDUSTRY ASSOCIATION, SALMON FOR

ALL; COLUMBIA RIVERKEEPER; NW

ENERGY COALITION; FEDERATION OF

FLY FISHERS; AMERICAN RIVERS, No. 05-35569

INC.,

Plaintiffs-Appellees,  D.C. No.

CV-01-00640-JAR

v.

NATIONAL MARINE FISHERIES

SERVICE; UNITED STATES ARMY

CORPS OF ENGINEERS; U.S.

BUREAU OF RECLAMATION,

Defendants,

FRANKLIN COUNTY FARM BUREAU

FEDERATION; GRANT COUNTY FARM

BOARD FEDERATION; WASHINGTON

FARM BUREAU FEDERATION;

STATE OF IDAHO; CLARKSON GOLF

& COUNTRY CLUB,

Defendants-Intervenors, 

12005
and 

NORTHWEST IRRIGATION UTILITIES;

PUBLIC POWER COUNCIL; PACIFIC

NORTHWEST GENERATING

COOPERATIVE; BPA CUSTOMER

GROUP,

Defendants-Intervenors- 

Appellants,

v.

STATE OF OREGON,

Plaintiff-IntervenorAppellee. 

NATIONAL WILDLIFE FEDERATION; 

IDAHO WILDLIFE FEDERATION;

WASHINGTON WILDLIFE FEDERATION;

SIERRA CLUB; TROUT UNLIMITED;

PACIFIC COAST FEDERATION OF

FISHERMEN’S ASSOCIATIONS;

INSTITUTE FOR FISHERIES RESOURCES;

IDAHO RIVERS UNITED; IDAHO No. 05-35646

STEELHEAD AND SALMON UNITED;  D.C. No.

NORTHWEST SPORT FISHING CV-01-00640-JAR

INDUSTRY ASSOCIATION, SALMON FOR

ALL; COLUMBIA RIVERKEEPER; NW

ENERGY COALITION; FEDERATION OF

FLY FISHERS; AMERICAN RIVERS,

INC.,

Plaintiffs-Appellees,

v. 

12006 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
NATIONAL MARINE FISHERIES 

SERVICE; UNITED STATES ARMY

CORPS OF ENGINEERS; U.S.

BUREAU OF RECLAMATION,

Defendants,

NORTHWEST IRRIGATION UTILITIES;

PUBLIC POWER COUNCIL; PACIFIC

NORTHWEST GENERATING

COOPERATIVE; BPA CUSTOMER

GROUP; FRANKLIN COUNTY FARM

BUREAU FEDERATION; GRANT

COUNTY FARM BOARD FEDERATION;

WASHINGTON FARM BUREAU 

FEDERATION; CLARKSON GOLF &

COUNTRY CLUB,

Defendants-Intervenors,

and

STATE OF IDAHO,

Defendant-IntervenorAppellant,

v.

STATE OF OREGON,

Plaintiff-IntervenorAppellee. 

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12007
NATIONAL WILDLIFE FEDERATION; 

IDAHO WILDLIFE FEDERATION;

WASHINGTON WILDLIFE FEDERATION;

SIERRA CLUB; TROUT UNLIMITED;

PACIFIC COAST FEDERATION OF

FISHERMEN’S ASSOCIATIONS;

INSTITUTE FOR FISHERIES RESOURCES;

IDAHO RIVERS UNITED; IDAHO

STEELHEAD AND SALMON UNITED;

NORTHWEST SPORT FISHING

INDUSTRY ASSOCIATION, SALMON FOR

ALL; COLUMBIA RIVERKEEPER; NW

ENERGY COALITION; FEDERATION OF

FLY FISHERS; AMERICAN RIVERS, No. 05-35570

INC., D.C. No.

Plaintiffs-Appellees,  CV-01-00640-JAR

v. AMENDED

NATIONAL MARINE FISHERIES OPINION

SERVICE; UNITED STATES ARMY

CORPS OF ENGINEERS; U.S.

BUREAU OF RECLAMATION,

Defendants-Appellants,

and

NORTHWEST IRRIGATION UTILITIES;

PUBLIC POWER COUNCIL; PACIFIC

NORTHWEST GENERATING

COOPERATIVE; BPA CUSTOMER

GROUP; FRANKLIN COUNTY FARM

BUREAU FEDERATION; GRANT

COUNTY FARM BOARD FEDERATION; 

12008 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
WASHINGTON FARM BUREAU 

FEDERATION; STATE OF IDAHO;

CLARKSON GOLF & COUNTRY CLUB,

Defendants-Intervenors,  v.

STATE OF OREGON,

Plaintiff-IntervenorAppellee. 

Appeal from the United States District Court

for the District of Oregon

James A. Redden, District Judge, Presiding

Argued and Submitted

July 13, 2005—Seattle, Washington

Filed July 26, 2005

Amended September 1, 2005

Before: A. Wallace Tashima, Sidney R. Thomas, and

Richard A. Paez, Circuit Judges.

Per Curiam Opinion

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12009
COUNSEL

Mark Eames, NOAA Office of General Counsel, Seattle,

Washington; Gayle Lear, Assistant Division Counsel, Northwestern Division, U.S. Army Corps of Engineers, Portland,

Oregon; Kelly A. Johnson, Acting Assistant Attorney General, Fred Disheroon, Ruth Ann Lowery, Ellen J. Durkee, and

Jennifer L. Scheller, Attorneys, Environment & Natural

Resources Division, U.S. Department of Justice, Washington,

D.C., for the federal defendants-appellants. 

Matthew A. Love and Sam Kalen, Van Ness Feldman, P.C.,

Seattle, Washington, for defendants-appellants BPA Customer Group. Lawrence G. Wasden, Attorney General, Clive

J. Strong, Deputy Attorney General, and Clay R. Smith, Deputy Attorney General, State of Idaho, Boise, Idaho, for

defendant-intervenor-appellant State of Idaho. 

Todd D. True and Stephen D. Mashuda, Earthjustice, Seattle,

Washington; Daniel J. Rohlf, Pacific Environmental Advocacy Center, Portland, Oregon, for plaintiffs-appellees

National Wildlife Federation. 

Hardy Myers, Attorney General, Mary H. Williams, Solicitor

General, David E. Leith, Assistant Attorney General, and Stephen K. Bushong, State of Oregon, Salem, Oregon, for

plaintiff-intervenor-appellee State of Oregon. 

Koward G. Arnett, Karnopp Petersen, LLP, Bend, Oregon;

David J. Cummings, Nez Perce Tribe, Lapwai, Idaho; Chris12012 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
topher B. Leahy, Fredericks, Pelcyger & Hester, LLC, Louisville, Colorado; Tim Weaver, Law Offices of Tim Weaver,

Yakima, Washington, for amici curiae Treaty Tribes. 

Robert D. Thornton and Paul S. Weiland, Nossaman, Guthner, Knox & Elliott, LLP, Irvine, California, for amicus curiae

National Association of Homebuilders. 

Rob McKenna, Attorney General, and Michael S. Grossman,

Assistant Attorney General, State of Washington, Olympia,

Washington, for amicus curiae State of Washington. 

John C. Bruning, Attorney General, David D. Cookson,

Assistant Attorney General, State of Nebraska, Lincoln,

Nebraska; Thomas R. Wilmoth, Special Assistant Attorney

General, Fennemore Craig, P.C., Lincoln, Nebraska, for

amicus curiae State of Nebraska. 

OPINION

PER CURIAM:

The defendants appeal the district court’s grant of a preliminary injunction, based on a violation of the Endangered Species Act (or “ESA”), 16 U.S.C. §§ 1531-1544, requiring the

United States to pass a specified amount of water through the

spillgates of four dams on the Snake River, and one dam on

the Columbia River during the summer months of 2005,

rather than passing the water through turbines for power generation. We affirm in part and remand in part. 

I

The Columbia River is the fourth largest river on the North

American continent. It drains approximately 259,000 square

miles, including territory in seven states and one Canadian

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12013
province. It flows for more than 1,200 miles from the base of

the Canadian Rockies to the Pacific Ocean. As part of the

cycle of life in the Columbia River system, every year hundreds of thousands of salmon and steelhead travel up and

down the river and its tributaries, hatching in fresh water,

migrating downstream to the sea to achieve adulthood, and

then returning upstream to spawn. The Snake River is the

Columbia River’s main tributary. 

As part of the modern cycle of life in the Columbia River

System, each year brings litigation to the federal courts of the

Northwest over the operation of the Federal Columbia River

Power System (“FCRPS” or “Columbia River System”)1 and,

in particular, the effects of system operation on the anadromous salmon and steelhead protected by the Endangered Species Act. 

No one disputes that the wild Pacific salmon population has

significantly decreased; indeed, in recent years, salmon runs

have declined to a small percentage of their historic abundance. There are now thirteen species of Columbia, Snake,

and Willamette River salmon and steelhead that are protected

by the Endangered Species Act.2 The district court found in

this case that “the listed species are in serious decline and not

1The FCRPS consists of 14 sets of dams and related facilities: Bonneville, The Dales, John Day, and McNary dams in the lower Columbia

River Basin; Chief Joseph, Grand Coulee, Libby, Hungry Horse, and

Albeni Falls dams in the upper Columbia River Basin; and Ice Harbor,

Lower Monumental, Little Goose, Lower Granite, and Dworshak Dams in

the lower Snake River Basin. The United States Bureau of Reclamation

manages the Grand Coulee and Hungry Horse dams; the remainder are

managed by the United States Army Corps of Engineers. 

2Snake River Chinook salmon (fall-run); Snake River Chinook salmon

(spring/summer-run); Snake River sockeye salmon; Upper Columbia

River steelhead; Snake River Basin steelhead; Lower Columbia River

coho salmon; Lower Columbia River steelhead; Middle Columbia River

steelhead; Upper Willamette River steelhead; Lower Columbia River Chinook salmon; Upper Willamette River Chinook salmon; Upper Columbia

River Chinook salmon (spring-run); and Columbia River chum salmon. 

12014 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
evidencing signs of recovery.” Each of the thirteen affected

stocks migrate at different times of the year to different parts

of the Columbia Basin. For example, Upper Columbia spring

Chinook adults return to their spawning grounds in the spring

of each year; Snake River fall Chinook adults return to the

Snake River Basin in the fall. Juveniles of these stocks generally migrate seaward between mid-April and early September.

The spring and summer Chinook, steelhead, and sockeye

salmon migrate as yearling juveniles in the spring. Subyearling fall Chinook migrate down the river during the mid-tolate summer. Some salmon migrate downstream after spending a year in fresh water; others migrate the same year. 

The primary focus of the present lawsuit is the survival of

the fall juvenile Chinook salmon and steelhead migrating

downstream to the Pacific Ocean. These fish must pass a

number of FCRPS dams on their journey to the sea and suffer

a very high mortality rate in doing so, sometimes as high as

92%. As the fish migrate downstream, they first encounter

reservoirs behind the dams, which slows their progress and

exposes them to predatory fish, such as the northern pikeminnow. After passage through each dam’s reservoir, the juvenile

salmon and steelhead must pass each dam. There are four

main methods by which salmon may navigate the Columbia

and Snake River hydroelectric projects while migrating from

upriver areas to the ocean: (1) spill over the dams; (2) passage

through turbines; (3) in-river bypass systems; and (4) transportation bypass systems. Of these options, passage through

turbines unquestionably causes the highest mortality rate. Historically, spill has been considered to cause the lowest mortality. However, spill must be carefully managed to avoid gas

supersaturation, which is harmful to the fish.3

3Falling water over the dam increases the amount of atmospheric gases

that are dissolved in the water. If the level of dissolved atmospheric gases

is too high, fish can experience “gas bubble trauma,” which is similar to

the “bends” experienced by human divers who return to the surface too

quickly. 

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12015
Each dam in the migration corridor of the mainstream

Snake and Columbia rivers has a bypass system. At some

dams, the bypass consists of screens in front of the turbine

intakes that divert the salmon and steelhead into a passageway

through the dam and downstream. At others, the bypass system diverts the fish into barges for transportation around the

dam. 

The operation of the Columbia River System is complex.

The Army Corps of Engineers and the Bureau of Reclamation

manage the dams for multi-purpose operations; the Bonneville Power Administration manages federal power generated

from the dams; and the Federal Energy Regulatory Commission plays a number of roles, including licensing of nonfederal hydro-power projects. Although the focus of this litigation is the effect of Columbia River System operation on

endangered species, in the day-to-day operation, federal agencies must manage the system to deliver needed power and

water to Northwest consumers. 

States also have an influence on the Columbia River System, directly in their governance of water diversions from the

river, and indirectly through their own fish and wildlife conservation programs. The operation of the Columbia River

System is also impacted by treaties with a number of federally

recognized Indian Tribes, which reserve to the tribes certain

fishing rights that are affected by the management of the

FCRPS.4

4

See, e.g., Treaty with the Nez Perces, 12 Stat. 957, Art. 3 (June 11,

1855); Treaty with the Tribes of the Middle Oregon (Confederated Tribes

of the Warm Springs Reservation of Oregon), 12 Stat. 963 (June 25,

1855); Treaty with the Yakima, 12 Stat. 951 (June 9, 1855); Treaty with

the Wallawalla, Cayuse, et al. (Confederated Tribes of the Umatilla

Indian Reservation), 12 Stat. 945 (June 9, 1855). In their amici brief, the

treaty tribes support the position of the National Wildlife Federation in

this action. 

12016 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
In the last several decades, the management of the Columbia River System has been strongly influenced by the Endangered Species Act, which requires federal agencies to, in

consultation with what is known as the “consulting agency,”

conserve species listed under the ESA. The ESA requires federal agencies to “insure that any action authorized, funded, or

carried out by such agency . . . is not likely to jeopardize the

continued existence of any endangered species or threatened

species or result in the destruction or adverse modification of

[designated critical] habitat. . . .” 15 U.S.C. § 1536(a)(2). To

ensure that the agency would meet its substantive ESA duties,

the ESA imposes a procedural consultation duty whenever a

federal action may affect an ESA-listed species. Thomas v.

Peterson, 753 F.2d 754, 763 (9th Cir. 1985). To that end, the

agency planning the action, usually known as the “action

agency,” must consult with the consulting agency. This process is known as a “Section 7” consultation. The process is

usually initiated by a formal written request by the action

agency to the consulting agency. After consultation and analysis, the consulting agency then prepares a biological opinion.

See generally Ariz. Cattle Growers’ Ass’n v. United States

Fish & Wildlife Serv., 273 F.3d 1229, 1239 (9th Cir. 2001).

The consulting agency evaluates the effects of the proposed

action on the survival of species and any potential destruction

or adverse modification of critical habitat in a biological opinion, 16 U.S.C. § 1536(b), based on “the best scientific and

commercial data available,” id. at § 1536(a)(2). The biological opinion includes a summary of the information upon

which the opinion is based, a discussion of the effects of the

action on listed species or critical habitat, and the consulting

agency’s opinion on “whether the action is likely to jeopardize the continued existence of a listed species or result in the

destruction or adverse modification of critical habitat. . . .” 50

C.F.R. § 402.14(h). In making its jeopardy determination, the

consulting agency evaluates “the current status of the listed

species or critical habitat,” the “effects of the action,” and

“cumulative effects.” 50 C.F.R. § 402.14(g)(2)-(3). “Effects

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12017
of the action” include both direct and indirect effects of an

action that will be added to the “environmental baseline.” 50

C.F.R. § 402.02. The environmental baseline includes “the

past and present impacts of all Federal, State or private

actions and other human activities in the action area” and “the

anticipated impacts of all proposed Federal projects in the

action area that have already undergone formal or early section 7 consultation.” Id. 

If the biological opinion concludes that jeopardy is not

likely and that there will not be adverse modification of critical habitat, or that there is a “reasonable and prudent alternative” to the agency action that avoids jeopardy and adverse

modification and that the incidental taking of endangered or

threatened species will not violate section 7(a)(2), the consulting agency can issue an “Incidental Take Statement” which,

if followed, exempts the action agency from the prohibition

on takings5 found in Section 9 of the ESA. 16 U.S.C.

§ 1536(b)(4); Aluminum Co. of America v. Administrator,

Bonneville Power Administration, 175 F.3d 1156, 1159 (9th

Cir. 1999). 

If the consulting agency concludes that an action agency’s

action may jeopardize the survival of species protected by the

ESA, or adversely modify a species’ critical habitat, the

action must be modified. Id. The consulting agency may recommend a “reasonable and prudent alternative” to the agency’s proposed action. Id. at § 1536(b)(3)(A). 

The issuance of a biological opinion is considered a final

agency action, and therefore subject to judicial review. Bennett v. Spear, 520 U.S. 154, 178 (1997); Ariz. Cattle Growers’

Ass’n, 273 F.3d at 1235. 

5

“The term ‘take’ means to harass, harm, pursue, hunt, shoot, wound,

kill, trap, capture, or collect, or to attempt to engage in any such conduct.”

16 U.S.C. § 1532(19). 

12018 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
The Endangered Species Act, as it applies here to protection of anadromous fish, requires action agencies to consult

the agency formerly known as the National Marine Fisheries

Service of the National Oceanic and Atmospheric Administration (“NMFS”),6

 to ensure that an agency’s actions do not

jeopardize an ESA-protected species or adversely modify

their critical habitat. 16 U.S.C. § 1536(a)-(b). 

Snake River fall Chinook salmon were listed as threatened

species in 1992. In 1993, NMFS issued a biological opinion

concluding that FCRPS operations would not jeopardize the

listed species. The district court held that NMFS’s action in

issuing the 1993 biological opinion was arbitrary and capricious. Idaho Dep’t of Fish & Game v. Nat’l Marine Fisheries

Serv., 850 F. Supp. 886, 900 (D. Or. 1994). The district court

found that NMFS had failed to give an adequate explanation

for several of the key assumptions that went into its jeopardy

analysis. This decision was vacated on appeal as moot

because NMFS had issued a subsequent biological opinion.

Idaho Dep’t of Fish & Game v. Nat’l Marine Fisheries Serv.,

56 F.3d 1071, 1075 (9th Cir. 1995). After further litigation

and agency action not directly relevant to this case, NMFS

issued a new biological opinion on December 21, 2000, (the

“2000 BiOp”) that superseded the previous biological opinions. 

In its 2000 BiOp, NMFS determined that the continued

operation of FCRPS as proposed by the action agencies would

jeopardize eight listed salmon and steelhead species; specifically, NMFS found that the “effects of the proposed or continuing action, the effects of the environmental baseline, and any

cumulative effects, and considering measures for survival and

recovery specific to other life stages” would leave the eight

species with too low a likelihood of survival and potential for

6The agency has now been renamed “NOAA Fisheries.” Because many

of the documents refer to the agency by its former name, it shall be referenced as “NMFS” throughout this opinion for convenience of reference.

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12019
population recovery. NMFS thus developed reasonable and

prudent alternatives to the proposed operation and analyzed

whether these alternatives, in conjunction with the environmental baseline and cumulative effects, would avoid jeopardizing the species. NMFS found these alternatives

insufficient. NMFS therefore assessed whether the additional

impact of off-site mitigation activities unrelated to FCRPS

operations, including hatchery and habitat initiatives, would

avoid jeopardy, and found that it did. 

Plaintiff National Wildlife Federation (“NWF”) brought

this present action challenging the 2000 BiOp in U.S. District

Court for the District of Oregon. The district court concluded

that the 2000 BiOp was invalid because to reach its jeopardy

determination, NMFS improperly relied on off-site federal

mitigation actions that had not undergone Section 7 consultation, and thus were not properly included in the environmental

baseline,7 and on non-federal mitigation actions that were not

reasonably certain to occur, and thus were not properly

included in cumulative effects. Nat’l Wildlife Fed’n v. Nat’l

Marine Fisheries Servs., 254 F. Supp. 2d 1196, 1211-12 (D.

Or. 2003). The district court remanded to provide NMFS an

opportunity to correct the 2000 BiOp. Id. at 1215. 

Rather than correct the 2000 BiOp, NMFS issued an

entirely new biological opinion on November 30, 2004 (the

“2004 BiOp”), which formed the basis of the federal agencies’ operating plans for the FCRPS during the summer of

2005. In the 2004 BiOp, NMFS conducted a jeopardy analysis

which utilized the novel approach of including in the environmental baseline the existing FCRPS, the nondiscretionary

7The 2004 BiOp concluded that NMFS could not distinguish the effects

of the discretionary and nondiscretionary FCRPS operations, and therefore

created a hypothetical “reference operation” to which it compared the discretionary proposed action. The reference operation was developed to

“maximize fish benefits” and it “overestimates the beneficial effects that

the Action Agencies can actually achieve.” 2004 BiOp at 5-6. 

12020 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
dam operations, and all past and present impacts from discretionary operations. As opposed to assessing whether the

salmon and steelhead would be jeopardized by the aggregate

of the proposed agency action, the environmental baseline,

cumulative effects, and current status of the species, NMFS

instead evaluated whether the proposed agency action, consisting of only the proposed discretionary operation of the

FCRPS, would have no net effect on a species when compared to the environmental baseline. By using this comparative approach rather than the aggregate approach, NMFS was

able to conclude that the proposed action would not jeopardize the continued existence of any listed species or destroy

or adversely modify critical habitat for three of these species.

NWF and the State of Oregon challenged the following

aspects of 2004 BiOp, specifically and as relevant to this

appeal: (1) the segregation of the existing FCRPS, the nondiscretionary dam operations, and all past and present impacts

of discretionary operations from the proposed discretionary

operations; (2) the basic analytical framework NMFS

employed to come to its no-jeopardy and critical habitat determinations; and (3) the critical habitat determinations which

plaintiffs alleged did not analyze what habitat conditions are

necessary for recovery.8

The district court granted summary judgment for NWF and

Oregon, holding that NMFS had violated the ESA in the issuance of its 2004 BiOp. The district court found the 2004 BiOp

legally insufficient for four independent reasons: 

• The opinion failed to conduct a jeopardy analysis

8The State of Oregon supports the substantive position of NWF, but

takes no position on the preliminary injunction. The State of Washington

supports NWF’s position that the 2004 BiOp is invalid, but opposes the

preliminary injunction remedy. The States of Idaho and Nebraska support

the federal government’s position on both the merits and the preliminary

injunction remedy. 

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12021
on the basis of all elements of the proposed

action, including the so-called non-discretionary

operations of the dams;

• The opinion failed to use an aggregation of the

impacts from the proposed action, the environmental baseline, and the cumulative impacts as

the basis for the jeopardy analysis;

• The opinion’s critical habitat determination was

flawed because it failed to determine separately

whether the proposed action would destroy or

adversely modify critical habitat necessary for

the recovery as well as survival of the listed species; and

• The opinion’s jeopardy analysis failed to address

both recovery and survival of the listed species.

The order granting summary judgment to the plaintiffs “invalidated” the 2004 BiOp. However, the district court specified that its summary judgment order was not final or

appealable. Following the district court’s decision to invalidate the 2004 BiOp, NWF moved for a preliminary injunction

requiring NMFS to: (1) withdraw the 2004 BiOp; (2) comply

with and implement all of the reasonable and prudent alternative mitigation actions described in the 2000 BiOp (with certain exceptions); (3) as to the 2005 summer flow, decrease the

water particle travel time by 10% in specified areas; and (4)

provide water spill over specified dams during the summer of

2005. 

The district court, based on its determination that the 2004

BiOp was procedurally and substantively flawed and its finding that the operations of FCRPS strongly contribute to the

endangerment of the listed species and will cause irreparable

injury if not changed, granted in part the motion for a preliminary injunction. The district court announced its intention to

12022 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
order the withdrawal of the 2004 BiOp, but declined to do so

until after a fall status conference. The court denied the

request to order the decrease of water particle travel time by

at least 10% in the specified areas. The court granted the

request to order summer spills at specified areas in order to

avoid irreparable harm to juvenile fall chinook and other

listed species. Specifically, the district court ordered the

affected agencies to: (1) provide spill from June 20, 2005,

through August 31, 2005, of all water in excess of that

required for station service, on a 24-hour basis, at the Lower

Granite, Little Goose, Lower Monumental, and Ice Harbor

Dams on the lower Snake River; and (2) provide spill from

July 1, 2005, through August 31, 2005, of all flows above

50,000 cubic feet per second, on a 24-hour basis, at the

McNary Dam on the Columbia River. 

The district court also held in its order that the respective

Records of Consultation and Statements of Decision issued by

the Army Corps of Engineers on January 3, 2005, and by the

Bureau of Reclamation on January 12, 2005, violated the ESA

because they were based on the invalid 2004 BiOp. 

The defendants filed an emergency motion for a stay of the

injunction order pending appeal. A motions panel denied the

defendants’ stay motion, but ordered an expedited hearing on

the preliminary injunction appeal. Oral argument on the preliminary injunction appeal was held July 13, 2005. The panel

expresses its appreciation to the parties for providing extensive briefing on short notice and on an accelerated time schedule. 

II

A district court’s order with respect to preliminary injunctive relief is subject to limited appellate review, and we will

reverse only if the district court “abused its discretion or

based its decision on an erroneous legal standard or on clearly

erroneous findings of fact.” United States v. Peninsula ComNAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12023
munications, Inc., 287 F.3d 832, 839 (9th Cir. 2002). “Our

review is limited and deferential.” Southwest Voter Registration Educ. Project v. Shelley, 344 F.3d 914, 918 (9th Cir.

2003) (en banc). In considering a preliminary injunction

appeal, we ordinarily do not decide the ultimate merits of the

case, but only the temporal rights of the parties until the district court renders judgment on the merits of the case based

on a fully developed record. Gilder v. PGA Tour, Inc., 936

F.2d 417, 422 (9th Cir. 1991). Mere disagreement with the

district court’s conclusions is not sufficient reason for us to

reverse the district court’s decision regarding a preliminary

injunction. Sports Forum, Inc. v. United Press Int’l, Inc., 686

F.2d 750, 752 (9th Cir. 1982); see also Ranchers Cattlemen

Action Legal Fund United Stockgrowers of Am. v. United

States Dep’t of Agric. (“R-CALF”), No. 05-35264, slip op. at

8751-52 (9th Cir. Jul. 25, 2005) (setting forth standard of

review). 

[1] The traditional preliminary injunction analysis does not

apply to injunctions issued pursuant to the ESA. Nat’l Wildlife Fed’n v. Burlington N. R.R., Inc., 23 F.3d 1508, 1510 (9th

Cir. 1994). “In cases involving the ESA, Congress removed

from the courts their traditional equitable discretion in injunction proceedings of balancing the parties’ competing interests.” Id. at 1511 (citing Friends of the Earth v. United States

Navy, 841 F.2d 927, 933 (9th Cir. 1988)). As the Supreme

Court has noted, “Congress has spoken in the plainest of

words, making it abundantly clear that the balance has been

struck in favor of affording endangered species the highest of

priorities.” TVA v. Hill, 437 U.S. 153, 194 (1978). Accordingly, courts “may not use equity’s scales to strike a different

balance.” Sierra Club v. Marsh, 816 F.2d 1376, 1383 (9th Cir.

1987); see also Marbled Murrelet v. Babbitt, 83 F.3d 1068,

1073 (9th Cir. 1996) (“Congress has determined that under

the ESA the balance of hardships always tips sharply in favor

of endangered or threatened species.”). 

12024 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
A

[2] Given this clear authority, we must at the onset reject

the argument of the federal appellants that the district court

erred as a matter of law by failing to conduct a traditional preliminary injunction analysis and, in particular, by failing to

weigh economic harm to the public in reaching its conclusion.

As the Supreme Court has instructed, such an analysis does

not apply to ESA cases because Congress has already struck

the balance. Id. Therefore, we conclude that the district court

did not apply an incorrect legal standard in this case. 

We decline to address the legal issues raised by the district

court’s summary judgment order. We review the merits only

in the very confined context of determining whether the district court abused its discretion in granting the preliminary

injunction. To establish a substantial likelihood of success on

the merits sufficient to pass appellate review of a district

court’s grant of a preliminary injunction, the plaintiffs were

only obligated to show “a fair chance of success.” Republic

of the Philippines v. Marcos, 862 F.2d 1355, 1362 (9th Cir.

1988) (en banc). Based on our review of the record and briefs

in this emergency appeal, we conclude that the plaintiffs have

met this burden by raising substantial questions as to whether

the agencies have violated Section 7 of the ESA by improperly circumscribing the scope of the consultation or failing to

aggregate the impacts of the proposed action. However, in

making this threshold determination, we express no opinion

on the ultimate merits of the district court’s summary judgment decision, leaving that final determination to the district

court in the first instance. 

B

We also conclude that the district court’s grant of a preliminary injunction was not based on clearly erroneous findings

of fact. Although the facts and scientific analysis underlying

the district court’s decision are hotly contested by the parties,

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12025
our review in the preliminary injunction context is very deferential. On appellate review in this context, we consider a finding of fact to be clearly erroneous if it is implausible in light

of the record, viewed in its entirety, Serv. Employees Int’l

Union v. Fair Political Practices Comm’n, 955 F.2d 1312,

1317 n.7 (9th Cir. 1992), or if the record contains no evidence

to support it, Oregon Natural Resources Council v. Marsh, 52

F.3d 1485, 1492 (9th Cir. 1995). Having reviewed the extensive, albeit incomplete, record provided to us by the parties in

this expedited proceeding, we find no reversible error in the

factual findings made by the district court. 

[3] One of the important factual findings made by the district court was that the federal operation of the Columbia and

Snake River dams “strongly contribute to the endangerment

of the listed species and irreparable injury will result if

changes are not made.” The federal appellants contest this

finding, arguing that the data show that returns of fall chinook

salmon have increased. The district court concluded otherwise

in its orders, finding in a 2004 order that the “predicted survival improvement for fall chinook juveniles has not materialized.” The government’s own recent data show that between

78-92% of juvenile fall chinook salmon that remain in-river

for their migration are killed by operation of the dams even

with use of mitigating measures, with a mean estimated kill

of 86% of the salmon migrating in-river.9 NWF strongly

argues that the government’s assertion of recovery is based on

a single, scientifically flawed, study. NWF also claims,

through expert testimony, that the increased returns were due

to large releases of hatchery fish, rather than successful fish

transport over dams, and that the mortality rate for migrating

juvenile salmon is actually increasing. The federal agencies

dispute this, and offer counter-testimony. The record is replete

with differing opinions by various experts. One of the few

9Although a non-trivial level of mortality would likely occur under freeflowing river conditions, FCRPS operations account for most of the mortality. 

12026 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
undisputed points, however, is that the fall chinook salmon

remain a species listed under the ESA as “likely to become

endangered in the foreseeable future.” 

[4] Our task in reviewing a district court’s preliminary

injunction decision is not to resolve these controversies.

“Clear error is not demonstrated by pointing to conflicting

evidence in the record.” United States v. Frank, 956 F.2d 872,

875 (9th Cir. 1991). Rather, “[a]s long as findings are plausible in light of the record viewed in its entirety, a reviewing

court may not reverse even if convinced it would have

reached a different result.” Wardley Int’l Bank, Inc. v. Nasipit

Bay Vessel, 841 F.2d 259, 262 n.1 (9th Cir. 1988) (citing

Anderson v. Bessemer City, 470 U.S. 564, 574 (1985)). Viewing the record as a whole with our deferential standard of

review, we cannot say that the district court’s factual finding

concerning irreparable harm was clearly erroneous. 

III

Having determined that the district court did not use an

incorrect legal standard in its preliminary injunction analysis

and did not make clearly erroneous factual findings, we must

decide whether the district court abused its discretion in granting the preliminary injunction. 

A

As we have discussed, the district court’s preliminary

injunction order was premised on its finding that the agencies

had violated both the substantive and procedural requirements

of ESA § 7. Thus, the question before the district court was

what interim remedy was appropriate to redress the ESA violations. 

[5] Although not every statutory violation leads to the “automatic” issuance of an injunction, in the context of the ESA,

“the test for determining if equitable relief is appropriate is

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12027
whether an injunction is necessary to effectuate the congressional purpose behind the statute.” Biodiversity Legal Found.

v. Badgley, 30 F.3d 1166, 1177 (9th Cir. 2002) (citing TVA,

437 U.S. at 194). We therefore have held that injunctive relief

was necessary to effectuate Congress’s clear intent by requiring compliance with the substantive and procedural provisions of the ESA. Id. at 1177 (holding that the district court

was “compelled” to grant injunctive relief to remedy a violation of the ESA); Sierra Club, 816 F.2d at 1384 (holding that

the Sierra Club was entitled to injunctive relief if the agency

violated substantive or procedural provisions of the ESA). 

Given this legal backdrop, we conclude that the district

court did not abuse its discretion in granting a preliminary

injunction. It had rejected the biological opinion upon which

the summer operations were premised, and it had concluded

that continuation of the status quo could result in irreparable

harm to a threatened species. Those are precisely the circumstances in which our precedent indicates that the issuance of

an injunction is appropriate. 

This case is unlike the circumstances presented in our

recent decision in R-CALF. In R-CALF, we concluded that the

district court had misread the governing statute. R-CALF, slip

op. at 8754. We also concluded that the agency had acted in

conformity with the governing statute. Id. at 8756-58. We further concluded that none of the reasons listed by the district

court supported its conclusion that the agency’s adoption of

the final rule at issue was arbitrary and capricious. Id. at

8758-65. 

[6] Here, in contrast, the district court’s conclusions were

well grounded in the governing statute; the agency had altered

its own interpretation of the statute significantly; and the

record supported the district court’s reasoning in declaring the

2004 BiOp to be invalid. Further, the operations involved in

this case have had a long history. The district court has monitored the situation carefully over the past few years and has

12028 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
found that the status quo will not lead to recovery of the listed

species. Thus, although we do not reach the merits of the

summary judgment order, the record supports the district

court’s analysis that the plaintiffs are likely to prevail on the

merits of their claim that the 2004 BiOp violates Section 7 of

the ESA and is arbitrary and capricious under the Administrative Procedure Act. Finally, as we have discussed, the standard for injunctive relief under the ESA is far different from

the usual standard governing preliminary injunctions that

applied in the R-CALF case. In ESA cases such as the one at

bar, “the balance has been struck in favor of affording endangered species the highest of priorities.” TVA, 437 U.S. at 194.

For these reasons, this case is quite distinguishable from RCALF, and we conclude that the district court did not commit

reversible error in deciding to grant a preliminary injunction.

B

Having concluded that the district court did not err in

deciding to grant preliminary injunctive relief, we must also

examine the nature and scope of relief ordered by the district

court. One of the primary complications of this case is that the

operations in question are, by necessity, ongoing. Thus, our

situation is unlike that of a timber sale, which can be postponed in order to permit the agency to correct the ESA violations before the planned operation commences. See, e.g.,

Native Ecosystems Council v. Dombeck, 304 F.3d 886, 900-03

(9th Cir. 2002) (enjoining timber sale for ESA and NEPA violations). Here, the district court was faced with a continuing

operation that it had concluded would cause irreparable harm

to threatened species. Thus, the district court was confronted

with two choices: (1) continue the status quo, the foundation

of which the court had rejected as violative of the ESA and

the continuation of which it had concluded could irreparably

harm listed species, or (2) order modifications. After considering the positions of the parties, the district court adopted

one of the plaintiffs’ suggestions: mandatory summer spills

over selected dams. It rejected the plaintiffs’ other major

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12029
request, namely that the court order a decrease in the water

particle travel time by 10% in specified areas.10

The district court’s selection of a remedy of selected spills

was based on expert opinion tendered by the plaintiffs and

evidence in the historical record. Frederick Olney, a former

fishery biologist for the U.S. Fish and Wildlife Service with

thirty-five years of experience in the field, testified by affidavit that spilling water for fish passage was a “cornerstone of

protection and mitigation programs” in the area and that there

was “regional agreement that spill is the safest passage route

through mainstream hydroelectric projects.” He testified that

“recent information indicates that transportation [of fish] is

not providing the benefits previously assumed,” citing the

2004 BiOp statement that “it is uncertain whether transport

provides a benefit or a detriment for Snake River fall Chinook.” Olney concluded that the plaintiffs’ request for summer spills would pose less risk for migrating fish than the

proposed operations. 

The plaintiffs also tendered the opinion of Stephen Pettit,

a former fisheries research biologist for the Idaho Department

of Fish and Game, who similarly concluded that the plaintiffs’

proposed spills would “reduce significantly, even substantially, the harmful effects ESA-listed salmon and steelhead

would otherwise experience under the 2004 BiOp.” 

In addition to the opinions of these experts, and others, the

district court considered the previous positive results of the

prior use of spills for assisting salmon migrating during the

summer months. The 2000 BiOp concluded that “relative to

other passage routes currently available, direct juvenile survival is highest through spillbays.” In reaching this conclusion, the agency took into consideration the possibility of gas

10The district court also appointed a technical advisor, Dr. Howard Horton, to aid it in understanding the various reports, studies and opinions

regarding the status of the listed species and effects of FCRPS. 

12030 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
bubble trauma and elevated temperatures. The agency also

concluded that spillway passage “should be the baseline

against which other passage methods are measured.” Because

“juvenile survival is generally highest through this passage

route,” the 2000 BiOp recommended that “measures that

increase juvenile fish passage over FCRPS project spillways

are the highest priority unless it can be shown that alternative

passage improvements would provide comparable survival.”

The district court’s action was in accord with the consulting

agency’s findings and recommendations in its 2000 BiOp,

which was the only operative document at the time, and was

in conformance with the historical belief that spillway passage

produced the highest survival of the species. This historical

assumption was not contested in the 2004 BiOp; rather, it

asserted that alternative transportation could provide comparable, but not necessarily better, survival rates. 

[7] In short, without summarizing all of the voluminous

evidence in the record, the district court had a more than sufficient basis upon which to conclude that summer spills would

provide the best and safest alternative to the planned operations contemplated in the 2004 BiOp that was rejected by the

court. 

The federal appellants and other defendants vigorously

contest the conclusions of the experts tendered by the plaintiffs. The defendants offered substantial expert countertestimony in opposition to the proposed spills, with experts

opining that:

• Because the migratory patterns and river conditions are so different, it is inappropriate to extrapolate the experience from previous spills

involving adult salmon at different locations and

times to the summer spills proposed by the plaintiffs to assist juvenile migrating salmon. 

• Although passage over a spillway may result in

higher survival, the falling water over the dam

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12031
increases the amount of atmospheric gases that

are dissolved in the water, which may cause “gas

bubble trauma” and damage fish. In addition,

spills may expose the fish to potentially dangerous high water temperatures.

• Research indicates that there is no apparent difference in adult return rates between fish that are

transported and those that remain in the river.

New research also indicates that a significant

number of salmon hold over in freshwater and

migrate to the ocean during their second year of

life, which may mean that hastening the transportation of salmon downstream may not necessarily

be beneficial.

• The total number of adult Snake River Chinook

Salmon that migrated upriver has increased significantly.

• It is highly imprudent and highly risky to try an

untested operation in a critically low water year.

Transportation rather than spillage is the safest

means of passage in a low water year.

• Ordering spills at certain locations will adversely

affect other endangered species. 

These are significant and serious concerns. However, it is

not our task to weigh the evidence presented to the district

court; rather we must decide whether the district court abused

its discretion. An abuse of discretion is “a plain error, discretion exercised to an end not justified by the evidence, a judgment that is clearly against the logic and effect of the facts as

are found.” Wing v. Asarco, Inc., 114 F.3d 986, 988 (9th Cir.

1997) (quoting Int’l Jensen, Inc. v. Metrosound U.S.A., Inc.,

4 F.3d 819, 822 (9th Cir. 1993)) (internal quotation marks

omitted). The abuse of discretion standard requires that we

12032 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
“not reverse a district court’s exercise of its discretion unless

we have a definite and firm conviction that the district court

committed a clear error of judgment in the conclusion it

reached.” SEC v. Coldicutt, 258 F.3d 939, 941 (9th Cir.

2001). 

[8] The federal appellants argue that the district court was

required to defer to agency expertise. Courts, as a general

matter, ought to defer to an agency’s scientific or technical

expertise. “Deference to the informed discretion of the

responsible federal agencies is especially important, where, as

here, the agency’s decision involves a high level of technical

expertise.” R-CALF, slip op. at 8753. However, “[t]he deference accorded an agency’s scientific or technical expertise is

not unlimited.” Brower v. Evans, 257 F.3d 1058, 1067 (9th

Cir. 2001) (citing Defenders of Wildlife v. Babbitt, 958 F.

Supp. 670, 679 (D.D.C. 1997)). Deference is not owed when

“ ‘the agency has completely failed to address some factor

consideration of which was essential to [making an] informed

decision.’ ” Id. (quoting Inland Empire Pub. Lands Council v.

Schultz, 992 F.2d 977, 981 (9th Cir. 1993) (internal citations

omitted)). Here, the district court had already invalidated the

agency biological opinion upon which the operations were

based, in large part because it omitted factors essential to the

analysis. As the district court noted, NMFS had completely

reversed course in its 2004 BiOp, particularly in its statutory

interpretation of the environmental baseline. “An agency

interpretation of a relevant provision which conflicts with the

agency’s earlier interpretation is ‘entitled to considerably less

deference,’ than a consistently held agency view.” INS v.

Cardoza-Fonseca, 480 U.S. 421, 446, n. 30 (1987) (quoting

Watt v. Alaska, 451 U.S. 259, 273 (1981)). The district court

had rejected the underlying premise of the agency’s methodology and the 2004 BiOp. Therefore, there was no formal

agency finding to which deference might arguably be owed.

Rather, the government chose to present its case through

expert affidavit. 

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12033
[9] Throughout the course of these proceedings, the government has adhered to its position that it would not alter its

planned summer dam operations which the district court had

determined could cause irreparable harm. Indeed, the government’s own 2000 BiOp had concluded that the present operations of the Columbia River System would jeopardize eight of

the listed species. In its summary judgment order, the district

court had made the factual finding that the listed species were

“in serious decline and not evidencing signs of recovery.”

Therefore, in the absence of an approved, final biological

opinion, the district court did not abuse its discretion in considering the record evidence. We conclude that the district

court did not abuse its discretion in ordering preliminary

injunctive relief. 

C

The federal appellants also suggest that, even if preliminary

injunctive relief were appropriate, the district court’s order

must be vacated because it is not narrowly tailored. The

appellants did not present this argument to the district court,

nor have they sought modification of the injunction. On

appeal, the appellants have declined to identify how the

injunction should be narrowly tailored, even under questioning. There is also some tension between appellants’ argument

on appeal that the district court is micromanaging the Columbia River System and its argument that the district court was

not specific or detailed enough in its order. The gist of the

federal appellants’ argument seems to be that the purported

lack of narrow tailoring should result in a vacation of the

entire injunction, rather than any modification designed to

achieve narrow tailoring. 

That being said, all sides agree that modifications to the

district court’s order have been required. Indeed, the district

court anticipated this by encouraging the parties “to engage in

discussions to reach a consensus on issues of spill.” The federal appellants have requested that we allow them to supple12034 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
ment the appellate record with declarations identifying

specific problems with the district court’s injunction. The

plaintiffs have opposed the motion; however, in the alternative, they have tendered supplemental declarations. 

[10] Without reviewing the tendered evidence or outlining

the evidence in the record indicating that specific issues at

certain sites may require modification of the preliminary

injunction, we conclude that there are issues that have arisen

after the issuance of the preliminary injunction that may

require modification of the district court order. It is inappropriate for us to decide those questions for the first time on

appeal, and we therefore deny the parties’ motions to supplement the record. Although we conclude that the district court

did not abuse its discretion in granting the preliminary injunction, we remand the question of whether modification or “narrow tailoring” of the order is required to the district court for

its consideration in the first instance. 

The BPA Customer Group has also argued that the district

court’s order should be vacated as not narrowly tailored. The

basis of the BPA Customer Group’s argument is different. It

argues that the order insufficiently relates the remedy to the

alleged ESA violation. Although the BPA Customer Group

raised this issue in their memorandum in opposition to the

preliminary injunction, the district court did not explicitly

address this issue in its preliminary injunction order. In light

of our decision to remand for consideration of modifications

to the preliminary injunction, we also remand this question to

the district court for its consideration in the first instance. We

urge the parties and the district court to resolve these

remanded issues as expeditiously as possible. 

IV

In sum, we affirm the district court’s issuance of a preliminary injunction, but remand to the district court the question

NAT’L WILDLIFE v. NAT’L MARINE FISHERIES 12035
of whether the injunction should be more narrowly tailored or

modified. 

AFFIRMED AND REMANDED.

12036 NAT’L WILDLIFE v. NAT’L MARINE FISHERIES