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



                and                    
NORTHWEST IRRIGATION UTILITIES;
PUBLIC POWER COUNCIL; PACIFIC
NORTHWEST GENERATING
COOPERATIVE; BPA CUSTOMER
                                       
GROUP,
          Defendants-Intervenors-
                        Appellants,
               v.
STATE OF OREGON,
              Plaintiff-Intervenor-
                          Appellee.
                                       

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;
NORTHWEST SPORT FISHING
                                              D.C. No.
                                           CV-01-00640-JAR
INDUSTRY ASSOCIATION, SALMON FOR
ALL; COLUMBIA RIVERKEEPER; NW
ENERGY COALITION; FEDERATION OF
FLY FISHERS; AMERICAN RIVERS,
INC.,
               Plaintiffs-Appellees,
                 v.
                                       
          NAT’L WILDLIFE v. NAT’L MARINE FISHERIES   12007



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-Intervenor-
                          Appellant,
                v.
STATE OF OREGON,
               Plaintiff-Intervenor-
                           Appellee.
                                       
12008     NAT’L WILDLIFE v. NAT’L MARINE FISHERIES



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;
                                       
          NAT’L WILDLIFE v. NAT’L MARINE FISHERIES    12009



WASHINGTON FARM BUREAU                
FEDERATION; STATE OF IDAHO;
CLARKSON GOLF & COUNTRY CLUB,
           Defendants-Intervenors,
               v.                     
STATE OF OREGON,
              Plaintiff-Intervenor-
                          Appellee.
                                      
       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
12012     NAT’L WILDLIFE v. NAT’L MARINE FISHERIES




                        COUNSEL

Mark Eames, NOAA Office of General Counsel, Seattle,
Washington; Gayle Lear, Assistant Division Counsel, North-
western Division, U.S. Army Corps of Engineers, Portland,
Oregon; Kelly A. Johnson, Acting Assistant Attorney Gen-
eral, 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 Cus-
tomer Group. Lawrence G. Wasden, Attorney General, Clive
J. Strong, Deputy Attorney General, and Clay R. Smith, Dep-
uty 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 Advo-
cacy 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 Ste-
phen 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; Chris-
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES       12013
topher B. Leahy, Fredericks, Pelcyger & Hester, LLC, Louis-
ville, Colorado; Tim Weaver, Law Offices of Tim Weaver,
Yakima, Washington, for amici curiae Treaty Tribes.

Robert D. Thornton and Paul S. Weiland, Nossaman, Guth-
ner, 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 prelim-
inary injunction, based on a violation of the Endangered Spe-
cies 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 gen-
eration. 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
12014       NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
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 hun-
dreds 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 anadro-
mous salmon and steelhead protected by the Endangered Spe-
cies 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 abun-
dance. 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
  1
     The FCRPS consists of 14 sets of dams and related facilities: Bonne-
ville, 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.
   2
     Snake 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 Chi-
nook salmon; Upper Willamette River Chinook salmon; Upper Columbia
River Chinook salmon (spring-run); and Columbia River chum salmon.
             NAT’L WILDLIFE v. NAT’L MARINE FISHERIES                12015
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 gener-
ally migrate seaward between mid-April and early September.
The spring and summer Chinook, steelhead, and sockeye
salmon migrate as yearling juveniles in the spring. Subyear-
ling fall Chinook migrate down the river during the mid-to-
late summer. Some salmon migrate downstream after spend-
ing 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 pikemin-
now. 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) trans-
portation bypass systems. Of these options, passage through
turbines unquestionably causes the highest mortality rate. His-
torically, spill has been considered to cause the lowest mortal-
ity. However, spill must be carefully managed to avoid gas
supersaturation, which is harmful to the fish.3
  3
    Falling 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.
12016        NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
   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 sys-
tem 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 Bonne-
ville Power Administration manages federal power generated
from the dams; and the Federal Energy Regulatory Commis-
sion plays a number of roles, including licensing of non-
federal hydro-power projects. Although the focus of this liti-
gation is the effect of Columbia River System operation on
endangered species, in the day-to-day operation, federal agen-
cies must manage the system to deliver needed power and
water to Northwest consumers.

   States also have an influence on the Columbia River Sys-
tem, directly in their governance of water diversions from the
river, and indirectly through their own fish and wildlife con-
servation 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.
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES        12017
   In the last several decades, the management of the Colum-
bia River System has been strongly influenced by the Endan-
gered 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 fed-
eral 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 pro-
cess 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 anal-
ysis, 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 opin-
ion, 16 U.S.C. § 1536(b), based on “the best scientific and
commercial data available,” id. at § 1536(a)(2). The biologi-
cal 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 jeopar-
dize 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
12018        NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
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 sec-
tion 7 consultation.” Id.

   If the biological opinion concludes that jeopardy is not
likely and that there will not be adverse modification of criti-
cal habitat, or that there is a “reasonable and prudent alterna-
tive” 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 consult-
ing 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 rec-
ommend a “reasonable and prudent alternative” to the agen-
cy’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. Ben-
nett 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).
             NAT’L WILDLIFE v. NAT’L MARINE FISHERIES               12019
   The Endangered Species Act, as it applies here to protec-
tion of anadromous fish, requires action agencies to consult
the agency formerly known as the National Marine Fisheries
Service of the National Oceanic and Atmospheric Administra-
tion (“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 capri-
cious. 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 opin-
ions.

   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; specifi-
cally, NMFS found that the “effects of the proposed or contin-
uing 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
  6
    The agency has now been renamed “NOAA Fisheries.” Because many
of the documents refer to the agency by its former name, it shall be refer-
enced as “NMFS” throughout this opinion for convenience of reference.
12020       NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
population recovery. NMFS thus developed reasonable and
prudent alternatives to the proposed operation and analyzed
whether these alternatives, in conjunction with the environ-
mental baseline and cumulative effects, would avoid jeopar-
dizing 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 consulta-
tion, 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 agen-
cies’ 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 environ-
mental baseline the existing FCRPS, the nondiscretionary
  7
    The 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 dis-
cretionary 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.
            NAT’L WILDLIFE v. NAT’L MARINE FISHERIES             12021
dam operations, and all past and present impacts from discre-
tionary 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, con-
sisting of only the proposed discretionary operation of the
FCRPS, would have no net effect on a species when com-
pared to the environmental baseline. By using this compara-
tive approach rather than the aggregate approach, NMFS was
able to conclude that the proposed action would not jeopar-
dize 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 non-
discretionary 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 deter-
minations; 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 issu-
ance 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
  8
    The 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.
12022      NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
        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 environ-
        mental 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 spe-
        cies; 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 “in-
validated” the 2004 BiOp. However, the district court speci-
fied that its summary judgment order was not final or
appealable. Following the district court’s decision to invali-
date 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 alterna-
tive mitigation actions described in the 2000 BiOp (with cer-
tain 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 find-
ing 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 prelimi-
nary injunction. The district court announced its intention to
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES       12023
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 pre-
liminary injunction appeal was held July 13, 2005. The panel
expresses its appreciation to the parties for providing exten-
sive briefing on short notice and on an accelerated time sched-
ule.

                               II

   A district court’s order with respect to preliminary injunc-
tive 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 Com-
12024      NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
munications, Inc., 287 F.3d 832, 839 (9th Cir. 2002). “Our
review is limited and deferential.” Southwest Voter Registra-
tion 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 dis-
trict 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 Wild-
life 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 injunc-
tion proceedings of balancing the parties’ competing inter-
ests.” 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). Accord-
ingly, 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.”).
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES        12025
                               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 pre-
liminary 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 dis-
trict 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 improp-
erly 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 judg-
ment 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 prelimi-
nary 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,
12026        NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
our review in the preliminary injunction context is very defer-
ential. On appellate review in this context, we consider a find-
ing 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 exten-
sive, 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 dis-
trict 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 sur-
vival improvement for fall chinook juveniles has not material-
ized.” 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
  9
    Although a non-trivial level of mortality would likely occur under free-
flowing river conditions, FCRPS operations account for most of the mor-
tality.
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES        12027
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 plausi-
ble 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)). View-
ing 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 grant-
ing 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 vio-
lations.

   [5] Although not every statutory violation leads to the “au-
tomatic” issuance of an injunction, in the context of the ESA,
“the test for determining if equitable relief is appropriate is
12028      NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
whether an injunction is necessary to effectuate the congres-
sional 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 requir-
ing compliance with the substantive and procedural provi-
sions of the ESA. Id. at 1177 (holding that the district court
was “compelled” to grant injunctive relief to remedy a viola-
tion 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 circum-
stances 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 fur-
ther 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 moni-
tored the situation carefully over the past few years and has
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES        12029
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 Administra-
tive Procedure Act. Finally, as we have discussed, the stan-
dard 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 endan-
gered species the highest of priorities.” TVA, 437 U.S. at 194.
For these reasons, this case is quite distinguishable from R-
CALF, 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 post-
poned in order to permit the agency to correct the ESA viola-
tions 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 vio-
lations). 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 consid-
ering 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
12030       NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
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 affida-
vit 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 Chi-
nook.” Olney concluded that the plaintiffs’ request for sum-
mer 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 substan-
tially, 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 sur-
vival is highest through spillbays.” In reaching this conclu-
sion, the agency took into consideration the possibility of gas
  10
    The district court also appointed a technical advisor, Dr. Howard Hor-
ton, to aid it in understanding the various reports, studies and opinions
regarding the status of the listed species and effects of FCRPS.
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES         12031
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 compa-
rable, 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 suffi-
cient basis upon which to conclude that summer spills would
provide the best and safest alternative to the planned opera-
tions 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 plain-
tiffs. The defendants offered substantial expert counter-
testimony in opposition to the proposed spills, with experts
opining that:

    •   Because the migratory patterns and river condi-
        tions are so different, it is inappropriate to extrap-
        olate the experience from previous spills
        involving adult salmon at different locations and
        times to the summer spills proposed by the plain-
        tiffs to assist juvenile migrating salmon.

    •   Although passage over a spillway may result in
        higher survival, the falling water over the dam
12032      NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
        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 danger-
        ous high water temperatures.

    •   Research indicates that there is no apparent dif-
        ference 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 transpor-
        tation of salmon downstream may not necessarily
        be beneficial.

    •   The total number of adult Snake River Chinook
        Salmon that migrated upriver has increased sig-
        nificantly.

    •   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, discre-
tion exercised to an end not justified by the evidence, a judg-
ment 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
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES        12033
“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 defer-
ence 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 method-
ology 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.
12034      NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
   [9] Throughout the course of these proceedings, the gov-
ernment 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 govern-
ment’s own 2000 BiOp had concluded that the present opera-
tions 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 con-
sidering 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 question-
ing. There is also some tension between appellants’ argument
on appeal that the district court is micromanaging the Colum-
bia 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 fed-
eral appellants have requested that we allow them to supple-
           NAT’L WILDLIFE v. NAT’L MARINE FISHERIES        12035
ment the appellate record with declarations identifying
specific problems with the district court’s injunction. The
plaintiffs have opposed the motion; however, in the alterna-
tive, 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 inappro-
priate for us to decide those questions for the first time on
appeal, and we therefore deny the parties’ motions to supple-
ment the record. Although we conclude that the district court
did not abuse its discretion in granting the preliminary injunc-
tion, we remand the question of whether modification or “nar-
row 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 prelimi-
nary injunction, but remand to the district court the question
12036     NAT’L WILDLIFE v. NAT’L MARINE FISHERIES
of whether the injunction should be more narrowly tailored or
modified.

  AFFIRMED AND REMANDED.
