                  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            No. 06-35011
ALL; COLUMBIA RIVERKEEPER; NW
ENERGY COALITION; FEDERATION OF
                                             D.C. Nos.
                                           CV-01-00640-JAR
FLY FISHERS; AMERICAN RIVERS,               05-00023-JAR
INC.; EASTERN OREGON IRRIGATORS
ASSOCIATION,
               Plaintiffs-Appellees,
                 v.
NATIONAL MARINE FISHERIES
SERVICE; UNITED STATES ARMY
CORPS OF ENGINEERS; U.S.
BUREAU OF RECLAMATION; DONALD
L. EVANS, in his official capacity
                                       




                            4271
4272     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO


as Secretary of Commerce; NOAA           
FISHERIES; D. ROBERT LOHN, in his
official capacity as Regional
Direct of NOAA Fisheries,
                          Defendants,
NORTHWEST IRRIGATION UTILITIES;
PUBLIC POWER COUNCIL; BPA
CUSTOMER GROUP; FRANKLIN
COUNTY FARM BUREAU FEDERATION;
GRANT COUNTY FARM BOARD
FEDERATION; WASHINGTON FARM
BUREAU FEDERATION; CLARKSON
GOLF & COUNTRY CLUB; STATE OF
                                         
MONTANA; KOOTENAI TRIBE OF
IDAHO,
             Defendant-Intervenors,
                 and
STATE OF OREGON,
                 Plaintiff-Intervenor-
                             Appellee,
STATE OF IDAHO,
              Defendant-Intervenor-
                            Appellant.
                                         
         NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO    4273



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                No. 06-35019
ENERGY COALITION; FEDERATION OF
                                                D.C. No.
                                        
FLY FISHERS; AMERICAN RIVERS,
INC.; EASTERN OREGON IRRIGATORS             CV-01-00640-JAR
ASSOCIATION,                                  AMENDED
                Plaintiffs-Appellees,          OPINION
                 v.
NATIONAL MARINE FISHERIES
SERVICE; UNITED STATES ARMY
CORPS OF ENGINEERS; U.S.
BUREAU OF RECLAMATION,
            Defendants-Appellants,
STATE OF OREGON,
               Plaintiff-Intervenor-
                            Appellee,
                and
                                        
4274     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO



DONALD L. EVANS, in his official      
capacity as Secretary of
Commerce; NOAA FISHERIES; D.
ROBERT LOHN, in his official
capacity as Regional Director of
NOAA Fisheries,
                        Defendants,
NORTHWEST IRRIGATION UTILITIES;
PUBLIC POWER COUNCIL; BPA
CUSTOMER GROUP; FRANKLIN              
COUNTY FARM BUREAU FEDERATION;
GRANT COUNTY FARM BOARD
FEDERATION; WASHINGTON FARM
BUREAU FEDERATION; STATE OF
IDAHO; CLARKSON GOLF &
COUNTRY CLUB; STATE OF
MONTANA; KOOTENAI TRIBE OF
IDAHO,
            Defendant-Intervenors.
                                      
       Appeal from the United States District Court
                for the District of Oregon
       James A. Redden, District Judge, Presiding

                   Argued and Submitted
          June 1, 2006—San Francisco, California

                   Filed April 9, 2007
                 Amended April 24, 2008

    Before: A. Wallace Tashima, Sidney R. Thomas, and
              Richard A. Paez, Circuit Judges.

                 Opinion by Judge Thomas
4278     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
                         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 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, Deputy Attor-
ney 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-
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
         NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO     4279
National Association of Homebuilders. Rob McKenna, Attor-
ney 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.

James L. Buchal, Murphy & Buchal LLP, Portland, Oregon,
for amicus curiae Columbia Snake River Irrigators Associa-
tion.

Russell C. Brooks, Bellevue, Washington; M. Reed Hopper
and Scott A. Sommerdorf, Pacific Legal Foundation, Sacra-
mento, California, for amicus curiae Washington Farm
Bureau Federation.


                         OPINION

THOMAS, Circuit Judge:

   These consolidated appeals bring us once more to the
Pacific Northwest, for another round in the complex and long-
running battle over salmon and steelhead listed under the
Endangered Species Act (“ESA”), 16 U.S.C. §§ 1531-1544.
In this ESA action brought by the National Wildlife Federa-
tion and other plaintiffs (collectively “NWF”), we consider a
November 2004 Biological Opinion (“2004 BiOp”) address-
ing the effects of proposed operations of Federal Columbia
River Power System (“FCRPS” or “Columbia River System”)
dams and related facilities on listed fish in the lower Colum-
bia and Snake Rivers. The 2004 BiOp, issued by the agency
formerly known as the National Marine Fisheries Service of
4280      NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
the National Oceanic and Atmospheric Administration
(“NMFS”),1 found that proposed FCRPS operations for 2004
through 2014 would not jeopardize the thirteen area salmonid
species that are listed as threatened or endangered, nor
adversely modify their critical habitat. NMFS and the State of
Idaho (collectively “NMFS”) appeal from the district court’s
determination that the 2004 BiOp was structurally flawed and
from certain portions of its remand order. We affirm.

                                   I

   The factual and procedural history of this case was detailed
in our prior opinion. NWF v. NMFS, 422 F.3d 782, 800 (9th
Cir. 2005). As background, and for convenience of reference,
we will briefly review the proceedings to date to place the
present controversy in context.

   Every year hundreds of thousands of salmon and steelhead
travel up and down the Columbia River and its tributaries,
hatching in fresh water, migrating downstream to the sea to
achieve adulthood, and then returning upstream to spawn. The
wild Pacific salmon population has significantly decreased in
recent years, and a number of species of Columbia, Snake,
and Willamette River salmon and steelhead are now protected
by the Endangered Species Act.2 Each of the affected stocks
migrates at a different time of the year to different parts of the
Columbia Basin.
  1
     The agency is now NOAA Fisheries. Because much of the record
before us uses the prior name, we shall refer to the agency as “NMFS” in
this opinion.
   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 FEDERATION v. STATE OF IDAHO                4281
   At issue in this case are the fall juvenile Chinook salmon
and steelhead migrating downstream to the Pacific Ocean.
These fish must pass a number of dams on their journey to the
sea and suffer a very high mortality rate in doing so. 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.

   A number of federal, state, and tribal entities are involved
in the operation of the Columbia River System. The U.S.
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. State regulation impacts the
system through governance of water diversions from the river
and state conservation programs. A number of federally rec-
ognized Indian Tribes retain treaty fishing rights in the waters
of the Columbia River System.3

    The issue before us is application of the ESA on the man-
agement of the Columbia River System. Section 7 of the ESA
requires federal agencies, in consultation with what is known
as the “consulting agency,” to conserve species listed under
the ESA. The Section 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
  3
    See, e.g., Treaty with the Nez Perces, art. 3, June 11, 1855, 12 Stat.
957; Treaty with the Tribes of the Middle Oregon (Confederated Tribes
of the Warm Springs Reservation of Oregon), June 25, 1855, 12 Stat. 963;
Treaty with the Yakima, June 9, 1855, 12 Stat. 951; Treaty with the Wal-
lawalla, Cayuse, et al. (Confederated Tribes of the Umatilla Indian Reser-
vation), June 9, 1855, 12 Stat. 945. In their amici brief, the treaty tribes
support the position of NWF in this action.
4282      NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
endangered species or threatened species or result in the
destruction or adverse modification of [designated critical]
habitat . . . .” 15 U.S.C. § 1536(a)(2). The ESA imposes a pro-
cedural consultation duty whenever a federal action may
affect an ESA-listed species. Thomas v. Peterson, 753 F.2d
754, 763 (9th Cir. 1985). The agencies charged with imple-
menting the ESA have promulgated a regulation clarifying
that “Section 7 and the requirements of this part apply to all
actions in which there is discretionary Federal involvement or
control.” 50 C.F.R. § 402.03 (emphasis added). Thus, where
there is such discretionary involvement or control, 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, investigation, and
analysis, the consulting agency then prepares a biological
opinion. See generally Ariz. Cattle Growers’ Ass’n v. U.S.
Fish & Wildlife Serv., 273 F.3d 1229, 1239 (9th Cir. 2001).
In this case, the action agencies are the U.S. Army Corps of
Engineers and the Bureau of Reclamation, while the consult-
ing agency is NMFS.

   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.§ 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 agen-
cy’s opinion on “whether the action is likely to jeopardize the
continued existence of a listed species or result in the destruc-
tion or adverse modification of critical habitat . . . .” 50 C.F.R.
§ 402.14(h)(3). In making its jeopardy determination, the con-
sulting agency evaluates “the current status of the listed spe-
cies or critical habitat,” the “effects of the action,” and
“cumulative effects.” Id. § 402.14(g)(2)-(3). “Effects of the
           NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO                  4283
action” include both direct and indirect effects of an action
“that will be added to the environmental baseline.” Id.
§ 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 consulta-
tion.” 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 endan-
gered 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 prohi-
bition on takings4 found in Section 9 of the ESA. 16 U.S.C.
§ 1536(b)(4); ALCOA v. BPA, 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. ALCOA, 175 F.3d at 1159. The con-
sulting agency may recommend a “reasonable and prudent
alternative” to the agency’s proposed action. 16 U.S.C.
§ 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.

   The ESA, as it applies here to the protection of anadromous
fish, requires action agencies — here the U.S. Army Corps of
  4
    “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).
4284     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
Engineers and the Bureau of Reclamation — to consult
NMFS to ensure that an agency’s actions do not jeopardize an
ESA-protected species or adversely modify their critical habi-
tat. 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 Idaho Department of Fish and Game chal-
lenged that opinion. In granting summary judgment for the
plaintiff, the district court held that NMFS’s action in issuing
the 1993 biological opinion was arbitrary and capricious
because NMFS had failed adequately to explain several of the
key assumptions in its jeopardy analysis. See Idaho Dep’t of
Fish & Game v. Nat’l Marine Fisheries Serv., 850 F. Supp.
886, 900 (D. Or. 1994). 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 Fish-
eries 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 biologi-
cal opinions.

   The 2000 BiOp 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 population recovery.
NMFS thus explored reasonable and prudent alternatives to
the proposed operation and analyzed whether these alterna-
tives, in conjunction with the environmental baseline and
cumulative effects, would avoid jeopardizing the species.
Because NMFS found these alternatives insufficient, it then
assessed whether the added impact of off-site mitigation
         NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO         4285
activities unrelated to FCRPS operations, including hatchery
and habitat initiatives, would avoid jeopardy, and found that
they would.

   NWF filed an ESA challenge to the 2000 BiOp in the Dis-
trict of Oregon, initiating this litigation. In May 2003, the dis-
trict court ruled that the 2000 BiOp was arbitrary and
capricious because it relied on (1) federal mitigation actions
that had not been subject to Section 7 consultation and (2)
non-federal mitigation actions that had not been shown rea-
sonably certain to occur. NWF v. NMFS, 254 F. Supp. 2d
1196, 1213 (D. Or. 2003). The court remanded to the agencies
for a new BiOp and revisions to the proposed operations,
leaving the 2000 BiOp in effect in the meantime.

   On remand, NMFS made several structural changes to its
jeopardy analysis. The 2004 BiOp’s jeopardy analysis
included in the environmental baseline for the proposed action
the existing FCRPS, various supposedly nondiscretionary
dam operations, and all past and present impacts from discre-
tionary operations. NMFS also adopted a novel “reference
operation” approach in the 2004 BiOp, purportedly in order
to account for the existence of the FCRPS dams. The refer-
ence operation consisted of the dams and a hypothetical
regime for operating them, which, according to NMFS, was
the most beneficial to listed fishes of any possible operating
regime. NMFS also found, though, that certain aspects of
FCRPS operations — such as operations relating to irrigation,
flood control, and power generation — were nondiscretion-
ary, given the dams’ existence, and that those aspects should
not be considered part of the action under ESA review. The
BiOp offers little detail on the nature and extent of the pur-
portedly nondiscretionary obligations or NMFS’s basis for
finding them to be nondiscretionary.

   Also, instead of assessing whether the listed fish would be
jeopardized by the aggregate of the proposed agency action,
the environmental baseline, cumulative effects, and current
4286      NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
status of the species, NMFS segregated its analysis, first eval-
uating whether the proposed agency action — consisting of
only the proposed discretionary operation of the FCRPS —
would have an appreciable net effect on a species. It consid-
ered additional context only if it found such an effect. By
using this so-called comparative approach rather than a more
holistic, aggregate approach, NMFS concluded that the pro-
posed action would not jeopardize the continued existence of
the listed fish. Although the 2004 BiOp did not point to any
improvement in the fishes’ status or the impacts of FCRPS
operations, its new approach attributed only a much smaller
portion of the fishes’ perilous condition to the proposed oper-
ations under review. The 2004 BiOp’s jeopardy analysis also
omitted any clear consideration of the impact of proposed
operations on listed species’ chances of recovery, which had
been a prominent feature of earlier analyses.

   On December 30, 2004, NWF filed a Second Supplemental
Complaint against NMFS, challenging the new 2004 BiOp.5
On May 26, 2005, the district court ruled on summary judg-
ment motions filed by NWF, the State of Oregon (which
intervened as a plaintiff), NMFS, and other parties. The court
held the 2004 BiOp invalid on several grounds raised by
NWF and declined to reach the various parties’ other claims.

   The district court concluded that there were several struc-
tural flaws with the 2004 BiOp’s jeopardy analysis, as well as
more modest defects in the BiOp’s analysis of impacts on crit-
ical habitat. First, the court determined that the agencies had
discretion to balance the FCRPS’s various purposes to comply
with ESA’s requirements, and that the 2004 BiOp impermiss-
ibly used the “reference operation” to redefine most FCRPS
ongoing operations as part of the “existence of the dams,”
instead of including those operations as part of the agency
  5
   Three months later, NWF filed a Third Supplemental Complaint,
adding claims against the Corps and Bureau of Reclamation that are not
before us.
           NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO               4287
action under review. Also, the court held that the 2004 BiOp’s
new, two-stage comparative analysis did not satisfy NMFS’s
obligation to make its jeopardy determination based on the
full natural and human context of the proposed action. The
court also objected to the 2004 BiOp’s complete omission of
recovery needs from its jeopardy analysis. Finally, the court
concluded that the 2004 BiOp did not adequately consider the
recovery implications of the proposed operation’s effects on
designated critical habitat for three listed species.

   On June 10, 2005, the district court granted in part NWF’s
motion for a preliminary injunction requiring NMFS to
increase flow and spill at certain FCRPS dams during the
summer of 2005. On review of that decision, we held that the
district court had not abused its discretion in granting NWF
a preliminary injunction, but remanded to the district court
“the question of whether the injunction should be more nar-
rowly tailored or modified.” NWF, 422 F.3d at 800.

   On September 26, 2005, the district court entered final
judgment under Federal Rule of Civil Procedure 54(b), as to
its May 2005 summary judgment decision on the merits of
NWF’s 2004 BiOp claims. The district court then remanded
to NMFS for yet another revision of the BiOp, which was pro-
ceeding at the time of oral argument. Among other things, the
remand order required NMFS to collaborate with interested
states and tribes and to provide a “failure report” if the
remand process appeared unlikely to produce a no-jeopardy
finding within the court’s remand timeframe. After the court
amended its Rule 54(b) order on October 24, 2005, to include
the October 10, 2005, remand order, NMFS appealed again.
We consider here NMFS’s challenges to the merits of the dis-
trict court’s May 2005 summary judgment decision, and to the
novel elements of the remand order.6
  6
   Other claims were raised on appeal by Columbia Snake River Irrigators
Association and Eastern Oregon Irrigators Association, plaintiffs in a sep-
arate action below. We address those claims in a memorandum disposition
in No. 05-35736 filed concurrently with this opinion.
4288       NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
   We review the district court’s decision and analysis de
novo. We may affirm the district court’s rejection of the 2004
BiOp, under the Administrative Procedure Act (“APA”), if
the agency action is arbitrary, capricious, an abuse of discre-
tion, or otherwise not in accordance with law. 5 U.S.C.
§ 706(2)(a). Although we may not substitute our judgment for
that of the agency, we must engage in a careful, searching
review to ensure that the agency has made a rational analysis
and decision on the record before it. Pac. Coast Fed’n of
Fishermen’s Ass’ns v. U.S. Bureau of Reclamation, 426 F.3d
1082, 1090 (9th Cir. 2005).

                                    II

   After a careful review of the record, we conclude that the
district court correctly determined that the jeopardy analysis
of the 2004 BiOp contained structural flaws that rendered it
incompatible with the ESA. Our conclusion is not altered by
the Supreme Court’s recent decision in National Association
of Home Builders v. Defenders of Wildlife, 127 S. Ct. 2518
(2007), which was filed after our opinion was published but
before we received the petition for rehearing.7 In Home Build-
ers, the Supreme Court granted Chevron deference to the reg-
ulation which provides that Section 7 consultation applies “to
all actions in which there is discretionary Federal involve-
ment or control,” 50 C.F.R. § 402.03 (emphasis added). 127
S. Ct. at 2534-35. The Court interpreted the regulation as clar-
ifying that Section 7 “covers only discretionary agency
actions and does not attach to actions . . . that an agency is
required by statute to undertake once certain specified trigger-
ing events have occurred. Id. at 2536 (emphasis in original).
The Court found the regulation to be a reasonable resolution
to the problem of an agency being unable to “simultaneously
  7
    A petition for rehearing was filed by the State of Idaho and a response
to the petition for rehearing was filed by the National Wildlife Federation.
Although the federal appellants requested, and received, an extension to
file petitions for rehearing, no such petition(s) were filed.
         NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO       4289
obey” both Section 7 and a separate statute which expressly
requires an agency to take a conflicting action. Id. at 2533-34.
We do not face this problem here, however, because in the
present case Congress has imposed broad mandates, rather
than directing the agency to take specific actions, and the
agencies are perfectly capable of simultaneously obeying Sec-
tion 7 and those mandates.

                               A

   [1] The district court properly held that NMFS may not use
a hypothetical “reference operation” in its jeopardy analysis
to exclude from the proposed actions’ impacts the effects of
related operations NMFS deems “nondiscretionary.” NMFS
admits that it chose the reference operation approach in order
to avoid “trying to precisely determine the extent of the
Action Agencies’ discretionary operation.” However, neither
the ESA nor Home Builders permits agencies to ignore poten-
tial jeopardy risks by labeling parts of an action nondiscre-
tionary. We cannot approve NMFS’s interpretation of this
rule as excluding from the agency action under review discre-
tionary agency actions taken pursuant to a broad congressio-
nal mandate.

   [2] First, we note that federal agencies, including NMFS,
have not previously taken such a cramped view of § 402.03’s
reference to “discretionary” federal action. Indeed, such an
approach is a drastic change from NMFS’s own approach in
the 1995 and 2000 BiOps. Because NMFS’s approach is a
novel one, completely at odds with NMFS’s prior scientific
approaches, it merits little deference. INS v. Cardoza-
Fonseca, 480 U.S. 421, 446 n.30 (1987) (“An agency inter-
pretation of a relevant provision which conflicts with the
agency’s earlier interpretation is entitled to considerably less
deference . . . .”) (internal quotation marks omitted).

   [3] Second, NMFS’s contention that competing mandates
for flood control, irrigation, and power production create any
4290      NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
immutable obligations that fall outside of agency discretion is
not persuasive. Indeed, NMFS’s interpretation is neither man-
dated nor intimated by the Court’s holding in Home Builders.
The Court’s concern in Home Builders was that “[a]n agency
cannot simultaneously obey the differing mandates set forth
in § 7(a)(2) of the ESA and § 402(b) of the CWA.” 127 S. Ct.
at 2534. In this context, compliance with the CWA provision
is problematic because the provision “affirmatively mandates
that [a specific action which conflicts with the ESA] ‘shall’ be
[taken] if the specified criteria are met. The provision operates
as a ceiling as well as a floor.” Id. at 2533. Here, in contrast,
Congress has imposed broad mandates which do not direct
agencies to perform any specific nondiscretionary actions, but
rather, are better characterized as directing the agencies to
achieve particular goals.

   The 2004 BiOp itself recognizes that Congress has not
quantified any of those broad goals, or otherwise specified the
manner in which the agencies must fulfill them. NMFS found,
for instance, that Congress has mandated that dam operations
include flood control, though “Congress has not prescribed
precisely how the Corps must achieve its flood control
responsibilities.” 2004 BiOp at 5-5. Similarly, Congress has
mandated that the BPA market and transmit “some level of
power, although the precise level is not defined.” Id. Thus, the
2004 BiOp recognizes that Congress has not specified the
manner in which the agencies must fulfill their various obliga-
tions. In other words, while the goals themselves may be man-
datory, the agencies retain considerable discretion in choosing
what specific actions to take in order to implement them. The
agencies are therefore obligated to satisfy the ESA’s require-
ments. See Pac. Coast Fed’n, 426 F.3d at 1084-85 (“The ESA
obligates federal agencies ‘to afford first priority to the
declared national policy of saving endangered species.’ ”)
(quoting TVA v. Hill, 437 U.S. 153, 185 (1978)).8
  8
   Moreover, at least some of the competing statutory mandates clearly
acknowledge that implementing agencies must accommodate wildlife
          NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO             4291
   NMFS may not avoid determining the limits of the action
agencies’ discretion by using a reference operation to sweep
so-called “nondiscretionary” operations into the environmen-
tal baseline, thereby excluding them from the requisite ESA
jeopardy analysis. And Home Builders cannot be read, as the
State of Idaho would have us do, to immunize discretionary
agency actions simply because they are taken in pursuit of a
non-discretionary goal. The concern that an agency cannot
“simultaneously obey” with both the ESA and the broad man-
dates relevant to this case is simply not at issue here.

    [4] ESA compliance is not optional. “[A]n agency cannot
escape its obligation to comply with the ESA merely because
it is bound to comply with another statute that has consistent,
complementary objectives.” Washington Toxics Coal. v. EPA,
413 F.3d 1024, 1032 (9th Cir. 2005). As the Court empha-
sized in Home Builders, “ESA’s no-jeopardy mandate applies
to every discretionary agency action—regardless of the
expense or burden its application might impose.” 127 S. Ct.
at 2537. When an agency, acting in furtherance of a broad
Congressional mandate, chooses a course of action which is
not specifically mandated by Congress and which is not spe-
cifically necessitated by the broad mandate, that action is, by
definition, discretionary and is thus subject to Section 7 con-
sultation. Because NMFS’s approach in the 2004 BiOp pro-
duces the opposite result, it is inconsistent with the ESA and
its accompanying regulations, and cannot stand.

needs. See Northwest Power Act, 16 U.S.C. § 839 (providing for purposes
of 1980 Pacific Northwest Electric Power Planning and Conservation Act
“to be construed in a manner consistent with applicable environmental
laws”); ALCOA, 175 F.3d at 1163 (“The Northwest Power Act’s goal of
providing economical power, however, does not supplant the BPS’s obli-
gation to comply with environmental mandates.”); Confederated Tribes &
Bands of the Yakima Indian Nation v. FERC, 746 F.2d 466, 473 (9th Cir.
1984) (finding Northwest Power Act places “fish and wildlife concerns on
an equal footing with power production”).
4292     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
                              B

   [5] The district court also properly concluded that the 2004
BiOp impermissibly failed to incorporate degraded baseline
conditions into its jeopardy analysis. The 2004 BiOp initially
evaluated the effects of the proposed action as compared to
the reference operation, rather than focusing its analysis on
whether the action effects, when added to the underlying
baseline conditions, would tip the species into jeopardy. Like
the district court, we cannot approve NMFS’s insistence that
it may conduct the bulk of its jeopardy analysis in a vacuum.

   [6] To “jeopardize the continued existence of” means “to
engage in an action that reasonably would be expected,
directly or indirectly, to reduce appreciably the likelihood of
both the survival and recovery of a listed species in the wild
by reducing the reproduction, numbers, or distribution of that
species.” 50 CFR § 402.02; 16 U.S.C. § 1536(a)(2). NMFS
argues that, under this definition, it may satisfy the ESA by
comparing the effects of proposed FCRPS operations on listed
species to the risk posed by baseline conditions. Only if those
effects are “appreciably” worse than baseline conditions must
a full jeopardy analysis be made. Under this approach, a listed
species could be gradually destroyed, so long as each step on
the path to destruction is sufficiently modest. This type of
slow slide into oblivion is one of the very ills the ESA seeks
to prevent.

   [7] Requiring NMFS to consider the proposed FCRPS
operations in their actual context does not, as NMFS argues,
effectively expand the “agency action” at issue to include all
independent or baseline harms to listed species. Nor does it
have the effect of preventing any federal action once back-
ground conditions place a species in jeopardy. To “jeopar-
dize” — the action ESA prohibits — means to “expose to loss
or injury” or to “imperil.” Either of these implies causation,
and thus some new risk of harm. Likewise, the suffix “-ize”
in “jeopardize” indicates some active change of status: an
           NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO                4293
agency may not “cause [a species] to be or to become” in a
state of jeopardy or “subject [a species] to” jeopardy. Ameri-
can Heritage Dictionary of the English Language (4th ed.).
Agency action can only “jeopardize” a species’ existence if
that agency action causes some deterioration in the species’
pre-action condition.

   Even under the so-called aggregation approach NMFS
challenges, then, an agency only “jeopardize[s]” a species if
it causes some new jeopardy. An agency may still take action
that removes a species from jeopardy entirely, or that lessens
the degree of jeopardy. However, an agency may not take
action that will tip a species from a state of precarious sur-
vival into a state of likely extinction. Likewise, even where
baseline conditions already jeopardize a species, an agency
may not take action that deepens the jeopardy by causing
additional harm.

   [8] Our approach does not require NMFS to include the
entire environmental baseline in the “agency action” subject
to review.9 It simply requires that NMFS appropriately con-
sider the effects of its actions “within the context of other
existing human activities that impact the listed species.”
ALCOA, 175 F.3d at 1162 n.6 (citing 50 C.F.R. § 402.02’s
definition of the environmental baseline). This approach is
consistent with our instruction (which NMFS does not chal-
lenge) that “[t]he proper baseline analysis is not the propor-
tional share of responsibility the federal agency bears for the
decline in the species, but what jeopardy might result from the
agency’s proposed actions in the present and future human
and natural contexts.” Pac. Coast Fed’n, 426 F.3d at 1093
(emphasis added).
  9
    We note that under NMFS’s jeopardy approach, the environmental
baseline serves only as a point of reference to determine the net effects of
a narrowly-defined action. Thus, whether an action is included in the base-
line determines whether its impacts are considered at all in the agency’s
basic jeopardy analysis.
4294     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
   [9] The current existence of the FCRPS dams constitutes an
“existing human activity” which is already endangering the
fishes’ survival and recovery. See ALCOA, 175 F.3d at 1162
n.6 (citing 50 C.F.R. § 402.02). Although we acknowledge
that the existence of the dams must be included in the envi-
ronmental baseline, the operation of the dams is within the
federal agencies’ discretion under both the ESA and the
Northwest Power Act, 16 U.S.C. § 839. Any proposed agency
action must be evaluated in the contest of this baseline in
order to properly determine whether the proposed actions will
jeopardize the listed fishes.

                               C

   [10] The district court also properly concluded that the
2004 BiOp was legally deficient because its jeopardy analysis
did not adequately consider the proposed actions’ impacts on
the listed species’ chances of recovery. ESA prohibits agency
action that is “likely to jeopardize the continued existence of”
any listed species. 16 U.S.C. § 1536(a)(2). The regulations
interpret this to prohibit any agency action “that reasonably
would be expected, directly or indirectly, to reduce apprecia-
bly the likelihood of both the survival and recovery of a listed
species in the wild.” 50 CFR § 402.02 (emphasis added).

   NMFS contends that this restriction bars only actions that
will both (1) reduce appreciably the likelihood of survival and
(2) reduce appreciably the likelihood of recovery, and that its
views are entitled to deference under Chevron U.S.A., Inc. v.
NRDC, 467 U.S. 837 (1984). Under this interpretation,
though, NMFS need only consider effects on survival: if there
is no appreciable reduction of survival odds, there can never
be jeopardy, even if recovery is completely impossible.
Because a species can often cling to survival even when
recovery is far out of reach, NMFS’s interpretation of the
jeopardy regulation reads “and recovery” entirely out of the
text. This disregard for the statutory and regulatory context
deserves no deference.
         NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO        4295
   Although we “will generally afford deference to the agen-
cy’s construction of its own regulation,” this deference is not
absolute. Regents of Univ. of Cal. v. Shalala, 82 F.3d 291, 294
(9th Cir. 1996); see also Webber v. Crabtree, 158 F.3d 460,
461 (9th Cir. 1998) (“Although we accord a high degree of
deference to an agency’s interpretation of its own regulation,
that interpretation cannot be upheld if it is plainly erroneous
or inconsistent with the regulation.”). Rather, the court con-
ducts a “two-pronged analysis.” Shalala, 82 F.3d at 294. First,
considering the “plain language of the regulation,” we must
inquire whether “[t]he words of the regulation [are] reason-
ably susceptible to the construction placed upon them [by the
agency], both on their face and in light of their prior interpre-
tation and application.” Id. (internal quotation marks omitted).
Second, we review the agency’s construction “in relation to
the governing statute,” to determine whether it is “consistent
with and in furtherance of the purposes and policies embodied
in the Congressional statute” authorizing the regulation. Id.
NMFS’s interpretation of the jeopardy regulation fails at both
stages.

   [11] As in Gifford Pinchot Task Force v. United States Fish
& Wildlife Service, 378 F.3d 1059 (9th Cir. 2004), we con-
clude that the jeopardy regulation requires NMFS to consider
both recovery and survival impacts. Gifford Pinchot held that
NMFS was required to consider recovery as well as survival
impacts in evaluating adverse modification of critical habitat,
rejecting the agency’s narrow interpretation of regulatory lan-
guage identical to that presented here. Specifically, we held
that “[b]ecause it is logical and inevitable that a species
requires more critical habitat for recovery than is necessary
for the species survival, the regulation’s singular focus
becomes ‘survival.’ ” Gifford Pinchot, 378 F.3d at 1069. Con-
cluding that ESA’s critical habitat provisions required protec-
tion — and thus agency consideration — of both survival and
recovery needs, we held that the regulation’s “singular focus”
on survival violated the ESA. Id. at 1070.
4296       NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
   We need not consider whether the ESA itself requires
NMFS to consider both survival and recovery (as Gifford Pin-
chot held was the case for critical habitat), because we con-
clude that the text of the jeopardy regulation is not
“reasonably susceptible” to the “survival only” interpretation
NMFS now gives it. As a general rule applicable to both stat-
utes and regulations, textual interpretations that give no sig-
nificance to portions of the text are disfavored. Hart v.
McLucas, 535 F.2d 516, 519 (9th Cir. 1979). NMFS’s reading
of the jeopardy regulation inexplicably reads “and recovery”
out of the text. Also, NMFS’s interpretation is unreasonable
“in light of [the regulation’s] prior interpretation and applica-
tion.” See Shalala, 82 F.3d at 294 (internal quotation marks
omitted). Until issuing the 2004 BiOp, the agency had consis-
tently interpreted 50 C.F.R. § 402.02 as requiring a joint anal-
ysis of both survival and recovery impacts. Nothing in its
prior approach indicates that NMFS may simply avoid any
consideration of recovery impacts, as it admits it has done here.10

   When the regulation was issued in its current form, in June
1986, the preamble and comments on the revised regulations
offered a reasonable explanation for the regulation’s use of
the phrase “reduce appreciably the likelihood of both the sur-
vival and recovery of a listed species.” 51 Fed. Reg. 19,934
(June 3, 1986). The comments noted that there was some con-
troversy over the reference to “both the survival and recov-
ery,” but explained that the standard referred to a “joint
survival and recovery concept.” Id. (emphasis added). The
1986 revisions added the word “both” “to emphasize that,
except in exceptional circumstances, injury to recovery alone
would not warrant [a jeopardy finding].” Id. (emphasis
  10
     Although the 2004 BiOp does not discuss recovery, NMFS argues that
it “implicitly” analyzed recovery in its survival analysis. However, we
may not consider this post hoc justification, or infer “an analysis that is
not shown in the record.” Gifford Pinchot, 278 F.3d at 1074; see also Pac.
Coast Fed’n, 426 F.3d at 1091 (“[W]e cannot infer an agency’s reasoning
from mere silence,” and “an agency’s action must be upheld, if at all, on
the basis articulated by the agency.”) (internal quotation marks omitted).
           NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO               4297
added). Thus, “in exceptional circumstances,” injury to recov-
ery prospects alone could result in a jeopardy finding. The
comments expressly acknowledged that “significant impair-
ment of recovery efforts or other adverse effects [besides sur-
vival impacts] which rise to the level of ‘jeopardizing’ the
‘continued existence’ of a listed species can also be the basis
for issuing a ‘jeopardy’ opinion.” Id. In order to recognize
such effects, and to apply the proper “joint survival and
recovery concept,” NMFS must analyze effects on recovery
as well as effects on survival.11

   We also note that this view of survival and recovery, as
intertwined needs that must both be considered in a jeopardy
analysis, is consistent with NMFS’s jeopardy analysis in ear-
lier BiOps, particularly the 1995 and 2000 BiOps in this very
dispute. Those BiOps plainly considered analysis of the listed
species’ prospects for recovery as essential to the jeopardy
analysis, and included repeated reference to, and measure-
ment of, the relevant species’ chances to survive proposed
operations “with an adequate potential for recovery.” NMFS
has offered no rational explanation for its sudden decision to
omit recovery needs from the 2004 BiOp’s analysis. Because
the agency has so dramatically changed its approach, its new
interpretation is entitled to less deference than we might usu-
ally give. Cardoza-Fonseca, 480 U.S. at 446 n.30.

   [12] The question before us is not whether, on the merits,
recovery risks in fact require a jeopardy finding here, but
whether, as part of the consultation process, NMFS must con-
duct a full analysis of those risks and their impacts on the
listed species’ continued existence. Although recovery
impacts alone may not often prompt a jeopardy finding,
  11
    We recognize that “these concepts [survival and recovery] are gener-
ally considered together in analyzing effects, and it is difficult to draw
clear-cut distinctions.” 51 Fed. Reg. 19,934. However, the agency may not
resolve this difficulty by ignoring recovery needs and focusing entirely on
survival, as it has claimed the right to do here.
4298      NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
NMFS’s analytical omission here may not be dismissed as
harmless: the highly precarious status of the listed fishes at
issue raises a substantial possibility that considering recovery
impacts could change the jeopardy analysis.12 The only rea-
sonable interpretation of the jeopardy regulation requires
NMFS to consider recovery impacts as well as survival.

                                  D

   [13] In sum, the district court correctly held that the 2004
BiOp’s analysis was structurally flawed. It properly deter-
mined that the agency may not use a hypothetical “reference
operation” in its jeopardy analysis to exclude from the pro-
posed action’s impacts the effects of related operations the
agency deems “nondiscretionary.” The district court also
properly concluded that the 2004 BiOp impermissibly failed
to incorporate degraded baseline conditions into its jeopardy
analysis. Finally, the district court correctly determined that
the 2004 BiOp was legally deficient because its jeopardy
analysis did not adequately consider the proposed action’s
impacts on the listed species’ chances of recovery.

   At its core, the 2004 BiOp amounted to little more than an
analytical slight of hand, manipulating the variables to
achieve a “no jeopardy” finding. Statistically speaking, using
the 2004 BiOp’s analytical framework, the dead fish were
really alive. The ESA requires a more realistic, common sense
examination. For these reasons, the district court’s rejection of
the 2004 BiOp’s jeopardy analysis was entirely correct.

                                  III

   [14] The district court properly held that NMFS violated
the ESA by failing to ensure that proposed FCRPS operations
  12
    We note, for example, the 2004 BiOp’s statement that the Snake River
sockeye’s continued near-total dependence on hatchery programs for sur-
vival may seriously harm its chances of recovery.
            NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO              4299
would not destroy or adversely modify critical habitat for any
listed fish. Specifically, the district court found inadequate
NMFS’s analysis of impacts on the recovery value of critical
habitat for Snake River Spring/Summer Chinook salmon,
Snake River Fall Chinook salmon, and Snake River sockeye
salmon, the only three listed species with designated critical
habitat at the time the 2004 BiOp was issued.13

   [15] The ESA mandates that federal agencies take no action
that will result in the “destruction or adverse modification” of
designated critical habitat. 16 U.S.C. § 1536(a)(2). “Destruc-
tion or adverse modification” is defined as follows:

       a direct or indirect alteration that appreciably dimin-
       ishes the value of critical habitat for both the sur-
       vival and recovery of a listed species. Such
       alterations include, but are not limited to, alterations
       adversely modifying any of those physical or biolog-
       ical features that were the basis for determining the
       habitat to be critical.

50 C.F.R. § 402.02. This regulation, as interpreted by NMFS,
“reads the ‘recovery’ goal out of the adverse modification
inquiry,” and requires agencies to consider alterations that
appreciably diminish the value of critical habitat for either
survival or recovery. Gifford Pinchot, 378 F.3d at 1069.

   The 2004 BiOp used two different methods to evaluate crit-
ical habitat impacts, apparently due to post-Gifford Pinchot
uncertainty, and found no adverse modification under either
method. The first method, the “Environmental Baseline
Approach,” used the BiOp’s environmental baseline14 as a ref-
erence point. This method considers first whether “the pro-
  13
     Critical habitat designations for nine other listed species were with-
drawn after a successful 2002 court challenge.
  14
     This indirectly raises the same baseline-definition problems addressed
above.
4300       NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
posed action is likely to alter an essential feature of the
critical habitat compared to the condition under the environ-
mental baseline,” and, if it does, “whether that alteration
appreciably diminishes the value of critical habitat for sur-
vival or recovery.” As an alternative, NMFS also used a “List-
ing Conditions Approach,” which is similar, but uses as a
reference point habitat conditions at the time the species was
listed. Because the “Listing Conditions” approach clearly
does not satisfy ESA, we consider only the “Environmental
Baseline” approach in any detail.15

   [16] We agree with the district court that NMFS’s adverse
modification analysis did not adequately consider recovery
needs and was therefore deficient under Gifford Pinchot, 378
F.3d at 1069. We agree with the district court that NMFS’s
critical habitat determination was arbitrary and capricious
because it (1) did not adequately consider the proposed
action’s short-term negative effects in the context of the
affected species’ life cycles and migration patterns, (2) relied
on uncertain long-term improvements to critical habitat to off-
set certain short-term degradation, and (3) concluded that the
species’ critical habitat was sufficient for recovery without
adequate information to make that determination.

                                    A

 [17] The 2004 BiOp disregarded our clear instruction that
NMFS “must consider near-term habitat loss to populations
  15
     Not surprisingly, the Listing Conditions approach found no hint of a
problem with any of the proposed action. The Listing Conditions approach
is entirely divorced from the statutory instruction to avoid “adverse modi-
fication,” 16 U.S.C. § 1536(a)(2), importing a reference point that is
incompatible with the statute’s plain language and clear purpose of
improving endangered species’ condition over time. Nothing in the stat-
ute’s language or purpose supports NMFS’s chosen meaning of “adverse
modification below conditions existing at time of listing.” Neither “ad-
verse” nor “modification” ordinarily implies measurement against condi-
tions at some remote point in the past.
           NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO                4301
with short life cycles.” Pac. Coast Fed’n, 426 F.3d at 1094
(rejecting agency’s no-jeopardy finding for failure to provide
adequate, reasoned analysis of short-term impacts on endan-
gered coho salmon). As we noted there, “[i]t is not enough to
provide water for [endangered fish] to survive in five years,
if in the meantime, the population has been weakened or
destroyed by inadequate water flows.” Id. at 1095. Here, the
2004 BiOp explicitly found that the proposed FCRPS opera-
tions would have significant negative impacts on each
affected species’ critical habitat through 2010, in spite of
planned mitigation efforts. However, it did not adequately
demonstrate that these impacts would not affect the fishes’
survival and recovery, in light of their short life-cycles and
current extremely poor habitat conditions.16

   First, for the Snake River Spring/Summer Chinook, NMFS
found that the proposed action would have a significant nega-
tive impact on “the essential habitat feature of safe passage in
the juvenile migration corridor” for five years, despite mitiga-
tion efforts. In spite of this, NMFS found no adverse modifi-
cation for the Spring/Summer Chinook “based primarily on
the determination that, by the sixth year of this proposed
action, the condition of critical habitat in the juvenile migra-
tion corridor would be improved.” In other words, NMFS
found that there was no adverse modification because it
ignored the short-term adverse modification and considered
only long-term impacts. This does not satisfy ESA’s require-
ments. See Gifford Pinchot, 378 F.3d at 1069.

  Effects on Snake River sockeye are both more uncertain
and likely more severe. NMFS found that Snake River sock-
eye will also suffer “significant” impairment of the safe pas-
sage feature of critical habitat between 2004 and 2009, and
  16
     As in Pacific Coast Federation, we cannot simply take the agency’s
word that the listed species will be protected under the planned operations:
“If this were sufficient, the NMFS could simply assert that its decisions
were protective and so withstand all scrutiny.” 426 F.3d at 1092.
4302     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
lower survival for the entire duration of the proposed action.
As with the Snake River Spring/Fall Chinook, despite the cur-
rent “extremely poor” habitat conditions, NMFS found no
adverse modification of sockeye habitat based mainly on its
conclusion that, by the sixth year of proposed operations, hab-
itat quality would be either unchanged or reduced by an
amount not considered “appreciable.” This also fails to satisfy
our rule in Gifford Pinchot.

   In addition, NMFS relied heavily on the fact that “almost
all” of the Snake River sockeye found in the FCRPS today are
hatchery fish, and that hatchery operations could replace fish
lost under the proposed FCRPS operation. At the same time,
NMFS explicitly found that continued reliance on the hatch-
ery operation itself threatens the sockeyes’ chances of recov-
ery: “The longer this ESU relies on the captive broodstock
program for its existence, the greater the risks associated with
domestication and loss of genetic diversity, which will
increase the difficulty of reestablishing a viable population in
the ESU’s native habitat.” However, NMFS’s adverse modifi-
cation analysis failed to consider the impact of prolonging the
sockeyes’ hatchery dependence on its eventual prospects for
recovery.

                               B

   [18] To the extent that NMFS found habitat conditions
would improve during the 2010-2014 period of operations, it
relied significantly on future installation of Removable Spill-
way Weirs (a type of surface bypass collector) and other
structural improvements to aid safe passage. We agree with
the district court that such improvements may not be included
as part of the proposed action without more solid guarantees
that they will actually occur. Although NMFS maintains that
“[t]he agencies are committed to installation of surface bypass
collectors at all dams where feasible, as exemplified by the
recent installation of such structures at three dams,” we are
not persuaded that even a sincere general commitment to
           NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO              4303
future improvements may be included in the proposed action
in order to offset its certain immediate negative effects, absent
specific and binding plans. Although the record does reflect
a general desire to install structural improvements where fea-
sible, it does not show a clear, definite commitment of
resources for future improvements.17 Also, while some struc-
tural improvements have already been made, these may nei-
ther substitute for nor guarantee the future improvements that
NMFS found would improve fish habitat starting from 2010
through 2014.

                                    C

   [19] The district court correctly held that NMFS inappro-
priately evaluated recovery impacts without knowing the in-
river survival levels necessary to support recovery. It is only
logical to require that the agency know roughly at what point
survival and recovery will be placed at risk before it may con-
clude that no harm will result from “significant” impairments
to habitat that is already severely degraded. Requiring some
attention to recovery issues does not improperly import ESA’s
separate recovery planning provisions into the section 7 con-
sultation process. Rather, it simply provides some reasonable
assurance that the agency action in question will not apprecia-
bly reduce the odds of success for future recovery planning,
by tipping a listed species too far into danger.

                                   IV

   Finally, NMFS contends that the district court’s October 7,
2005, remand order exceeded the scope of its authority. Spe-
cifically, NMFS challenges the remand order’s requirements
that NMFS provide a “failure report” to the district court if it
  17
     It may well be that the agencies lack the power to guarantee the
improvements in question. However, if this is the case, the proper course
is to exclude them from the analysis and consider only those actions that
are in fact under agency control or otherwise reasonably certain to occur.
4304     NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
believes the agencies will be unable to develop a proposed
action that avoids jeopardy to listed fish within the district
court’s remand timeframe, and that the agency consult with
interested tribes and states during the remand. We have juris-
diction over this challenge because the remand order is
included in the district court’s amended final judgment under
Rule 54(b) entered on October 24, 2005. “The district court
has broad latitude in fashioning equitable relief when neces-
sary to remedy an established wrong,” Alaska Ctr. for the
Env’t v. Browner (“ACE”), 20 F.3d 981, 986 (9th Cir. 1994),
and we review the district court’s choice of remedies within
that scope for abuse of discretion, United States v. Alisal
Water Corp., 431 F.3d 643, 654 (9th Cir. 2005). We conclude
that the disputed portions of the remand order are within the
district court’s authority, so long as they are enforced as writ-
ten, and not as a broader license to direct the remand proceed-
ings.

  The “failure report” requirement falls within the district
court’s power. The remand order’s precise command is as fol-
lows:

    If, at any time during the remand period, NOAA
    concludes the Action Agencies are not making suffi-
    cient progress in developing a proposed action and/
    or RPA that avoids jeopardy to the listed species,
    NOAA shall advise the court of that circumstance
    immediately and shall issue a ‘failure report’ similar
    to that required in the 2000 BiOp, that advises the
    court and the parties of those additional measures,
    including the breaching of dams, that may be neces-
    sary to achieve a valid no-jeopardy finding.

NMFS does not challenge the district court’s requirement of
regular status reports every 90 days during the remand, and
such reporting requirements are clearly permissible. See Tele-
comms. Research & Action Ctr. v. FCC, 750 F.2d 70, 81
(D.C. Cir. 1984). Nor does NMFS challenge the court’s dis-
         NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO        4305
cretionary authority to impose a deadline for the remand pro-
ceedings. See Nat’l Org. of Veterans’ Advocates v. Sec’y of
Veterans Affairs, 260 F.3d 1365, 1381 (Fed. Cir. 2001) (set-
ting 120-day deadline for rule-making). The “failure report”
requirement here is a reasonable combination of a time limit
and progress reports and is appropriate under the circum-
stances of this case. The district court reasonably found that
such specific direction was necessary in light of the agency’s
conduct on earlier remands and the urgency of the listed spe-
cies’ situation.

  The other requirement NMFS challenges is this:

    During the remand period, [the agencies] shall col-
    laborate with the sovereign entities, including the
    States of Idaho, Montana, Oregon, and Washington,
    and the Tribes who are parties or amici in the action
    . . . to achieve the goals of:

    (a) Developing items to be included in the pro-
    posed action; and

    (b) Clarifying policy issues and reaching agree-
    ment or narrowing the areas of disagreement on sci-
    entific and technical information.

This collaboration requirement is justified both as a reason-
able means to ensure that NMFS complies with ESA’s man-
date that agencies “use the best scientific and commercial data
available” in their decision-making, 16 U.S.C. § 1536(a)(2),
and as a reasonable procedural restriction given the history of
the litigation. However, we note that the requirement does not
on its face direct the substance of the agencies’ actions on
remand, and may not be interpreted to do so.

  Courts may, at least in some circumstances, require specific
actions from an agency on remand. In ACE, 20 F.3d at 986-
87, which addressed the EPA’s persistent failure to establish
4306       NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO
total maximum daily loads for Alaskan waters as required by
the CWA, we approved significant, but carefully tailored,
control of the EPA’s proceedings on remand. We held that
“[i]n tailoring the relief granted, the district court correctly
recognized that in order to bring about any progress toward
achieving the congressional objectives of the CWA, the EPA
would have to be directed to take specific steps.” Id. at 986.
Such discretion is also necessary here.

   Of course, there are also limits to the courts’ power to con-
trol an agency’s conduct on remand. See FPC v. Transconti-
nental Gas Pipe Line Corp., 423 U.S 326, 333 (1976) (finding
that the court of appeals had “overstepped the bounds of its
reviewing authority” by ordering a direct evidentiary report to
the court). In ACE, we noted with approval that “the [district]
court was careful to leave the substance and manner of
achieving [CWA] compliance entirely to the EPA.” ACE, 20
F.3d at 986-87. Thus, the district court’s remedy fell within
its “traditional, equitable, and interstitial role to fashion [a]
remedy” for the agencies’ dereliction of their statutory duties.
Id. at 987.

   [20] Here, FCRPS operations have been the subject of per-
petual litigation since the fish in question were first listed in
the early 1990s. The analytical approach of the 2004 BiOp,
issued under court order after a remand in 2003, broke sharply
from NMFS’s previous analyses in the 1995 and 2000 BiOps,
and did so in ways that lacked any reasonable foundation in
ESA’s statutory mandates. We hold that on this record,
requiring consultation with states and tribes constitutes a per-
missible procedural restriction rather than an impermissible
substantive restraint.18 The district court’s chosen remedy was
“reasonably calculated to remedy an established wrong,” and
was not an abuse of discretion. NRDC v. Sw. Marine, Inc.,
  18
    We find far less intrusion into agency procedures here than in the situ-
ation the Second Circuit found impermissible in Sierra Club v. United
States Army Corps of Engineers, 701 F.2d 1011 (2d Cir. 1983).
         NAT’L WILDLIFE FEDERATION v. STATE OF IDAHO       4307
236 F.3d 985, 1000 (9th Cir. 2000) (internal quotation marks
omitted) (approving remedy to enforce compliance with
CWA permit issued by agency, and finding no encroachment
on agency’s authority).

                               V

  In short, after a careful review of the record, we affirm the
judgment of the district court. Its rejection of the 2004 BiOp
was entirely appropriate, and it did not abuse its discretion in
entering the remand order.

  AFFIRMED.
