                  FOR PUBLICATION
  UNITED STATES COURT OF APPEALS
       FOR THE NINTH CIRCUIT

PACIFIC COAST FEDERATION OF             
FISHERMEN’S ASSOCIATIONS;
INSTITUTE FOR FISHERIES RESOURCES;
NORTHCOAST ENVIRONMENTAL
CENTER; KLAMATH FOREST
ALLIANCE; OREGON NATURAL
RESOURCES COUNCIL; THE
WILDERNESS SOCIETY;
WATERWATCH OF OREGON;
DEFENDERS OF WILDLIFE;
HEADWATERS,
              Plaintiffs-Appellants,
                and
MIKE THOMPSON, Representative,                No. 03-16718
                           Plaintiff,
                 v.                            D.C. No.
                                            CV-02-02006-SBA
UNITED STATES BUREAU OF                        OPINION
RECLAMATION; NATIONAL MARINE
FISHERIES SERVICE,
             Defendants-Appellees,
KLAMATH WATER USERS
ASSOCIATION; TULELAKE IRRIGATION
DISTRICT; WILLIAM HEINEY; AMOS
HOYT,
            Defendant-Intervenors-
                          Appellees,
                 v.
YUROK TRIBE; HOOPA VALLEY
TRIBE,
              Plaintiff-Intervenors.
                                        
                            14293
14294       PACIFIC COAST v. BUREAU   OF   RECLAMATION
         Appeal from the United States District Court
            for the Northern District of California
        Saundra B. Armstrong, District Judge, Presiding

                    Argued and Submitted
         February 16, 2005—San Francisco, California

                    Filed October 18, 2005

   Before: Dorothy W. Nelson, William A. Fletcher, and
            Raymond C. Fisher, Circuit Judges.

                Opinion by Judge D.W. Nelson
14296      PACIFIC COAST v. BUREAU   OF   RECLAMATION


                         COUNSEL

Kristen L. Boyles (argued), and Michael Mayer (on the
briefs), Earthjustice, Seattle, Washington, for the appellants.

John A. Bryson (argued), and David C. Shilton, S. Jay Govin-
dan (on the briefs), Department of Justice, Washington, D.C.,
for the appellees.
           PACIFIC COAST v. BUREAU   OF   RECLAMATION    14297
Robin Lee Rivett (argued), and Andrew T. Lloyd, Pacific
Legal Foundation, Sacramento, California; Russell C. Brooks,
Pacific Legal Foundation, Bellevue, Washington (on the
briefs), for defendant-intervenor-appellees Klamath Water
Users Association et al.


                         OPINION

D.W. NELSON, Circuit Judge:

   Eight organizations representing environmental and fish-
eries interests sued the United States Bureau of Reclamation
(BOR) and the National Marine Fisheries Service (NMFS) for
injunctive and declaratory relief, alleging violations of the
federal Endangered Species Act (ESA), 16 U.S.C. §§ 1531-
1544. The lawsuit concerned the federal government’s efforts
to operate an irrigation project in accordance with its respon-
sibilities under the ESA to protect the threatened Southern
Oregon/ Northern California Coast (SONCC) coho salmon
and its habitat. On appeal, the Pacific Coast Federation of
Fishermen’s Associations and the other plaintiffs (collectively
referred to as Pacific Coast) contend that the government’s
actions are arbitrary and capricious, in violation of the ESA.
They argue that the government’s plan employs a phased
approach but does not analyze how the first two phases,
encompassing eight years of a ten year plan, will avoid jeop-
ardy to the coho salmon. Appellees, the federal agencies, and
defendant/intervernor Klamath Water Users Association
(KWUA) urge that the plan reflects the agency’s best judg-
ment in the face of scientific uncertainty and contains suffi-
cient analysis to support the NMFS’s conclusion that its
proposed action will avoid jeopardy to the coho. The district
court struck down parts of the NMFS’s original plan, but
upheld the eight years of short-term measures that are the sole
issue in this appeal. We conclude that the short-term measures
are arbitrary and capricious, and remand the case to the dis-
14298        PACIFIC COAST v. BUREAU       OF   RECLAMATION
trict court for the issuance of injunctive relief in accordance
with this opinion.

               I. Legal and Factual Background

  A. The Endangered Species Act

   This case requires us to review a biological opinion (BiOp)
prepared by the NMFS as part of its obligations under the
ESA to ensure that federal actions in the operation of a federal
irrigation project do not jeopardize anadromous fish species.1
We begin with a brief overview of the ESA and the consulta-
tion process so that the legal and procedural context of our
review is clear.

   The ESA obligates federal agencies “to afford first priority
to the declared national policy of saving endangered species.”
Tenn. Valley Auth. v. Hill, 437 U.S. 153, 185 (1978). Section
7 of the ESA establishes a consultation process to insure that
“any action authorized, funded, or carried out by [a federal]
agency . . . is not likely to jeopardize the continued existence
of any endangered . . . or threatened species or result in the
destruction or adverse modification of [critical] habitat . . . .”
16 U.S.C. § 1536(a)(2). When an action has the potential to
affect an anadromous fish species, the NMFS has responsibil-
ity for consultation.

   Before undertaking any action, the federal agency must
determine whether any threatened or endangered species
might be present in the area of the proposed action. Id. at
(c)(1). If such a species might be present, the agency must
prepare a biological assessment to determine whether the spe-
cies is likely to be affected by the proposed action. Id. The
  1
    “Anadromous” fish species, like the SONCC coho salmon, spend por-
tions of their lives in both fresh and salt water. All such species spawn in
fresh water. See http://www.nmfs.noaa.gov/habitat/habitatprotection/
anadfish/index.htm.
           PACIFIC COAST v. BUREAU   OF   RECLAMATION     14299
biological assessment serves as a basis for the formal consul-
tation with the NMFS.

  During formal consultation, the NMFS must prepare a bio-
logical opinion, or BiOp, which determines the effects that the
proposed action might have on the listed species or its critical
habitat. Id. at (b)(3)(A). If the NMFS determines that the pro-
posed activity might cause jeopardy to a listed species or
adversely modify its habitat, the agency must suggest “rea-
sonable and prudent alternatives” (RPAs) to the proposed
action that would avoid jeopardy or adverse modification of
habitat. Id. The implementing regulation defines RPAs as:

    alternative actions identified during formal consulta-
    tion that can be implemented in a manner consistent
    with the intended purpose of the action, that can be
    implemented consistent with the scope of the Federal
    agency’s legal authority and jurisdiction, that is eco-
    nomically and technologically feasible, and that the
    Director believes would avoid the likelihood of jeop-
    ardizing the continued existence of listed species or
    resulting in the destruction or adverse modification
    of critical habitat.

50 C.F.R. § 402.02. In this case, the NMFS determined that
the BOR’s proposed activities — the operation of a federal
irrigation system — would cause jeopardy to the SONCC
coho salmon, and it therefore developed the RPA that is at the
heart of this appeal.

  B. The Klamath River Basin and the Klamath Project

   The Klamath River basin straddles northern California and
southern Oregon. At the center of this case is a fish population
that is unique to the region, the SONCC coho salmon. The
SONCC coho spawns and matures in the main stem and tribu-
taries of the Klamath River.
14300        PACIFIC COAST v. BUREAU     OF   RECLAMATION
   The Klamath River basin supports a variety of agricultural
activities that are possible in part because of irrigation water
from the Klamath Project, a federally funded irrigation system
established in the early 20th century. The Klamath Project
consists of a number of dams and reservoirs. The coho salmon
population populates the main stem and tributaries of the
Klamath River until its passage is blocked by the Iron Gate
Dam, which is the component of the Klamath Project closest
to the Pacific Ocean. The flows past the Iron Gate dam into
the Klamath River determine to a great extent the quantity of
water available in the river. At issue in this appeal are the
NMFS’s determinations regarding the quantity of water that
the BOR must release from behind the Iron Gate Dam to the
Klamath River.

   A number of factors make water management especially
difficult in the Klamath River Basin. See generally Pac. Coast
Fed’n of Fisherman’s Ass’ns v. BOR, 138 F.Supp. 2d 1228,
1230-31 (N.D. Cal. 2001) (“PCFFA I”); Kandra v. United
States, 145 F.Supp. 2d 1192, 1196-98 (D. Or. 2001). The pri-
mary reservoir is relatively shallow, and is home to popula-
tions of two different species of endangered fish, known as
suckers, that require maintenance of certain minimum water
levels. Kandra, 145 F.Supp 2d at 1196-98. Marshlands in two
national wildlife refuges are irrigated by the Klamath Project
to create bird habitat. Id. at 1196. Several tribes in the area
have treaty rights to Klamath River fish, and the Department
of Interior must meet the United States’ fiduciary duty to
maintain these resources. Id. at 1197. Numerous farmers have
contracts for irrigation water that the BOR must supply each
growing season. PCFFA I, 138 F.Supp. 2d at 1231. The
Klamath Basin has been the focus of previous cases dealing
with endangered species conservation and water use and man-
agement.2
  2
   See, e.g., Bennett v. Spear, 520 U.S. 154 (1997) (regarding endangered
suckers; holding related to standing); Klamath Water Users Protective
             PACIFIC COAST v. BUREAU       OF   RECLAMATION          14301
  C. The SONCC Coho Salmon

   The SONCC coho ranges throughout the North Pacific
Ocean. During the twentieth century, populations of coho
declined substantially in California and Oregon. The BiOp
states that the number of wild coho in the Klamath River is
“extremely low, and has been declining for most of the past
two decades.” The population of the SONCC coho is esti-
mated to have declined from an estimated range of 50,000 to
125,000 wild coho in the 1940s to fewer than 6,000 wild coho
in 1996. The SONCC coho salmon was listed as a threatened
species under the ESA in 1997.3 The major factors threatening
the SONCC coho include logging, grazing, dams, and water
withdrawal for irrigation. The facts below are drawn from the
NMFS’s description of the SONCC coho’s life cycle and
assessment of its habitat needs in the BiOp.

   The SONCC coho has a three-year life cycle, spending half
its life in fresh water and half in salt water. Coho eggs typi-
cally hatch in March. Coho fry emerge two weeks after hatch-

Ass’n v. Patterson, 204 F.3d 1206 (9th Cir. 1999) (addressing contract
issues relating to water allocation; holding that the BOR’s obligations
under the ESA allow it to override rights of water users); Moden v. U. S.
Fish & Wildlife Serv., 281 F.Supp. 2d 1193 (D. Or. 2003) (holding that
delisting of the fish residing in reservoir is not supported); Kandra, 145
F.Supp. 2d at 1192 (upholding the BOR’s implementation of conservation
measures against challenge by irrigators); PCFFA I, 138 F.Supp. 2d at
1228 (overturning the BOR’s operation plan for failure to consult with the
NMFS as required by the ESA).
   3
     The NMFS recently reconfirmed the SONCC coho’s status as a threat-
ened species in response to a lawsuit challenging the listing of a different
subgroup of coho salmon. See Alsea Valley Alliance v. Evans, 161 F.Supp.
2d 1154 (D.Or. 2001), appeal dismissed for lack of jurisdiction sub nom.
Alsea Valley Alliance v. Dep’t of Commerce, 358 F.3d 1181 (9th Cir.
2004). See Endangered and Threatened Species: Final Listing Determina-
tion for 16 ESUs of West Coast Salmon, and Final 4(d) Protective Regula-
tions for Threatened Salmonid ESUs, 70 Fed. Reg. 37,160, 37,193 (June
28, 2005) (to be codified at 50 C.F.R. pts 223 and 224).
14302      PACIFIC COAST v. BUREAU   OF   RECLAMATION
ing, and spend up to 15 months in fresh water. The fry’s
preferred habitat is shallow areas near stream banks. Fry
become smolt after 15 months and migrate to the sea between
March and June. After about three years, coho return to the
same streams in which they were born to spawn, migrating
upstream between September and February, and spawning
between November and January. Sufficient water flows must
be available in the main stem of the Klamath River to enable
the fish to migrate upstream during September through Febru-
ary and to migrate downstream at maturity from March
through June. Habitat conditions in the main stem are also
important because degraded habitat or low flow in tributaries
causes coho fry to seek additional habitat in the main stem.

   During the spring months, March through June, newly
hatched fry need shaded habitat near stream banks and
migrating smolt need sufficient water in the river to leave trib-
utaries and migrate to the sea. The BiOp makes clear that
NMFS considers these the most critical months in which to
provide an adequate amount of water in the main stem
because of the needs of the fry and smolt. The NMFS reports
that studies in other basins show that increased flow during
these months resulted in “lower mortality due to migratory
delay, predation, and exposure to potentially poor main stem
habitat conditions.” During the summer months, the primary
concerns are to ensure that there is sufficient habitat in the
main stem for juveniles displaced from tributaries by poor
water quality or competition, and that the water temperatures
are sufficiently cool. From October through February, the pri-
mary concern is maintaining sufficient water in the main stem
for upstream migration and access to tributaries. The NMFS
notes that in fall and winter water often flows freely past the
Iron Gate Dam, resulting in “uncontrolled releases” of water.

  D. Prior Scientific Assessments of the Klamath River Basin

   The BiOp at issue here is the product of several iterations
of scientific study and review, including two previous BiOps
           PACIFIC COAST v. BUREAU   OF   RECLAMATION     14303
and two government studies of the basin that reached conflict-
ing conclusions. The NMFS issued the first BiOp for the
Klamath Project in 1999. At this time, a government-
commissioned scientific assessment of the flow needs of
anadromous species in the Klamath River basin was released.
Known as Phase I of the “Hardy Report,” that assessment pro-
vided interim recommendations on flow levels needed to sup-
port aquatic life.

   In 2001, a severe drought limited water availability in the
basin. Kandra, 145 F.Supp. 2d at 1198. Two BiOps, one for
the SONCC coho and one for the other endangered fish that
inhabit the reservoir, called for maintenance of high levels of
water in both the reservoir and the main stem of the river. The
BOR complied with the BiOps and, as a result, did not deliver
water to irrigators. Significant agricultural losses followed.

   Following the dry 2001 irrigation season, the National
Research Council (NRC) was asked by the Department of
Interior to “independently review the scientific and technical
validity of the government’s biological opinions.” The NRC
Report, released in February 2002, found that there was not
scientific support for the flow recommendations in the
NMFS’s coho salmon BiOp. The report reviewed existing sci-
entific literature and data on coho in the Klamath River basin.
It concluded that “incremental depletions beyond those that
are reflected in the recent historical record could be accom-
plished only with increased risk to coho salmon. At the same
time, the available information provides little support for ben-
efits presumed to occur through the increase of flows beyond
those of the last decade.” The conclusion questioned the
validity of the 2001 BiOp. The NMFS requested clarification
from the NRC, which responded that “the NRC committee did
not conclude that NMFS must be wrong in its recommenda-
tions on main-stem flows.” In its BiOp, the NMFS attributed
the conclusions of the NRC report to “lack of information on
distribution and abundance of coho . . . and the lack of studies
focused on coho and factors limiting its population in the
14304        PACIFIC COAST v. BUREAU    OF   RECLAMATION
Klamath River Basin.” The NMFS did not dismiss the NRC
Report, but it did not adopt its conclusions in full.

   Phase II of the “Hardy Report” was released in draft form
in November 2001. Its conclusions about flow requirements
conflict with those of the NRC.4 The Phase II report, calling
itself the “best available science,” used site-specific habitat
modeling and estimates of the unimpaired flows in the main
stem to arrive at a recommendation for flows for each river
reach. The report determined that flows lower than approxi-
mately 1000 cubic feet per second (cfs) during the late sum-
mer would likely expose the SONCC coho to dangerously
high water temperatures, thereby increasing the risk of harm
to the species.

  E. The Current Biological Opinion

   The process through which the current BiOp was created
began when the BOR prepared its most recent long-range bio-
logical assessment in February 2002. The BOR proposed
maintaining a flow regime that varied river flows by “water
year type,” meaning that less water need be provided in years
in which less precipitation has fallen in the region, reflecting
natural variations in river flows. For each type of “water year”
(for instance, dry or wet), the BOR used the historic average
water flow for that type over the previous ten-year period to
set its goals by type of year for the next ten years of operation.
Any available water beyond that needed to meet the goal
would be allotted for irrigation. In addition, the BOR would
establish a water bank to store 100,000 total acre feet of water
to meet the flow requirements.

   When the NMFS reviewed the proposed operations plan in
the BOR’s biological assessment to prepare the current BiOp,
it determined that if the Klamath Project were operated as the
  4
    The NRC report did not consider the Hardy Phase II report in making
its findings because it was in draft form.
           PACIFIC COAST v. BUREAU   OF   RECLAMATION    14305
BOR intended, it would cause jeopardy to the SONCC coho
and adversely modify its critical habitat. The NMFS was con-
cerned that the BOR’s use of the minimum flow over the past
ten years as the planning target for establishing monthly flows
would drive down the average flow in the Klamath River
from below its ten-year average, which would lead to adverse
effects to habitat and individual coho in the main stem.
Among the NMFS’s concerns were that decreased flows
would reduce the amount of suitable coho fry habitat, make
it more difficult for smolt to migrate downstream, and prevent
adult coho from accessing tributaries during their upstream
migration. In the BiOp, therefore, the NMFS developed an
RPA to replace the BOR’s proposed plan of operations. The
RPA is the subject of the instant appeal.

   The RPA covers operations for the Klamath Project from
2002 until 2012. An organizing principle of the RPA is that
the BOR should bear responsibility only for the share of water
losses caused by the Klamath Project. Because the project irri-
gates 57 percent of land in the basin, the RPA provided that
the BOR would provide 57 percent of the water needed for
the coho, and establish an intergovernmental workgroup to
“develop the other 43 [percent] of the flows.” The RPA per-
mitted the BOR to use a “water bank” to provide its share of
the water.

   The RPA is divided into three phases. Phase I, lasting from
2002 through 2005, calls upon the BOR to gradually develop
resources in the water bank, begin development of the inter-
governmental task force, and conduct scientific studies. Dur-
ing Phase I, the BOR must provide, at a minimum, the flows
that were established in its biological assessment, supplement-
ing those flows in the spring and/or summer by use of the
water bank.

 Phase II, which is to last from 2006 to 2010, requires the
BOR increase the water bank to 100,000 acre feet and provide
14306      PACIFIC COAST v. BUREAU   OF   RECLAMATION
the greater of the 57 percent share or the flows proposed in
the biological assessment.

   During Phase III, which encompasses water years 2010 and
2011, NMFS anticipates that 100 percent of the salmon’s flow
needs will be met through the BOR’s 57 percent share and the
43 percent contribution from unspecified sources. The discus-
sion in this section explains how the NMFS calculated the
long-term flow levels that it believed were necessary to avoid
the likelihood of jeopardy to the coho. The agency determined
that the species could withstand a 20 percent reduction in hab-
itat from what it would have received under an unimpaired
flow regime, and calculated the flows that must be provided
to achieve this quantity of habitat. The agency also deter-
mined that in summer months, flows of less than 1000 cfs
would threaten coho in the main stem with dangerously high
water temperatures, and required maintenance of flows of
1000 cfs or greater.

  F. The Proceedings Below

   The litigation below began with an unsuccessful request by
Pacific Coast for a temporary restraining order in response to
interim measures initiated before the BiOp was finalized. The
NMFS completed the final BiOp on May 31, 2002. After
33,000 chinook, coho, and steelhead salmon died in an unex-
plained fish kill in the Klamath River between September 20
and 27, 2002, Pacific Coast filed an amended complaint
against the federal defendants.

   The parties filed cross-motions for summary judgment, on
which the district court ruled on July 14, 2003. The district
court overturned a significant aspect of the RPA, finding the
requirement that the BOR provide only 57 percent of the
long-term flows to be arbitrary and capricious. The court con-
cluded that the NMFS had inappropriately considered the
effects of actions that were not “reasonably certain to occur”
when it determined that the coho would receive 100 percent
           PACIFIC COAST v. BUREAU   OF   RECLAMATION     14307
of the flows through a collaborative process. The federal
defendants do not appeal this ruling, nor does Pacific Coast
challenge the long-term flow levels established for Phase III.

   At issue in this appeal is the district court’s determination
that Phases I and II of the RPA, or the short-term measures,
were not arbitrary and capricious. Pacific Coast challenged
the flow levels established in Phases I and II, arguing that the
Phase I flows were the same flows rejected by the NMFS as
insufficient in its review of the BOR’s biological assessment
and that the Phase II flows provided only 57 percent of the
flows that the NMFS recognized the coho required. The court
acknowledged that the RPA “does not explicitly engage in an
analysis of what effect the water flows in Phases I and II, with
the addition of the available water from the water bank, will
have on the coho salmon or their critical habitat.” However,
the court found that the NMFS had determined that providing
less water during the short-term would not jeopardize the
coho. The court reasoned:

    [T]he statements by the NMFS do not reflect a con-
    clusion that it is necessary to consistently provide
    100% of the long-term target flows throughout each
    phase of the program in order to avoid jeopardy to
    the salmon. In fact, implicit in the RPA’s phased
    approach is the ultimate conclusion that maintaining
    a percentage of the long-term flow rates with the
    additional water provided by the water bank during
    Phase I and II will not jeopardize the salmon or
    adversely modify their critical habitat, provided that
    the long-term flow rates are eventually met by Phase
    III of the program.

   The court ordered the NMFS to revise its BiOp to address
the deficiencies identified in Phase III of the RPA, but speci-
fied that the BiOp and the RPA would remain in effect until
a revised BiOp was issued. Pacific Coast timely filed the
instant appeal. The federal defendants initially cross-appealed
14308      PACIFIC COAST v. BUREAU   OF   RECLAMATION
the decision to strike down Phase III, but voluntarily dis-
missed the appeal prior to briefing.

                        II. Discussion

  A. Standard of Review

   The district court’s grant of summary judgement is
reviewed de novo. Buono v. Norton, 371 F.3d 543, 545 (9th
Cir. 2004). The BiOp is a final agency decision subject to
review under § 706 of the Administrative Procedure Act
(APA). Bennett v. Spear, 520 U.S. 154, 178-79 (1997). Such
decisions may be set aside if “arbitrary, capricious, an abuse
of discretion, or otherwise not in accordance with law.” 5
U.S.C. § 706(2)(A). Review under this standard is narrow; the
reviewing court may not substitute its judgment for that of the
agency. Marsh v. Ore. Natural Res. Council, 490 U.S. 360,
375-76 (1989). We will sustain an agency action if the agency
has articulated a rational connection between the facts found
and the conclusions made. Motor Vehicle Mfrs. Ass’n v. State
Farm Mutual Auto. Ins. Co., 463 U.S. 29, 43 (1983). “Even
when an agency explains its decision with ‘less than ideal
clarity,’ a reviewing court will not upset the decision on that
account ‘if the agency’s path may reasonably be discerned.’ ”
Alaska Dep’t of Envt’l Conserv. v. EPA, 540 U.S. 461, 497
(2004) (quoting Bowman Transp., Inc. v. Arkansas-Best
Freight Sys., Inc., 419 U.S. 281, 286 (1974)).

   While our review is deferential, our inquiry must “be
searching and careful.” Marsh, 490 U.S. at 378. We must
determine whether the agency’s decision was “based on a
consideration of the relevant factors and whether there has
been a clear error of judgment.” Id. Courts defer to the evalu-
ations of agencies when the evidence presents conflicting
views because “an agency must have discretion to rely on the
reasonable opinions of its own qualified experts even if, as an
original matter, a court might find contrary views more per-
suasive.” Id. However:
           PACIFIC COAST v. BUREAU   OF   RECLAMATION     14309
    if the agency has relied on factors which Congress
    has not intended it to consider, entirely failed to con-
    sider an important aspect of the problem, offered an
    explanation for its decision that runs counter to the
    evidence before the agency, or is so implausible that
    it could not be ascribed to a difference in view or the
    product of agency expertise

the agency action may be overturned as unlawful. Motor
Vehicle Mfrs. Ass’n, 463 U.S. at 43.

  B. The RPA’s Short-Term Flow Requirements Are Arbitrary
  and Capricious

   The BiOp and its RPA govern the BOR’s actions for ten
years. However, the BOR is not required to provide the full
quantity of water that the NMFS deems necessary for the
coho until year nine. During the first eight years of implemen-
tation, the BOR is required to provide at most 57 percent of
the species’ total water needs. We must determine whether the
NMFS’s decision to delay the provision of the full quantity of
water for eight years is supported by the record before us. We
conclude that it is not. The BiOp contains no analysis of the
effect on the SONCC coho of the first eight years of imple-
mentation of the RPA, and thus we cannot sustain the agen-
cy’s decision.

  1. Phases I and II Cannot be Sustained on the Basis of
  Implicit Reasoning

   The district court reasoned that the agency had implicitly
considered, in imposing the three-phase RPA, that all phases
would ensure against jeopardy to the coho. The federal defen-
dants assert that the district court properly found that the
adoption of the phased approach implicitly recognized the
agency’s determination that such an approach would avoid
jeopardy.
14310      PACIFIC COAST v. BUREAU   OF   RECLAMATION
   [1] We cannot adopt the district court’s reasoning. It is a
basic principle of administrative law that the agency must
articulate the reason or reasons for its decision. See, e.g.,
Motor Vehicle Mfrs., 463 U.S. at 43; SEC v. Chenery Corp.,
332 U.S. 194, 196-97 (1947); Gifford Pinchot Task Force v.
U.S. Forest Serv., 378 F.3d 1059, 1072 n.9 (9th Cir. 2004);
Ariz. Cattle Growers Ass’n. v. U.S. Fish & Wildlife Serv., 273
F.3d 1229, 1236 (9th Cir. 2001). Although “ ‘a decision of
less than ideal clarity’ ” may be upheld “ ‘if the agency’s path
may reasonably be discerned,’ we cannot infer an agency’s
reasoning from mere silence. . . . Rather, ‘an agency’s action
must be upheld, if at all, on the basis articulated by the agency
itself.’ ” Beno v. Shalala, 30 F.3d 1057, 1073-74 (9th Cir.
1994) (quoting Motor Vehicle Mfrs., 463 U.S. at 43, 50, 57).
The agency is obligated to “articulate[ ] a rational connection
between the facts found and the choices made.” NRDC v.
Dep’t of Interior, 113 F.3d 1121, 1126 (9th Cir. 1997) (inter-
nal citations omitted).

   [2] Thus, the RPA cannot be sustained, as the district court
held, by reliance on the agency’s unstated assumptions about
the effects of Phases I and II. In a recent ESA case, we
rejected a similar assertion that an agency “implicitly recog-
nized the central role of recovery in its critical habitat analy-
sis,” because when reviewing a biological opinion, we rely
only “on what the agency actually said” in the BiOp to deter-
mine whether the agency considered the appropriate factors.
Gifford Pinchot Task Force, 378 F.3d at 1072 & n.9 (internal
quotation marks omitted). Indeed, in an ESA case where we
approved the use of a phased approach, we noted specifically
that the agency’s analysis revealed that it “considered the rel-
evant factors and reasonably found that the [species] could
survive the loss of habitat” during a four-year period in which
an agency gradually acquired replacement habitat. S.W. Ctr.
for Biological Diversity v. BOR, 143 F.3d 515, 523 (9th Cir.
1998). To permit an agency to “implicitly” conclude that a
species would not be jeopardized by a proposed activity, and
not require the agency to articulate a basis for its conclusion,
           PACIFIC COAST v. BUREAU   OF   RECLAMATION     14311
“would reject the bedrock concept of record review.” Gifford
Pinchot Task Force, 378 F.3d at 1072 n.9. We thus examine
the BiOp in its entirety to determine whether “the agency’s
path” to its conclusion that Phases I and II of the RPA would
avoid jeopardy to the coho “may reasonably be discerned.”
Motor Vehicles Mfrs., 463 U.S. at 43.

  2. The Analysis of Phases I and II does not Provide a
  Reasoned Explanation for the Agency’s Decision

   [3] Our review of the BiOp has been “searching and care-
ful,” as we have attempted to identify the basis for the agen-
cy’s conclusions that the coho will not be jeopardized during
the first two phases of the RPA. Marsh, 490 U.S. at 378. The
agency’s analysis of the beneficial effects of the long-term
flows, in combination with the absence of analysis of the
effects of the substantially lower short-term flows, lead us to
conclude that the reasoning behind the agency’s plan cannot
be reasonably discerned. In fact, the agency’s decision
appears to conflict with the analysis in the BiOp. The BiOp
contains no analysis that suggests that the agency determined
that, during the eight-year period encompassed by Phases I
and II, the coho would receive sufficient protection against
jeopardy under the proposed plan of operations.

   Even the sections of the BiOp relied on by the federal
defendants in their briefing and at oral argument to support
their assertion that the agency provides “extensive analysis”
of the effect of the RPA over the full ten-year period provide
only minimal support for their argument. Almost all of the
analysis in the RPA is concentrated on justification of the
long-term flow requirement, and there is little substance to the
discussions of Phases I and II.

   The federal defendants assert that the BiOp “explains
NMFS’ rationale for concluding that the short-term and long-
term measures will avoid the likelihood of jeopardy.” The
section that defendants cite (1) describes the RPA; (2) dis-
14312       PACIFIC COAST v. BUREAU   OF   RECLAMATION
cusses how the RPA attempts to strike a balance between the
NRC and Hardy Reports; and (3) details negotiations between
the NMFS and the BOR on development of the RPA. The
closest this section comes to providing any analysis that the
RPA will not jeopardize the coho is the following:

    Given that coho are primarily tributary spawners,
    that main-stem spawning and rearing habitat is likely
    not limiting at the current population size, and recog-
    nizing the importance of the main stem as a migra-
    tory corridor for adult and down-stream migrating
    smolts, NMFS thinks that the approach contained in
    this RPA sufficiently addresses the adverse effects of
    the Klamath Project to the SONC[C] coho salmon
    and its critical habitat by incrementally improving
    smolt migration habitat over conditions that would
    be achieved in the [biological assessment] and those
    suggested in the NRC interim report.

Although this language suggests, as the district court indi-
cated, that the agency believed that the RPA would avoid
jeopardy to the coho, this assertion alone is insufficient to sus-
tain the BiOp and the RPA. The agency essentially asks that
we take its word that the species will be protected if its plans
are followed. If this were sufficient, the NMFS could simply
assert that its decisions were protective and so withstand all
scrutiny.

   [4] The federal defendants urge that the NMFS provided “a
detailed evaluation of the effect of each phase of the RPA.”
Although some of the discussion on the referenced pages is
“detailed,” it does not discuss the effects of each phase on
SONCC coho. The section on Phase I, for example, contains
an extensive discussion of why the water year types in BOR’s
proposal should be modified to better reflect natural variabil-
ity, but does not describe the effect that the modification
would have on salmon or its habitat.
             PACIFIC COAST v. BUREAU     OF   RECLAMATION         14313
   Phase I also establishes the water bank requirement. It pro-
vides that each year, an increasing volume of water must be
delivered via the water bank. The BiOp explains that this
“should improve instream flows” and “could be used to . . .
improve downstream smolt survival and improve coho fry
survival.” This statement supports the NMFS’s assertion that
it believed the RPA would protect the coho, but it does not
show how the addition of water from the bank will affect
water levels or water temperature in the main stem of the
river.

   The discussion of Phase II is even more conclusory. The
section describes how the NMFS arrived at the BOR’s 57 per-
cent responsibility, but it does not analyze how providing only
57 percent of the long-term flows will avoid jeopardy to the
coho.5 Rather than explain how providing 57 percent of the
long-term flows will avoid jeopardy to the salmon, the discus-
sion of Phase II explains that the Project provides irrigation
to 57 percent of the land in the upper Klamath Basin. The
flow level appears to be justified solely on the basis of the
Klamath Project’s share of responsibility for the water use.
The proper baseline analysis is not the proportional 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. See Aluminum Co. of Am. v. Adm’r, Bonneville
Power Admin., 175 F.3d 1156, 1162 n.6 (9th Cir. 1999); see
also Nat’l Wildlife Fed’n v. Coleman, 529 F.2d 359, 373-74
(5th Cir. 1976). Nothing in this section shows that the agency
considered the effect on the coho of providing only slightly
   5
     The district court overturned the 57 percent requirement only of the
long-term flows, holding that the RPA dependence on the participation of
third parties to provide the remaining 43 percent of the flows needed to
avoid jeopardy was not appropriate because the beneficial effects of the
proposed collaborative effort were not “reasonably certain to occur.” 50
C.F.R. § 402.02 (defining “indirect effects” as those “reasonably certain
to occur”).
14314      PACIFIC COAST v. BUREAU   OF   RECLAMATION
more than half of the long-term flow needs for the first eight
years of implementation.

   When we compare the analysis of Phases I and II to that
provided in the discussion of the long-term flow levels estab-
lished in Phase III, the deficiencies of the Phase I and II anal-
yses become more apparent. In the section establishing the
long-term flow levels, the BiOp detailed by season how the
coho will benefit from increased flows. The agency estimated
the amount of habitat that would have been available under an
unimpaired flow regime. From this, the NMFS determined
that, in order to avoid jeopardy during the critical March
through June period, the BOR must provide a water flow that
would result in a loss of only 20 percent of the habitat that
would have been available under unimpaired flow conditions.
During the summer months, when increased water tempera-
ture is of great concern, the BiOp determined that a minimum
flow of 1000 cfs must be provided to avoid the adverse effects
of high water temperatures.

   Notably, during dry and critically dry years, under the
regime proposed in Phases I and II, the flows could be sub-
stantially lower during the summer. For instance, during a dry
water year, in Phase I, the BOR must provide between 542
and 749 cfs of water in the months of July through September
(and less in a critically dry year), while in Phase II the flows
could be as low as 570 cfs (57 percent of the full 1000 cfs).
Nothing in the discussion of Phases I and II explains why the
coho population would not face jeopardy from these signifi-
cantly lower flows during the summer months of the first
eight years of implementation.

   [5] The discussion of the long-term flows in Phase III con-
tains the analysis that supports the long-term flow recommen-
dations. It is clear how the agency determined that the flow
levels would improve coho habitat and increase the likelihood
of the species’ survival. By contrast, the discussion of the
flows called for in Phases I and II does not explain how the
            PACIFIC COAST v. BUREAU   OF   RECLAMATION     14315
agency determined that these flows would be protective. The
kind of analysis provided in the discussion of Phase III is con-
spicuously absent from the agency’s discussion of Phases I
and II.

   [6] The scant analysis in Phases I and II is more troubling
when we consider the duration of each Phase and the three-
year life cycle of the SONCC coho. Phase I spans 2002
through 2005; Phase II lasts from 2006 to 2009. Phase III —
when the coho will be provided with 100 percent of NMFS’s
estimated flow needs — lasts only two years, from 2010 to
2011. Phases I and II occupy eight years of the ten-year plan.
Five full generations of coho will complete their three-year
life cycles — hatch, rear, and spawn — during those eight
years. Or, if there is insufficient water to sustain the coho dur-
ing this period, they will not complete their life cycle, with
the consequence that there will be no coho at the end of the
eight years. If that happens, all the water in the world in 2010
and 2011 will not protect the coho, for there will be none to
protect. It is not sufficient for the agency to impose these
flows without explaining how the flows will protect critical
habitat and ensure that sufficient water is in the main stem for
coho to survive during these first five generations.

   In a previous ESA case involving salmon, we stressed that
the agency must consider near-term habitat loss to populations
with short life cycles, and faulted the agency for only consid-
ering the impact of its actions over a ten-year period. Pac.
Coast Fed. of Fisherman’s Ass’ns. v. NMFS, 265 F.3d 1028,
1037-38 (9th Cir. 2001). “Given the importance of the near-
term period on listed species survival it is difficult to justify
NMFS’s choice not to assess degradation over a time frame
that takes into account the actual behavior of the species in
danger.” Id. at 1038. Here, the agency’s assertion that it deter-
mined that the RPA would not cause jeopardy to the coho is
difficult to accept when it is evident that the agency “entirely
failed to consider an important aspect of the problem” —
namely, that the species it must protect will experience five
14316      PACIFIC COAST v. BUREAU   OF   RECLAMATION
generational cycles over the time span governed by Phases I
and II of the RPA. Motor Vehicle Mfrs. Ass’n, 463 U.S. at 43.
An agency does not avoid the likelihood of jeopardy to a
listed species when it disregards the life cycle of the species
in crafting the measures designed to protect it. Nor can the
agency provide only partial protection for a species for sev-
eral generations without any analysis of how doing so will
affect the species.

   A repeated theme of the federal defendants’ argument is
that the BiOp represents the agency’s best judgment in the
face of the conflicting conclusions of the NRC report and the
Hardy Phase II study. Defendants assert that the science is
uncertain, and thus “there are no specific quantitative target
flows that determine jeopardy because there is no specific sci-
entific information relating coho salmon population size to
specific quantities of main-stem habitat as represented by
flow.” However, Phase III clearly presents “specific quantita-
tive target flows” that the NMFS concluded were necessary to
avoid jeopardy. The federal defendants ask us to disregard
their quantitative conclusions in favor of their assertions that
the first eight years of the RPA will avoid jeopardy.

   [7] The federal defendants argue that the agency is not
required to provide quantitative analysis, and that the analysis
for Phases I and II reflects NMFS’s qualitative determination
that the RPA would not jeopardize the SONCC coho. How-
ever, this court has held that “while the [NFMS] can draw
conclusions based on less than conclusive scientific evidence,
it cannot base its conclusions on no evidence.” Nat’l Ass’n. of
Home Builders v. Norton, 340 F.3d 835, 847 (9th Cir. 2003)
(internal citations omitted); see also Bennett, 520 U.S. at 176
(“The obvious purpose of the requirement that each agency
‘use the best scientific and commercial evidence available’ is
to ensure that the ESA not be implemented haphazardly, on
the basis of speculation or surmise.”) (quoting 16 U.S.C.
§ 1536 (a)(2)). In Phase III of the RPA, NMFS establishes
necessary flow levels; for Phases I and II, the RPA reduces
            PACIFIC COAST v. BUREAU   OF   RECLAMATION     14317
those flows by nearly half, but does not explain why this
reduction does not jeopardize the coho.

   We remand the case to the district court for the issuance of
appropriate injunctive relief. See Sierra Club v. Marsh, 816
F.2d 1376, 1384 (9th Cir. 1987) (holding that plaintiff was
entitled to injunctive relief if the agency violated a substantive
or procedural provision of the ESA). We emphasize that the
interim injunctive relief should reflect the short life-cycle of
the species. It is not enough to provide water for the coho to
survive in five years, if in the meantime, the population has
been weakened or destroyed by inadequate water flows.

                        CONCLUSION

   [8] We conclude that the RPA is arbitrary and capricious
because it fails to analyze the effects of eight of ten years of
the proposed action on the SONCC coho, a species that has
a three-year life cycle. The agency has not demonstrated that
it has followed the mandate of the ESA to avoid the likeli-
hood of jeopardy to the SONCC coho. We remand to the dis-
trict court to craft appropriate injunctive relief.

  REVERSED and REMANDED for the issuance of
injunctive relief.
