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• Miccosukee Tribe of Indians of Florida v. United States, 566 ...

• Sierra Forest Legacy v. Sherman, 646 F.3d 1161 (9th Cir. 2011)

• San Luis & Delta-Mendota Water Authority v. United States, 672 ...

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

• SAN LUIS & DELTA-MENDOTA WATER AUTH. v. Salazar, 666 F. ...

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• 97 Cal. Daily Op. Serv. 7390, 97 Daily Journal D.A.R. ...

• Aluminum Company of America Columbia Aluminum Corporation Columbia Falls

Aluminum ...

• American Rivers v. US Army Corps of Engineers, 271 F. ...

• American Textile Mfrs. Institute, Inc. v. Donovan, 452 U.S. 490 ...

• Animal Defense Council Friends of the Desert Friends of the ...

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Natural Resources Defense Council v. Kempthorne, 506 F. Supp. 2d 322 - CourtListener.... Page 1 of 63

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Natural Resources Defense Council v. Kempthorne, 506 F.

Supp. 2d 322 (D. Cal. 2007)

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District Court, D. California

Date Filed: May 25th, 2007

Status: Precedential

Citations: 506 F. Supp. 2d 322

Docket Number: 1:05-CV-01207 OWW (TAG)

Fingerprint: 9427e876b649a88520725e022d4549428d79cb53

506 F.Supp.2d 322 (2007)

NATURAL RESOURCES DEFENSE

COUNCIL, et al., Plaintiffs,

v.

Dirk KEMPTHORNE, in his official capacity

as Secretary of the Interior, et al., Defendants,

California Department of Water Resources,

Defendant-Intervenor,

State Water Contractors, DefendantIntervenor,

San Luis & Delta-Mendota Water Authority, et

al., Defendant-Intervenors.

No. 1:05-CV-01207 OWW (TAG).

United States District Court, E.D. California.

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May 25, 2007.

*323 *324 *325 *326 *327 Andrea Arnold Treece, Deborah S. Reames, Michael Ramsey Sherwood,

Earthjustice Legal Defense Fund Incorporated, Oakland, CA, Hamilton Candee, Katherine Scott

Poole, Natural Resources Defense Council, Trent William Orr, Law *328 Office of Trent W. Orr, San

Francisco, CA, for Plaintiffs.

James A. Maysonett, Keith W. Rizzardi, Department of Justice, Wildlife and Marine Resources

Section, Washington, DC, for Defendants.

Daniel Joseph O'Hanlon, Clifford W. Schulz, Kronick, Moskovitz, Tiedemann & Girard, Jon David

Rubin, Diepenbrock Harrison, Brenda Washington Davis, Christian Charles Scheuring, John Robert

Hewitt, Ronda Azevedo Lucas, California Farm Bureau Federation, Deborah A. Wordham, California

Attorney General's Office, Andrew Morrow Hitchings, Somach, Simmons & Dunn, Kevin M.

O'Brien, Steven Paul Saxton, Downey Brand LLP, Sacramento, CA, Christopher H. Buckley, Jr.,

Gibson Dunn and Crutcher, Washington, DC, Gregory K. Wilkinson, Anthony Leon Beaumon, Best

Best & Krieger, LLP, Riverside, CA, Mark Diaz Servino, Best Best and Krieger LLP, Irvine, CA,

Clifford Thomas Lee, California Attorney General's Office, San Francisco, CA, J. Mark Atlas, Frost

Krup and Atlas, Willows, CA, for Defendants-Intervenors.

ORDER GRANTING IN PART AND DENYING IN PART PLAINTIFFS' MOTION FOR

SUMMARY JUDGMENT (DOC. 231/232)

OLIVER W. WANGER, District Judge.

I. INTRODUCTION

This case concerns the effect on a threatened species of fish, the Delta smelt (Hypomesus

transpaeificus)

[1], of the coordinated operation of the federally-managed Central Valley Project

("CVP") and the State of California's State Water Project ("SWP"), among the world's largest water

diversion projects. Both projects divert large volumes of water from the California Bay (SacramentoSan Joaquin) Delta ("Delta") and use the Delta to store water.

For over thirty years, the projects have been operated pursuant to a series of cooperation agreements.

In addition, the projects are subject to ever-evolving statutory, regulatory, contractual, and judiciallyimposed requirements. The Long-Term Central Valley Project and State Water Project Operations

Criteria and Plan ("2004 OCAP" or "OCAP") surveys how the projects are currently managed in light

of these evolving circumstances. At issue in this case is a 2005[2] biological opinion ("BiOp"), issued

by the United States Fish and Wildlife Service ("FWS" or "Service") pursuant to the Endangered

Species Act ("ESA"), which concludes that current project operations described in the OCAP and

certain planned future actions will not jeopardize the continued existence of the Delta smelt or

adversely modify its critical habitat.

The Delta smelt is a small, slender-bodied fish endemic to the Delta. Historically, Delta smelt could

be found throughout the Delta. Although abundance data on the smelt indicates that the population

has fluctuated wildly in the past, it is undisputed that, overall, the population has declined

significantly in recent years, to its lowest reported volume in fall 2004.

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In this case, Plaintiffs, a coalition of environmental and sportfishing organizations, challenge the 2005

BiOp's no jeopardy and no adverse modification findings as arbitrary, capricious, and contrary to law

under the Administrative Procedure Act, 5 U.S.C. §§ 702 et seq. Before the court for decision is

Plaintiffs' motion for summary judgment. Among other things, Plaintiffs *329 allege that the BiOp

fails to consider the best available science, relies upon uncertain (and allegedly inadequate) adaptive

management processes to monitor and mitigate the potential impacts of the OCAP, fails to

meaningfully analyze whether the 2004 OCAP will jeopardize the continued existence of the Delta

smelt, fails to consider the OCAP's impact upon previously designated critical habitat, and fails to

address the impacts of the entire project.

Separate opposition briefs were filed by the Federal Defendants (Doc. 242), the Department of Water

Resources ("DWR") (Doc. 246), and the State Water Contractors ("SWC") (Doc. 241), along with a

final brief filed collectively by San Luis & Delta-Mendota Water Authority, Westlands Water

District, and the California Farm Bureau Federation ("the San Luis Parties") (Doc. 247).

II. THE ENDANGERED SPECIES ACT

A recent Ninth Circuit opinion in National Wildlife Federation v. National Marine Fisheries Service,

481 F.3d 1224 (9th Cir.2007) [hereinafter "NWF v. NMFS"], succinctly summarizes the relevant

provisions of the ESA:

The ESA requires federal agencies to "insure that any action authorized, funded, or

carried out by such agency . . . is not likely to jeopardize the continued existence of any

endangered species or threatened species or result in the destruction or adverse

modification of [designated critical] habitat. . . ." 15 U.S.C. § 1536(a)(2). The ESA

imposes a procedural consultation duty whenever a federal action may affect an ESAlisted species. Thomas v. Peterson, 753 F.2d 754, 763 (9th Cir.1985). To that end, the

agency planning the action, usually known as the "action agency," must consult with the

consulting agency. This process is known as a "Section 7" consultation. The process is

usually initiated by a formal written request by the action agency to the consulting

agency. After consultation, investigation, and analysis, the consulting agency then

prepares a biological opinion. See generally Ariz. Cattle Growers' Ass'n v. U.S. Fish &

Wildlife, 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 consulting

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 opinion, 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 agency's opinion on "whether the

action is likely to jeopardize the continued existence of a listed species or result in the

destruction or adverse modification of critical habitat. . . ." 50 C.F.R. § 402.14(h)(3). In

making its jeopardy determination, the consulting agency evaluates "the current status of

the listed species or critical habitat," the "effects of the action," and "cumulative effects."

Id. § 402.14(g)(2)-(3). "Effects of the 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

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private actions and other human activities in the action area" and "the anticipated impacts

of all proposed Federal projects in the action area that have already undergone formal or

early section 7 consultation." *330 Id. If the biological opinion concludes that jeopardy is

not likely and that there will not be adverse modification of critical habitat, or that there

is a "reasonable and prudent alternative[]" to the agency action that avoids jeopardy and

adverse modification and that the incidental taking of endangered or threatened species

will not violate section 7(a)(2), the consulting agency can issue an "Incidental Take

Statement" which, if followed, exempts the action agency from the prohibition on takings

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).

* * * * * *

The issuance of a biological opinion is considered a final agency action, and therefore

subject to judicial review. Bennett v. Spear, 520 U.S. 154, 178, 117 S.Ct. 1154, 137

L.Ed.2d 281 (1997); Ariz. Cattle Growers' Ass'n, 273 F.3d at 1235.

Id. at 1230.

III. FACTUAL BACKGROUND

For over thirty years the state and federal agencies charged with management of the CVP and SWP

have operated the projects in an increasingly coordinated manner pursuant to a Coordinated Operating

Agreement ("COA"). The COA, which dates to 1986, has evolved over time to reflect, among other

things, changing facilities, delivery requirements, and regulatory restrictions. The most recent

document surveying how the COA is implemented in light of these evolving circumstances is the

2004 Operating Criteria and Plan ("2004 OCAP" or "OCAP") issued June 30, 2004. (AR 489-728.)[3]

A. Overview of the 2004 OCAP.

The OCAP begins with a "Purpose of Document" section which states:

This document has been prepared to serve as a baseline description of the facilities and

operating environment of the Central Valley Project (CVP) and State Water Project

(SWP). The Central Valley Project Operations and Criteria Plan (CVP-OCAP) identifies

the many factors influencing the physical and institutional conditions and decisionmaking

process under which the project currently operates. Regulatory and legal instruments are

explained, alternative operating models and strategies described.

The immediate objective is to provide operations information for the Endangered Species

Act, Section 7, consultation. The long range objective is to integrate CVP-OCAP into the

proposed Central Valley document. It is envisioned that CVP-OCAP will be used as a

reference by technical specialists and policymakers in and outside the Bureau of

Reclamation (Reclamation) in understanding how the CVP is operated. The CVP-OCAP

includes numeric and nonnumeric criteria and operating strategies. Emphasis is given to

explaining the analyses used to develop typical operating plans for simulated hydrologic

conditions.

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All divisions of CVP are covered by this document, including the Trinity River Division,

Shasta and Sacramento Divisions, American River Division and Friant Division.

(AR 506.)[4]

The introductory chapter provides an overview of all of the physical components *331 of the CVP

and SWP (AR 507-520), as well as all of the relevant legal authorities affecting CVP operations (508-

512).

Chapter 2, explains, among other things, that water needs assessments have been performed for each

CVP water contractor, to confirm each contractor's past beneficial use in order to anticipate future

demands. (AR 521.) Chapter 2 also reviews the 1986 COA and how it is implemented on a daily basis

by Reclamation and DWR. (AR 523-25.) Also provided is a detailed overview of the "changes in

[the] operations coordination environment since 1986," which include:

Changes due to temperature control operations on the Sacramento River;

Increases in the minimum release requirements on the Trinity River;

Implementation of CVPIA 3406(b)(2) and Refuge Water Supply contracts;

Commitments made by the CVP and SWP pursuant to the Bay-Delta Accord and the

subsequent implementation of State Water Resources Control Board ("SWRCB")

Decision-1641;

The Monterey Agreement;

The Operation of the North Bay Aqueduct (which was not included in the 1986 COA).

The SWP's commitment to make up for 195,000 acre-feet of pumping lost to the CVP

due to SWRCB Decision 1485;

Implementation of the Environmental Water Account; and

Constraints imposed by various endangered species act listings, including that of the

Sacramento River Winter-Run Chinook Salmon, the Sacramento River Spring-Run

Chinook Salmon, the Steelhead Trout, and the Delta Smelt (which resulted in the

issuance of biological opinions in 1993, 1994, and 1995 concerning CVP/SWP

operations and the South Delta Temporary Barriers Biological Opinion in 2001)

(AR 525-28.) The OCAP also reviews the regulatory standards imposed by SWRCB D-1641, which

include water quality standards based on the geographic position of the 2-parts-per-thousand isohale

(otherwise known as "X2"), a Delta export restriction standard known as the export/inflow (E/I) ratio,

minimum Delta outflow requirements, and Sacramento River and San Joaquin River flow standards.

(AR 530-537.) In addition to imposing requirements, D-1641 granted the Bureau and DWR

permission to use each project's capabilities in a coordinated manner. (AR 537-38.)

This is not a complete overview of the projects' operations covered in the OCAP. Numerous

regulatory and operational changes have taken place in recent years. As the OCAP's "Purpose of

Document" section explains, the immediate objective of the OCAP is to lay out all such regulatory

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and other operational information so that ESA Section 7 consultation can proceed to evaluate how

project operations will effect the Delta smelt under various projected future conditions.

B. Applying the ESA to Project Operations.

Because endangered and/or threatened species, including the Delta smelt, reside in the area affected

by the CVP and SWP, the 2004 OCAP, administered on behalf of the federal government by the

Bureau of Reclamation ("Bureau"), must comply with various provisions of the ESA. Specifically,

prior to authorizing, funding, or carrying out any action, the acting federal agency (in this case, the

Bureau) must first consult with FWS and/or NMFS to "insure that [the] action . . . is not likely to

jeopardize the continued existence of any endangered *332 species or threatened species or result in

the destruction or adverse modification of habitat of such species which is determined . . . to be

critical. . . ." 16 U.S.C. § 1536(a)(2) [ESA § 7(a)(2)]. This form of consultation is called "formal

consultation," and concludes with the issuance of a biological opinion. 50 C.F.R. § 402.02.

Alternatively, under certain circumstances, a federal agency may pursue "early consultation," on

behalf of an agency or private party (referred to as a "prospective applicant") who will require formal

approval or authorization to undertake a project. Id. Early consultation may be requested when the

prospective applicant "has reason to believe that an endangered species or a threatened species may be

present in the area affected by this project and that implementation of such action will likely affect

such species." 50 C.F.R. § 402.11(b). The result of early consultation is a "preliminary biological

opinion," the contents of which are "the same as for a biological opinion issued after formal

consultation except that the incidental take statement provided with a preliminary biological opinion

does not constitute authority to take listed species." § 402.11(e). Subsequently, the preliminary

biological opinion may be "confirmed" after the prospective applicant applies to the federal agency

for a permit or license. Once a request for confirmation is received, the FWS must either confirm that

the preliminary biological opinion stands as the final biological opinion or must request that the

federal agency initiate formal consultation. § 402.11(f).

In this case, the 2004 OCAP BiOp[5] contemplates increases in water diversions and the construction

of new facilities in the Delta. (AR 256-271.) The maximum daily diversion rate in Clifton Court

Forebay will increase from 6,680 cubic feet per second (CFS) to 8,500 CFS (27% increase in

pumping) and eventually to 10,300 CFS (54% increase). Permanent barriers within the south Delta

will be constructed and operated. An intertie between the California Aqueduct and the Delta-Mendota

Canal will be constructed and operated. Water deliveries from the American River will be doubled.

New deliveries of CVP water to the Freeport Regional Water Project will be made. Water transfers

resulting in an annual 200,000 to 600,000 acre-feet increase in Delta exports will result. (AR 256,

339-40, 357-59, 371, 382-83, 465.)

The Bureau submitted some of these operational changes for formal consultation with FWS

concerning their impact on the Delta smelt, while other changes were subject only to early

consultation:

This biological opinion covers formal and early consultation for the operations of the

CVP and SWP. The formal consultation effects described in this biological opinion cover

the proposed 2020 operations of the CVP including the Trinity River Mainstem ROD

(Trinity ROD) flows on the Trinity River, the increased *333 water demands on the

American River, the delivery of CVP water to the proposed Freeport. Regional Water

Project (FRWP), water transfers, the long term Environmental Water Account (EWA),

the operation of the Tracy Fish Facility, and the operation of the SWP-CVP intertie. The

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effects of operations of the SWP are also included in this opinion and include the

operations of the North Bay Aqueduct, the Suisun Marsh Salinity Control. Gates, the

Skinner Fish Facility and water transfers.

Early consultation effects include the effects of operations of components of the South

Delta Improvement Program (SDIP). These operations include pumping of 8500 cubic

feet per second (cfs) at the SWP and Banks Pumping Plant (hereafter referred to as 8500

Banks), permanent barrier operations in the South Delta, the long term EWA, water

transfers, and CVP and SWP operational integration. There are two separate effects

sections in this biological opinion, one for Formal Consultation and one for Early

Consultation. In addition, there is an incidental take for formal consultation and a

preliminary incidental take for early consultation.

(AR 2, 248.)[6]

C. History of This Lawsuit.

On July 30, 2004, FWS issued a Biological Opinion (the "2004 OCAP BiOp"), addressing both

formal and early consultation for the above-described OCAP actions. (AR 1.)[7]

On August 4, 2004, the Ninth Circuit decided Gifford Pinchot Task Force v. United States Fish &

Wildlife Serv., 378 F.3d 1059, 1069 (9th Cir.2004), which held that the FWS's definition of "adverse

modification" to critical habitat is an impermissible interpretation of the ESA because it focuses on

whether critical habitat modifications would impact the survival of a species, effectively ignoring the

statutorily-mandated goal of "recovery." On November 4, 2004, in response to this ruling, the Bureau

requested reinitiation of consultation to address critical habitat issues.

Plaintiffs in this case, a coalition of nonprofit conservation organizations, filed suit on February 15,

2005, alleging that the 2004 OCAP BiOp was legally inadequate in light of Gifford Pinchot and

should be invalidated. (Doc. 1.) Plaintiffs named as defendants the Department of the Interior and the

FWS. (Id.)

On February 16, 2005, FWS issued an amended BiOp (the "2005 OCAP BiOp," "OCAP BiOp," or

"BiOp"), which superceded the 2004 OCAP BiOp. (AR 247.) The 2005 OCAP BiOp concludes that

the coordinated operation of the SWP and CVP, including the proposed future actions, will not

jeopardize the Delta smelt's continued existence. (AR at 469.) Although the BiOp recognizes that

existing protective measures may be inadequate, the FWS concluded that certain proposed protective

measures, including the EWA and a proposed "adaptive management" *334 protocol would provide

adequate protection. (Id.)

Since the filing of this complaint, Federal Defendants have reinitiated § 7 consultation and contend

this case should be dismissed as moot, or stayed for a voluntary remand of the 2005 BiOp without

vacatur.

Plaintiffs filed a supplemental complaint on May 20, 2005, challenging the amended BiOp on various

grounds. (Doc. 128 pt. 8.)

D. Delta Smelt Abundance.

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Smelt once were one of the most common pelagic[8] fish in the Delta, having previously occupied the

waters from "Suisun Bay and Montezuma Slough, upstream to at least Verona on the Sacramento

River, and Mossdale on the San Joaquin River." (AR 365.) Smelt abundance has "declined

irregularly" for at least the past 20 years. (AR 365-67.) FWS relies primarily upon two indices to

monitor Delta smelt abundance, calculated from the Summer Tow Net Survey ("TNS") and the Fall

Midwater Trawl ("FMWT"). (AR 366-67, 1022.) The TNS index, which measures the abundance and

distribution of juvenile Delta smelt, constitutes "one of the more representative indices because the

data have been collected over a wide geographic area (from San Pablo Bay upstream through most of

the Delta) for the longest period of time (since 1959)." (AR 370.) Since 1983, except for three years

(1986, 1993, and 1994), the TNS has remained consistently lower than ever previously recorded. (Id.)

The FMWT index, which measures the abundance and distribution of late juveniles and adult Delta

smelt from San Pablo Bay to Rio Vista on the Sacramento River and Stockton on the San Joaquin

River, is the second longest running survey (since 1967). The BiOp reviewed the FMWT trends as

follows:

Although this index has fluctuated widely (AR 9201-02, 9222), it has "declined

irregularly over the past 20 years." (AR 370-71.) Since 1983, the FMWT has registered

more low indices for more consecutive years than previously recorded. Until recently,

except for 1991, this index has declined irregularly over the past 20 years. Since 1983,

the delta smelt population has exhibited more low fall midwater trawl abundance indices,

for more consecutive years, than previously recorded. The 1994 FMWT index of 101.7 is

a continuation of this trend. This occurred despite the high 1994 summer townet index for

reasons unknown. The 1995 summer townet was a low index value of 319 but resulted in

a high FMWT index of 898.7 reflecting the benefits of large transport and habitat

maintenance flows with the Bay-Delta Accord in place and a wet year. The abundance

index of 128.3 for 1996 represented the fourth lowest on record. The abundance index of

305.6 for 1997 demonstrated that the relative abundance of delta smelt almost tripled

over last years results, and delta smelt abundance continued to rise, peaking in 1999 to an

abundance index of 863, only to fall back down to the low abundance indexes of 139 for

2002 and 213 for 2003.

(AR at 371.)

The 2004 FMWT index, which was not discussed in the BiOp, was calculated to be 74, the lowest

ever recorded. (AR 9202.) (This omission forms the basis of one of Plaintiffs' challenges to the BiOp.)

The survey was apparently released in December 2004, and was specifically cited to FWS in February

2005.

*335 At the hearing on the summary judgment motions, Federal Defendants in substance argued that

despite years of study, the abundance data for the annual Delta smelt population is fraught with

uncertainties and "not enough is known about the species" to accurately and finitely measure with

certainty the project's effects on Delta smelt. FWS maintains the one to two year life expectancy of

the smelt also contribute to this lack of certainty.

E. Relationship Between Abundance and Project Operations.

The BiOp cites several reasons for the smelt's decline. First, since the mid 1800s, mining, agricultural

use, and levee construction caused the loss of a large portion of smelt habitat. (AR at 365.) Second,

recreational boating in the Delta has resulted in the presence and propagation of "predatory non-native

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fish" and an increase in the rate of smelt erosion resulting from boat wakes. (Id.) Third, reduced water

quality "from agricultural runoff, effluent discharge and boat effluent has the potential to harm the

pelagic larvae and reduce the availability of the planctonic food source." (Id. at 366.) Finally, the

BiOp acknowledges that "delta smelt have been increasingly subject to entrainment,' upstream or

reverse flows of waters in the Delta and San Joaquin River, and constriction of low salinity habitat to

deep-water river channels of the interior Delta." (Id.) The BiOp acknowledges that these final adverse

effects are "primarily a result of the steadily increasing proportion of river flow being diverted from

the Delta by the Projects, and occasional droughts." (Id. (emphasis added).) The BiOp in no way

quantifies the contribution of each of these factors to the smelt's decline. The parties dispute the extent

to which project operations jeopardize the smelt.

F. Relationship Between Smelt and "X2."

Smelt are euryhaline (tolerant of a wide range of salinities), but generally occur in water with less

than 10-12 parts per thousand (ppt) salinity. (AR at 362.) For a large part of its life span, Delta smelt

are thought to be associated with the "freshwater edge of the mixing zone," where the salinity is

approximately 2 parts per thousand (often referred to as "X2"). (AR at 366.) The summer TNS index

increases dramatically whenever X2 is located between Chipps and Roe islands. (Id.) Whenever the

location of X2 shifts upstream of the confluence of the Sacramento and San Joaquin, either as a result

of water diversions or natural conditions, smelt abundance decreases. (Id. at 371.)

G. The Concept of "Salvage."

The BiOp's "no jeopardy" conclusion relies on the concept of "salvage," which refers generally to the

process of using mechanical devices to screen fish that would otherwise be entrained in project

facilities (e.g., pumps) into holding tanks for transport to other parts of the Delta. (See e.g., AR 321.)

Unlike many other fish species in the Delta, Delta smelt do not survive the salvage process, "either

due to stress and injury from handling, trucking and release, or from predation in or near the salvage

facilities, the release sites, or in Clifton Court Forebay." (AR at 413.) As a result, for Delta smelt,

FWS uses the terms salvage and entrainment essentially interchangeably. (See id.) ("To simplify

predictions of the difference in salvage (and by extension entrainment) between model scenarios. . . .

")[9]

Previous BiOps regarding CVP and SWP operations used salvage to set take limits. For example, the

1995 BiOp's incidental *336 take statement set take exceedence levels for Delta smelt based on "[m]

onthly average delta smelt salvage at the Federal and State Fish Facilities from 1980 to 1992 by water

year type." (AR at 11765.) Essentially, take limits were set according to how much salvage had

occurred in the past.

More recently, project managers, fisheries officials, and other experts came to the consensus that the

salvage approach was insufficient on its own. For example, one DWR biologist noted that the singular

focus on historic salvage had problems:

Higher levels of take are allowed in below normal years merely because this is what the

projects "took" historically. However, the population is more condensed in below normal

years and possibly more vulnerable to entrainment.

(AR 5532.) Experts advocated (a) further research into the relationship between the position of the

Delta smelt and environmental conditions (AR 4881); and (b) the adoption of a flexible management

approach, which would allow new information to be "folded back into the operation and conservation

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strategies." (AR 4870.) The result was a "layered" approach to managing the smelt, made up of more

protective take limits than previously imposed along with the implementation of an adaptive

management protocol.

I. Revised Take Exceedence Levels Used In the BiOp.

The BiOp includes "hard" take limits,[10] based on historic "salvage density estimates," adjusted to

account for operational constraints under the 2004 OCAP and presumed increased environmental

water flows. Separate take limits were established for formal and early consultation purposes.

The revision of the take limits began with historic catch data from periodic samples of salvaged fish.

(See AR 413.) Data about the volume of water diverted during the collection period is then used to

estimate the fish per volume of water diverted. This is referred to as the "salvage density."[11] (Id.)

Historically, salvage density varied greatly depending on whether the year was wet (above normal),

dry (below normal, dry, or critical) year. Wet and dry year data were analyzed separately. (Id.) The

estimates were then inputted into a computer modeling system, CASIM II, to estimate take under

varying assumptions about future project operations, including programs designed to improve

environmental conditions, such as the Environmental Water Account. (AR 413-14.)

Several different scenarios or "Studies" were run through CALSIM II and included in the BiOp. For

example, Study No. 1 reflects the 1995 regulatory base case, without any changes in project

operations and without the addition of any environmental water programs. Study No. 4a estimates a

take level for flow conditions planned under the operations subject to final consultation (changes to

flows in the Trinity River, future development levels, and the operation of the Freeport Regional

Water Project and the Intertie). Study 4a included flow adjustments required by D-1641 and VAMP,

along with projected CVPIA (b)(2) flows, but did not include operation of the EWA. Study No. 5a

was similar to 4a, except that it added projected *337 EWA flows. Separately, in Study No. 5,

CALSIM II simulated flow modifications projected to occur as a result of "those projects subject to

early consultation," specifically the increased pumping and permanent barriers called for in the

planned South Delta Improvement Project ("SDIP"). (AR 374, 414-19; Sommer Decl. ¶ 5.) Each

modeling scenario was run separately for various water year types (Wet, Above Normal, Below

Normal, Dry, and Critically Dry) and independently estimated take at CVP and SWP facilities.

The BiOp based its conclusions for formal consultation on the results of the Study No. 5a, and for

early consultation on the results of Study No. 5. The results of the modeling scenarios for Study No.

5a are set forth in several tables at pages 414 through 419 of the AR. The following table summarizes

the changes in estimated take for Study No. 5a, for each type of water year, relative to the 1995 base

case. In other words, the positive figures represent the number of additional smelt that will be taken

per month under formal consultation relative to the 1995 base case (Study No. 1) while negative

numbers represent how many fewer smelt will be taken per month relative to the 1995 base case.[12]

Table 1:

Summary of Results for CVP Salvage Under Study No. 5a

---------------------------------------------------------------------------

Above Below

Wet Normal Normal Dry Critically

Month Year Year Year Year Dry Year

---------------------------------------------------------------------------

Adults

December -1 -1 -3 -3 -41

January -13 -13 -12 -10 -98

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February -33 -36 +63 -60 +9

March +29 -40 -83 -19 +1

Largely Juveniles

April 0 0 -16 +5 0

May 0 0 -9017 -14469 -11652

June 0 0 0 -2910 0

July 0 +11 +7 -74 0

Net: December-March -17 -89 -35 +28 -130

Net: April-July 0 +11 -9025 -17448 -1165

---------------------------------------------------------------------------

Table 2:

Summary of Results for SWP Salvage Under Study No. 5a

---------------------------------------------------------------------------

Above Below

Wet Normal Normal Dry Critically

Month Year Year Year Year Dry Year

---------------------------------------------------------------------------

Adults

December -6 -6 -16 -15 -11

January -76 -87 -82 -87 -104

February +86 -94 0 0 +51

March +98 +91 +63 0 +2

*338

Largely Juveniles

April -60 -77 -365 -144 0

May -27188 -25933 -31122 -32083 -7269

June -1096 -129 -53 1267 0

July 0 +282 +318 +493 +175

Net: December-March +102 -95 -35 -102 -62

Net: April-July -28346 -25857 -31213 -33000 -7095

For the CVP, CALSIM II predicts significant reductions in smelt salvage during the months of

December through July in below normal and dry years, when compared to the regulatory base case.[13]

However, under certain scenarios, CVP salvage increases during other months of the year relative to

the regulatory base case, because pumping is predicted to increase during these months to make up for

water released from storage for fish protection purposes. For the SWP, salvage stays relatively level

for the months of December through March. However, salvage decreases for the months of April

through July relative to the regulatory base case.

Based on CALSIM II Study 5a, FWS calculated the amount of "combined salvage" (i.e., for both

projects) estimated under the formal consultation scenario, for each month, according to water year

type. The BiOp rounded the numbers up to the nearest 100 and used those figures to set incidental

take limits by water year type. (AR 471-472.)

Table 3:

Incidental Take Limits by Water Year Type

(For Both CVP and SWP)

--------------------------------------------------------------------------

Water Year Type

--------------------------------------------------------------------------

Below Normal, Dry,

Month Wet or Above Normal or Critical

------------------------------------------------------------

October 100 100

November 100 100

December 700 400

Monthly January 3000 1900

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Incidental February 2300 1700

Take March 1300 1300

April 1000 1100

May 37800 30500

June 45300 31700

July 3500 2500

*339

August 100 100

September 100 100

--------------------------------------------------------------------------

Because these incidental take levels are based on predictions produced by CALSIM II Study 5a, they

do not assume any smelt protection actions under the DSRAM, but do assume continued availability

of the EWA water. (AR 374, 471.)

FWS determined that the level of anticipated take "is not likely to result in jeopardy to the smelt

because this level of take is at or below historical levels of take." (AR 474.)

However, the BiOp also acknowledges that "the operations of the Projects under formal consultation

as described in the Project Description will result in adverse effects to delta smelt through entrainment

at the CVP and SWP and by drawing delta smelt into poorer quality habitat in the south delta." (AR

422 (emphasis added).) The BiOp concludes that "with the inclusion of [certain] conservation

measures described [in the BiOp] and the implementation of the [Delta Smelt Risk Assessment

Matrix], these adverse effects would be avoided or minimized." (Id. (emphasis added).) "[W]ith these

conservation measures in place, the re-operation of the Trinity River, the increased level of

development on the American River, the Freeport Diversion, the Suisun Marsh Salinity Control

Gates, the Barker Slough Diversion, or due to changes to X2 . . . are not expected to result in adverse

effects to delta smelt." (AR 423.)

FWS' conclusions admit project operations will result in adverse effects to delta smelt, which are

unquantified, and can only be avoided by conservation measures and implementation of the DSRAM.

H. "Conservation Measures."

The "conservation measures" contemplated are listed in the Summary of Effects section of the BiOp

and include: (1) the Environmental Water Account ("EWA"); (2) Central Valley Project Improvement

Act (b)(2) water; (3) State Water Resource Control Board's Water Rights Decision 1641; (4) the

Vernalis Adaptive Management Plan ("VAMP"); and (5) the DSRAM adaptive management plan.

(AR 466-68.)

1. CVPIA (b)(2) Water.

According to the 1992 Central Valley Project Improvement Act, the CVP must "dedicate and manage

annually 800,000 acre-feet of Central Valley Project yield for the primary purpose of implementing

the fish, wildlife, and habitat restoration purposes and measures authorized by this title; to assist the

State of California in its efforts to protect the waters of the San Francisco Bay/Sacramento-San

Joaquin Delta Estuary; and to help to meet such obligations as may be legally imposed upon the

Central Valley Project under State or Federal law following the date of enactment of this title,

including but not limited to additional obligations under the Federal Endangered Species Act." Title

XXXXIV of the Reclamation Projects Authorization and Adjustment Act of 1992, Pub.L. 102-575,

106 Stat. 4600, 4706 (1992). (See AR 372.)

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FWS, in consultation with the Bureau and other agencies, may use this "(b)(2) water" to meet Water

Quality Control Plan (WQCP) obligations and any other requirements imposed by law after 1992.

"For example, (b)(2) water has been used to maintain flows on Clear Creek to provide adequate

spawning and rearing habitat for Chinook salmon. Water exports at the CVP have also been reduced

using (b)(2) water to reduce entrainment of salmon or *340 delta smelt at the salvage facilities. This

ongoing action provides a benefit to delta smelt in most years." (AR 372.)

The base CVP yield committed to fish restoration is fixed by statute and is mandatory. This fixed

supply is subject to reduction up to 25% in critically dry years under CVPIA 3406(b)(2)(C).

2. Environmental Water Account.

The Environmental Water Account ("EWA") is "an adaptive management tool that aims to protect

both fish and water users as it modifies water project operations in the Bay-Delta." (AR 373.)

The EWA provides water for the protection and recovery of fish beyond that which

would be available through the existing baseline of regulatory protection related to

project operations. The EWA buys water from willing sellers or diverts surplus water

when safe for fish, then banks, stores, transfers and releases it as needed to protect fish

and compensate water users for deferred diversions.

(Id.)

The EWA has been used to benefit smelt by allowing for the curtailment of project export pumping

during critical time periods. (Id.) The EWA could also be used to increase in-stream flows or increase

outflows in the Delta, both of which would benefit the smelt. (Id.) The EWA is not fixed by statute

nor is annual funding assured, and the water supply it provides, though reasonably anticipated, is not

immutable.

3. Water Rights Decision 1641.

State Water Resource Control Board Decision 1641 (D-1641) imposes certain minimum flow and

water quality objectives upon the projects:

D-1641 includes specific outflow requirements throughout the year, specific export

restraints in the spring, and export limits based on a percentage of estuary inflow

throughout the year. D-1641 obligates the SWP and CVP to comply with the objectives

in the 1995 Bay-Delta Plan. The Service issued a biological opinion on the Bay-Delta

plan to the Environmental Protection Agency on November 2, 1994. The water quality

objectives in the 1995 Bay-Delta Plan and in D-1641 are designed to protect in-Delta

agricultural, municipal and industrial, and fishery uses and vary throughout the year and

by water year type. . . . D-1641 will also protect delta smelt by providing transport,

habitat and attraction flows.

(AR 373 (citations omitted).)

The D-1641 requirements are mandatory under the projects' operating permits. The water to satisfy

D-1641 comes from 3406(b) (2) yield and supplemental sources the Bureau utilizes.

4. Vernalis Adaptive Management Plan (VAMP).

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The Vernalis Adaptive Management Plan (VAMP) is an experimental program that had its origin in

D-1641. (AR 373.) It provides for flows on the lower San Joaquin River and export curtailments at

the projects. (Id.) VAMP's purpose is to "provide pulse flows on the San Joaquin River and improve

habitat conditions in the Delta by reducing exports at the CVP and SWP" over a 31 day period in

April and May for the benefit of Chinook salmon and Delta smelt. (Id.) Currently, water used to

reduce exports at the CVP under VAMP is accounted for as CVPIA (b)(2) water. (Id.) If export

reductions are taken, the EWA is used to supply contractors to make up for the transfers. VAMP

flows "allow larval and juvenile smelt to avoid becoming entrained at the export facilities and to move

downstream to Suisun Bay." (Id.)

*341 The VAMP water supply is not irrevocably fixed or assured.

I. Delta Smelt Risk Assessment Matrix (DSRAM).

The BiOp's other, primary protection for the smelt is the implementation of a new adaptive

management protocol, known as the Delta Smelt Risk Assessment Matrix ("DSRAM"). The DSRAM

utilizes a list of trigger criteria to precipitate responses. (AR at 344.) The criteria are:

(1) the previous year's FMWT index;

(2) the risk of smelt entrainment based upon the location of X2;

(3) the estimated duration of the smelt spawning period, based on water temperature;

(4) the presence of spawning female smelt;

(5) the proximity of the smelt to project pumping facilities; and

(6) a salvage trigger for adult and juvenile smelt. (AR 346.)

1. The DSRAM Process.

If any trigger criteria is met or exceeded, a Delta Smelt Working Group ("DSWG") is convened. The

DSWG consists of representatives from FWS, the California Department of Fish and Game, DWR,

the United States Environmental Protection Agency, the Bureau, and the California Bay-Delta

Authority. (See AR 344-45.) The DSWG then recommends corrective actions to a Water Operations

Management Team ("WOMT"). (Id.) The OCAP BiOp identifies four specific actions that the DSWG

and WOMT must consider taking if one or more trigger criteria occur: (1) export reductions at one or

both of the projects; (2) changes in the south Delta barrier operations; (3) changes in San Joaquin

River flows; and (4) changes in the operation of the Delta cross channel.[14] The DSRAM does not

contain defined action criteria, but instead leaves any response wholly to the discretion of the two

groups who administer the DSRAM (DSWG and WOMT).

2. DSRAM Implementation.

The BiOp acknowledges although FWS is "confident that use of the DSRAM will reduce the

frequency with which actual salvage exceeds the median predicted salvage, the exceedence frequency

could be as high as 50%." (AR 471.) There is no analysis of the duration or consequences from such

exceedence. The DSRAM provides no operating criteria or action schedule, specifying when

mitigation actions must be taken. It is not possible to predict what, how and when DSRAM measures

will be implemented.

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J. Recent Experience with DSRAM.

DWR offered post-record evidence regarding the manner in which DSRAM has actually been

implemented since its inception. This post-record activity could not have been considered by the

agency. A motion to strike the proffered evidence was sustained. The offer of proof includes two "fish

actions" that were taken in 2005 in response to "triggers" and a third that was planned but avoided

when project water increased in early 2006, a wet year. DWR's offer of proof is to show positive

experience in operation of the DSRAM.

K. Recent Procedural History.

The Federal Defendants acknowledge that "[s]hortly before the 2005 OCAP BiOP was completed, a

fall midwater trawl survey of delta smelt revealed a substantial *342 decline in the population index

for the species" to the lowest ever. (Doc. 242-1, at 4.) The Federal Defendants do not concede that the

existence of this data renders the BiOp arbitrary and capricious, because "limited analysis of this data

existed, and the Service relied on the raw data, and its own professional judgments as the best

available scientific and commercial data available." (Id.) Nevertheless, "the CALFED agencies have

continued to assemble and analyze new data and information." (Id.) For example, scientists from

CALFED agencies "recently" developed a document based upon the new data: the Interagency

Ecological Program Synthesis of 2005 Work to Evaluate the Pelagic Organism Decline (POD) in the

Upper San Francisco Estuary (the "IEP POD Synthesis"). This document led the Federal Defendants

to conclude that the OCAP for the CVP and SWP may affect Delta smelt in a manner or to an extent

not previously considered. (IEP POD Synthesis, Doc. 240, Attachment 1.)

On July 6, 2006, the Bureau requested that the FWS re-initiate consultation concerning the impact of

the OCAP on the Delta smelt. (Doc. 240.) In a July 6, 2006 letter to the FWS, the Bureau

acknowledged that "emerging data indicates an apparent substantial decline in the Delta smelt

population index." (Doc. 240-2.)

1. No Dismissal or Stay.

In light of the second re-initiation of consultation, federal defendants sought dismissal on prudential

mootness grounds, a voluntarily remand without vacatur, or a stay pending the completion of

reconsultation. (See Does. 242-1, 273.) The motion for stay was joined by the DWR (Doc. 277), and

various Defendant-Intervenors (Doc. 274). Plaintiffs opposed because Federal Defendants refused to

withdraw the challenged BiOp and stated their intent to continue CVP and SWP operations under the

disputed BiOp and its incidental take statements during the time period necessary to complete reconsultation, now projected to be July 2008, more than two and one-half water years following the

effective date of the disputed BiOp. (See Doc. 279.)

Defendants' motion to dismiss on prudential mootness grounds was denied:

Plaintiffs' concerns have not been fully addressed by the reinitation of consultation.

Federal Defendants are relying in part on the challenged BiOps in operating the CVP and

intend to continue to do so. The controversy over whether the BiOps and OCAP should

have continued viability is real and substantial and this court could provide relief, in the

form of a decision invalidating the BiOps followed by hearings on interim remedies.

Under these circumstances, it is not appropriate to deem this case prudentially moot.

(Doc. 301 at 18 (footnotes omitted).)

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The motion for voluntary remand without vacatur was denied based on the general standard for

vacatur set forth in Natural Resources Defense Council v. U.S. Dept. of the Interior, 275 F.Supp.2d

1136, 1143 (C.D.Cal.2002), which considers "the seriousness of the order's deficiencies" and "the

disruptive consequences of an interim change that may itself be changed." No evidence or argument

was presented regarding the nature of the prejudice that might result from invalidating the BiOp (id. at

20), and numerous factual and legal disputes exist regarding the seriousness of the order's deficiencies

(see id. at 27). The court was left to speculate what consequences to the species would result if

injunctive relief were ordered against continued implementation of the disputed BiOp.

The stay motion, based on the primary jurisdiction doctrine, was denied on the authority of Lockyer v.

Mirant Corp., 398 F.3d 1098, 1109 (9th Cir.2005) (a party *343 seeking a stay "must make out a clear

case of hardship or inequity in being required to go forward, if there is even a fair possibility that the

stay for which he prays will work damage to someone else."). The' order held: "Plaintiffs are entitled

to have their complaint decided on the merits, particularly given the fact that Defendants continue to

rely on the challenged BiOps as if they were lawfully enacted." (Doc. 301 at 33.) The apparent

increasing jeopardy to the smelt by and after February of 2005 militates against further delay while

FWS continue "to study" the issue of jeopardy, an exercise that has continued for almost a decade.

IV. POST-RECORD EVIDENTIARY DISPUTES

A. Objections to Declaration of Ted Sommer.

DWR offers the post-record declaration of Ted Sommer, Ph.D, to explain (1) the concept of salvage

and its relationship to the take exceedence levels in the BiOp; (2) the operation of DSRAM; (3) and

the manner in which DSRAM has been implemented since its inception.

Generally, "the focal point for judicial review should be the administrative record already in

existence, not some new record made initially in the reviewing court." Camp v. Pitts, 411 U.S. 138,

142, 93 S.Ct. 1241, 36 L.Ed.2d 106 (1973). However, the Ninth Circuit recognizes three main

exceptions to this rule, allowing courts to consider extra-record evidence:

(1) if necessary to determine "whether the agency has considered all relevant factors and

has explained its decision,"

(2) "when the agency has relied on documents not in the record," or (3) "when

supplementing the record is necessary to explain technical terms or complex subject

matter."

Southwest Ctr. for Biological Diversity v. U.S. Forest Service, 100 F.3d 1443, 1450 (9th Cir.1996). A

court may also consider extra-record evidence "when plaintiffs make a showing of agency bad faith."

Nat'l Audubon Soc. v. U.S. Forest Sera, 46 F.3d 1437, 1447 n. 9 (9th Cir.1993).

DWR maintains that the Sommer declaration explains "technical or complex subject matters"

admissible under the exception for evidence "necessary to explain technical or complex subject

matters." (Doc. 246-1 at 5-6 n. 5.) Plaintiffs move to strike the declaration on the ground that subject

matters covered by Mr. Sommer are "neither technical nor complex." (Doc. 305 at 4 n. 1.) Rather,

Plaintiffs contend that the declaration is offered to explain the agency's post-BiOp experience with

DSRAM in an effort to counter the Plaintiffs' argument that the DSRAM is wholly discretionary and

contains no defined standards or enforceable requirements.

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Generally, "post hoc rationalizations of the agency . . . cannot serve as a sufficient predicate for

agency action." Am. Textile Manuf. Inst. v. Donovan, 452 U.S. 490, 539, 101 S.Ct. 2478, 69 L.Ed.2d

185 (1981); see also Sierra Club v. Bosworth, 199 F.Supp.2d 971, 986 (N.D.Cal. 2002) (refusing to

consider post hoc explanations that were "neither addressed nor supported by the record"). DWR does

not disagree with this general principle, but instead insists that the declaration is offered only to

explain complex and technical aspects of the incidental take exceedence levels and the DSRAM.

Paragraphs 11 through 15 of the Sommer Declaration concern the implementation measures taken

under the DSRAM after the BiOp issued. There is no basis in the law for the admission of this postrecord evidence. DWR does not assert otherwise. Plaintiffs' motion to strike is GRANTED as to

paragraphs 11 through 15.

*344 The information contained in the remainder of the Sommers declaration is drawn directly from

the BiOp itself, explaining in plain language how the incidental take limits were set and how DSRAM

operates. Although, much of the same information can be found in the BiOp, the subject matters

covered are technical and complex and Dr. Sommer's declaration clarifies or explains them. This

exception saves the remaining paragraphs of the Sommers declaration to explain the incidental take

limits.

The motion to strike is DENIED IN PART as to the past record evidence paragraphs only.[15]

B. Federal Defendants' Renewed Objections to Previously Admitted Extra-Record Documents.

The May 13, 2006 memorandum decision admitted certain extra-record documents, for limited

purposes (Doc. 219), including Document 10 (a Powerpoint presentation by Michael Dettinger given

to the Bay-Delta Authority on December 8, 2004 entitled "Uncertainties & CALFED Planning What

Are Current Observations and Models Saying?") for two purposes. First, "for the limited purpose[] of

determining whether []FWS failed to adequately consider the climate change issue and the scientific

significance of any such failure. . . .;" but not legal opinions. (Doc. 219 at 25.) Second, to the extent

appropriate, all twenty two extra record documents presented by Plaintiffs, including Document 10,

may be referenced to aid the court's understanding of various technical concepts under the "technical

terms and complex subject matter exception." (Id. at 32.)

In the footnote to their opposition brief, Federal Defendants renew their objection to consideration of

any of the documents under the technical terms and complex subject matter exception. (Doc. 242-1 at

22 n. 12.) The May 13, 2006 memorandum decision notes: "Defendants and Defendant Intervenors

suggest that Plaintiff has failed to establish that the existing record is inadequate to explain the

technical terms, but point to no authority requiring such a showing." (Doc. 219 at 30.) Federal

Defendants now assert: "numerous courts, including the Supreme Court and district courts in this

Ninth Circuit, have held that a record may not be supplemented for explanatory purposes unless the

existing record has been demonstrated inadequate." (Doc. 242-1 at 22 n. 12.), citing an unpublished

district court decision, City of Santa Clarita v. United States Dept. Of Interior, 2005 WL 2972987 at

*2 n. 3 (C.D.Cal.2005):

. . . Plaintiffs bear the burden of making an initial showing that the administrative record

is inadequate for effective judicial review and that one of the exceptions to record review

applies. Animal Defense Council v. Hodel, 840 F.2d at 1436-38 (affirming district court

order limiting review to administrative record and prohibiting discovery because

plaintiffs did not show record presented was insufficient for review or *345 that any of

the exceptions to record review were applicable). . . .

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(emphasis added).

A district court decision not cited by Defendants, Karuk Tribe of Cal. v. U.S. Forest Serv., 379

F.Supp.2d 1071, 1087 (N.D.Cal.2005), reiterated this holding:

The Ninth Circuit allows a reviewing court to consider extra-record materials in an APA

case only under four narrow exceptions: (1) when it needs to determine whether the

agency has considered all relevant factors and has explained its decision; (2) when the

agency has relied upon documents or materials not included in the record; (3) when it is

necessary to explain technical terms or complex matters; and (4) when a plaintiff makes a

showing of agency bad faith. Southwest Center for Biological Diversity v. United States

Forest Service, 100 F.3d 1443, 1450 (9th Cir.1996). For extra-record material to be

considered, a plaintiff must first make a showing that the record is inadequate. Animal

Defense Council v. Hodel, 840 F.2d 1432, 1437 (9th Cir.1988) ("The [plaintiff] makes no

showing that the district court needed to go outside the administrative record to determine

whether the [agency] ignored information"). At the *1088 same time, "[a] satisfactory

explanation of agency action is essential for adequate judicial review, because the focus

of judicial review is not on the wisdom of the agency's decision, but on whether the

process employed by the agency to reach its decision took into consideration all the

relevant facts." Asarco, Inc. v. U.S. Environmental Protection Agency, 616 F.2d 1153,

1160 (9th Cir.1980).

(emphasis added).[16]Karuk Tribe, and Animal Defense Council v. Hodel, 840 F.2d 1432, 1437 (9th

Cir.1988), on which it relies, do stand for the proposition that, before admitting documents under any

exception to the general rule against extra-record evidence, a court should require that a plaintiff make

an initial showing that the existing record is insufficient. Here, defendants maintain that those,

documents plaintiffs have referenced to explain complex or technical matters, are "the cart before the

horse," because Plaintiffs *346 have not shown the existing record is inadequate.

First, Federal Defendants objection is arguably untimely. They did not cite cases requiring a

preliminary showing of insufficiency when the motion to augment was briefed and heard. Nor did

Federal Defendants timely move for reconsideration of the May 13, 2006 ruling on the motion to

augment. Striking the challenged documents now, would cause prejudice to Plaintiffs, who relied

upon these rulings to prepare their dispositive motions.

Even assuming a timely and specific objection, on the merits, Plaintiffs' extra-record documents were

properly admitted. Of these twenty-two documents, Plaintiffs' papers only referenced eight: Docs. 9,

10, 11, 12, 13, 20, 21 & 22. With the exception of Documents 12 and 22, all were admitted on

multiple grounds. (Documents 12 and 22 were admitted for the limited purpose of explaining

technical materials.) The documents and the bases for their admission are as follows:

Document 9: Summary of Annual Joint Meeting of California Bay-Delta Authority and

Bay-Delta Public Advisory Committee (December 8-9, 2004). Admitted "for the limited

purpose of determining whether USFWS failed to adequately consider the EWA/ CVPIA

(b)(2) issue," "for the limited purposes of determining whether USFWS failed to

adequately consider the climate change issue and the scientific significance of any such

failure . . .," and, as appropriate, to explain complex and technical matters:

Document 10: Climate Change Uncertainties & CALFED Planning: What Are Current

Observations and Models Saying? Powerpoint presentation by Michael Dettinger, U.S.

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Geological Survey at the Scripps Institute for Oceanography, et al. to Bay-Delta

Authority (December 8, 2004).

Admitted "for the limited purposes of determining whether USFWS failed to adequately

consider the climate change issue and the scientific significance of any such failure," and

as appropriate, to explain complex and technical matters.

Document 11: Summary of Annual Joint Meeting of California Bay-Delta Authority and

Bay-Delta Public Advisory Committee (February 9-10, 2005).

Admitted "for the limited purpose of showing that USFWS failed to consider relevant

Delta smelt population data and its scientific significance," and, as appropriate, to explain

complex and technical matters.

Document 12: Letter from H. Candee and K. Poole, NRDC, to S. Thompson re

Consultation on OCAP: Significant New Delta Smelt Information, Service (Feb. 14,

2005).

Admitted only to explain, as appropriate, complex and technical matters.

Document 13: Delta smelt abundance trends, Powerpoint presentation by Chuck Armor,

DFG, to Bay-Delta Authority

Admitted "for the limited purpose of showing that USFWS failed to consider relevant

Delta smelt population data and its scientific significance," and, as appropriate, to explain

complex and technical matters.

Document 20: Supplemental Biological Opinion on CVP and SWP Operations, April 1,

2004 through March 31, 2006 (Feb. 27, 2004).

Admitted "for the limited purpose of determining whether USFWS failed to adequately

consider the EWA/ CVPIA(b)(2) issue," and, as appropriate, *347 to explain complex

and technical matters.

Document 21: Future Water Availability in the West: Will there be enough? Powerpoint

presentation by M. Dettinger to 24th Annual Conference on Water, Climate and

Uncertainty: Implications for Western Water Law, Policy, and Management (June 11-13,

2003).

Admitted "for the limited purposes of determining whether USFWS failed to adequately

consider the climate change issue and the scientific significance of any such failure . . .,"

and, as appropriate, to explain complex and technical matters.

Document 22: Letter from John W. Keys, Bureau, to Hon. George Miller, House of

Representatives re Bureau's renewal of CVP water contracts (Dec. 23, 2004).

Admitted only to explain, as appropriate, complex and technical matters.

With the exception of Documents 12 and 22, Plaintiffs were permitted to reference these documents

to show whether FWS adequately considered included subject matter to support the BiOp. Although

Plaintiffs did not expressly demonstrate that the record was insufficient, a finding of insufficiency can

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be implied from the rulings admitting the documents. For example, Document 10, the powerpoint

presentation regarding "Climate Change Uncertainties & CALFED Planning" presented to the BayDelta Authority on December 8, 2004, references climatological information and issues not otherwise

discussed in the administrative record, bearing on whether FWS failed to adequately consider the

climate change issue. The same reasoning applies to Documents 9, 10, 11, 13, 20 & 21. As for

Documents 12 and 22, were which were only admitted under the complex and technical matters

exception, no prior showing of insufficiency was made. However, Documents 12 and 22 were only

referenced as secondary citations or for context. Even if, any document was admitted in error, no

prejudice has resulted.

V. STANDARD OF REVIEW

Summary judgment is appropriate where there are no genuine issues of material fact and the moving

party is entitled to judgment as a matter of law. Fed. R. Civ. Pro. 56(c). This is a challenge to the

lawfulness of a biological opinion brought under the ESA and the Administrative Procedure Act

("APA"). Agency decisions made under the ESA are governed by the APA, which requires that the

agency action be upheld unless it is found to be "arbitrary, capricious, an abuse of discretion, or

otherwise not in accordance with law," or "without observance of procedure required by law." 5

U.S.C. § 706(2)(A), (D). The inquiry is designed to "ensure that the agency considered all of the

relevant factors and that its decision contained no clear error of judgment." Pacific Coast Fed'n of

Fishermen's Ass'ns v. NMFS, 265 F.3d 1028, 1034 (9th Cir. 2001). Agency action should only be

overturned if the agency has "relied on factors which Congress has not intended it to consider, entirely

failed to consider an important aspect of the problem, offered an explanation for its decision that runs

counter to the evidence before the agency, or is so implausible that it could not be ascribed to a

difference in view or the product of agency expertise." Id. In sum, a court must ask "whether the

agency considered the relevant factors and articulated a rational connection between the facts found

and the choice made." Id. "A biological opinion is arbitrary and capricious and will be set aside when

it has failed to articulate a satisfactory explanation for its conclusions or when it has entirely failed to

consider an important aspect of the problem." *348 Greenpeace v. NMFS, 80 F.Supp.2d 1137, 1147

(W.D.Wash.2000). Alternatively, a biological opinion may also be invalid if it fails to use the best

available scientific information as required by 16 U.S.C. § 1536(a)(2). Id. at 1150.

As a general rule, a court must defer to the agency on matters within its expertise. See National

Wildlife Federation v. National Marine Fisheries Service, 422 F.3d 782, 798 (9th Cir.2005).

However, "[t]he deference accorded an agency's scientific or technical expertise is not unlimited." Id.

"Deference is not owed when the agency has completely failed to address some factor consideration

of which was essential to [making an] informed decision." Id. (internal citations and quotations

omitted).

A final BiOp is final agency action for judicial review purposes. American Rivers, infra, 126 F.3d at

1124-25.

VI. SUMMARY OF PLAINTIFFS' MOTION

Plaintiffs move for summary judgment on the following grounds:

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(1) First, the BiOp did not utilize the Best Available Science by: (a) failing to reference the "most

recent Delta Smelt abundance data," namely the 2004 Fall Midwater Trawl Data; and (b) failing to

consider the possible effects that climate change might have on the smelt's habitat.

(2) Second, the BiOp unlawfully relies upon the DSRAM as a mitigation measure because the

DSRAM process is "entirely discretionary, uncertain, and unenforceable." In addition, Plaintiffs

allege that Federal Defendants acted arbitrarily and capriciously by relying upon the EWA, CVPIA(b)

(2), and/or VAMP programs as water sources necessary to implement the DSRAM. Plaintiffs allege

that Federal Defendants have (a) failed to demonstrate that EWA, CVPIA and/or VAMP will continue

to be available over the 20-year term of the BiOp and (b) failed to demonstrate that DSRAM can

reliably operate without water assets from those programs.

(3) Third, there is no rational connection between the evidence in the record and the BiOp's "no

jeopardy" conclusion. Specifically, Plaintiffs allege (a) that the BiOp's focus on salvage as the

measure of harm to the species underestimates project impacts and results in a meaningless take limit;

and (b) that the BiOp fails to explain how its no jeopardy conclusion can be justified in light of the

identified adverse effects of the project, along with indirect and cumulative effects.

(4) Fourth, the BiOp failed to adequately analyze whether the OCAP's impacts on the Delta smelt's

critical habitat are consistent with the smelt's recovery. In addition, the Federal Defendants failed to

adequately take into account smelt habitat areas other than defined by X2.

(5) Finally, the BiOp is unlawfully narrow in its scope because it (a) fails to provide a comprehensive

analysis of the effects of constructing facilities required to carry out long term CVP and SWP

operations and (b) fails to analyze the impacts of the projects delivering the full amount of water

authorized under CVP and SWP water service contracts.

VII. DISCUSSION

A. Threshold Issues.

1. ESA 60-day notice requirement.

The San Luis Parties argue that Plaintiffs have not complied with the ESA's citizen suit notice

requirement, 16 U.S.C. § 1540(g)(2)(A)(i), that written notice be given to "the Secretary, and to any

alleged violator" at least sixty days in advance of filing suit. Failure to give this notice is a bar to

bringing suit under the ESA. Southwest Ctr. for Biological Diversity *349 v. U.S. Bureau of

Reclamation, 143 F.3d 515, 520 (9th Cir.1998).

In American Rivers v. National Marine Fisheries Serv., 126 F.3d 1118, 1124-25 (9th Cir.1997), the

Ninth Circuit held that issuance of a biological opinion is a final agency action that is properly pled as

a challenge under the APA, rather than as a citizen suit claim under the ESA. Failure to comply with

the 60-day notice requirement does not deprive the court of jurisdiction. Id.

The San Luis Parties advocate an approach that ignores American Rivers,[17] taken in an unpublished

district court opinion, Pacific Coast Fed' of Fisherman's Ass'ns v. U.S. Bureau of Reclamation, 2006

WL 1469390 at *27 n. 8 (N.D.Cal. 2006). Pacific Coast Federation declined to apply American

Rivers' general rule because the injunctive relief the Plaintiffs sought went beyond simply having the

biological opinion invalidated. The Pacific Coast Federation Plaintiffs sought to have any new

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biological opinion first reviewed by the court. This requested relief fell outside the scope of the APA

but was "within the scope of the ESA and thus trigger[ed] the notice period requirement." Id. Here,

the requested relief is invalidation of the BiOp, a remedy undeniably available under the APA.

American Rivers controls. There was no need to comply with the ESA 60-day notice requirement. The

district court has jurisdiction over APA review of the BiOp.

2. Jurisdiction to Review Challenges to Early Consultation and Preliminary Biological Opinion.

Defendants contend the case is not ripe for decision. The BiOp covers not only current operations, but

also a variety of future actions, some subject to formal consultation, others to early consultation: This

biological opinion covers formal and early consultation for the operations of the CVP and SWP. The

formal consultation effects described in this biological opinion cover the proposed 2020 operations of

the CVP including the Trinity River Mainstem ROD (Trinity ROD) flows on the Trinity River, the

increased water demands on the American River, the delivery of CVP water to the proposed Freeport

Regional Water Project (FRWP), water transfers, the long term Environmental Water Account

(EWA), the operation of the Tracy Fish Facility, and the operation of the SWP-CVP intertie. The

effects of operations of the SWP are also included in this opinion and include the operations of the

North Bay Aqueduct, the Suisun Marsh Salinity Control Gates, the Skinner Fish Facility and water

transfers.

Early consultation [issues address] the effects of operations of components of the South

Delta Improvement Program (SDIP). These operations include pumping of 8500 cubic

feet per second (cfs) at the SWP and Banks Pumping Plant (hereafter referred to as 8500

Banks), permanent barrier operations in the South Delta, the long term EWA, water

transfers, and CVP and SWP operational integration. There are two separate effects

sections in this biological opinion, one for Formal Consultation and one for Early

Consultation. In addition, there is an incidental take for formal consultation and a

preliminary incidental take for early consultation.

(AR 2, 248.)

The San Luis Parties object that the early consultation portions of the BiOp are not final agency action

and any challenges to the early consultation process are not subject to judicial review. Early

consultation, *350 by definition, results in only a "preliminary opinion" and in a preliminary

incidental take statement that "does not constitute authority to take lifted species." 50 C.F.R. § 402.11

(e). Upon request for "confirmation" of a preliminary biological opinion, FWS will review the

proposed action to determine if there have been "significant changes in the action as planned or in the

information used during early consultation." § 402.11(f). Within 45 days of such request, FWS must

either confirm the preliminary biological opinion or request formal consultation. Id.

Plaintiffs concede that they "are not challenging the validity of FWS's early consultation or its

preliminary biological opinion regarding certain segregated components of the 2004 OCAP." (Doc.

306 at 37.) Rather, Plaintiffs argue that the portion of the BiOp covering formal consultation is flawed

because it fails to examine the full impacts of all aspects of the 2004 OCAP. (Doc. 306 at 37.)

Plaintiffs maintain the formal consultation should have covered certain planned actions included in

the early consultation that are interdependent with other planned actions not included in either

consultation. This claim is cognizable, as it challenges the scope of the formal consultation and the

completeness of evaluation of overall OCAP operations on jeopardy to the smelt, not the lawfulness

of the early consultation on future actions.

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B. The Biological Opinion Unlawfully Relies Upon Uncertain, Unenforceable Mitigation Measures.

The BiOp concludes that the "operations of the Projects under formal consultation . . . will result in

adverse effects to the delta smelt through entrainment at the CVP and SWP facilities and by drawing

delta smelt into poorer quality habitat in the south delta. However with the inclusion of the

conservation measures described above and the implementation of the DSRAM, these adverse effects

would be avoided or minimized." (AR 467 (emphasis added).) The "conservation measures"

mentioned in the BiOp's conclusion are various regulatory mechanisms already in place to "provide

protection to delta smelt and/or their habitats," including D-1641, the EWA, CVPIA (b)(2) water, and

VAMP. (AR 421-22, 466-67.)

1. Law Governing Mitigation Measures.

Mitigation measures must be "reasonably specific, certain to occur, and capable of implementation;

they must be subject to deadlines or otherwise-enforceable obligations; and most important, they must

address the threats to the species in a way that satisfies the jeopardy and adverse modification

standards." Ctr. for Biological Diversity v. Rumsfeld, 198 F.Supp.2d 1139, 1152 (D.Ariz.2002) (citing

Sierra Club v. Marsh, 816 F.2d 1376 (9th Cir.1987)); see also NWF v. NMFS, 481 F.3d 1224 at *12

& n. 16 ("Although the record does reflect a general desire to install structural improvements [to

benefit fish] where feasible, it does not show a clear, definite commitment of resources for future

improvements.").

Plaintiffs allege that, in depending on the DSRAM and the other "conservation measures" to support

its no jeopardy conclusion, the BiOp unlawfully relies upon uncertain, unenforceable mitigation

measures which do not constitute a clear, definite commitment of resources. Specifically, Plaintiffs

argue: (a) the DSRAM process is "entirely discretionary, uncertain, and unenforceable" and (b) the

biological opinion unjustifiably assumes that the other, currently operational "conservation

measures" (e.g., the EWA and CVPIA(b) (2) water) will continue to be available for use by DSRAM

in the future.

*351 2. The DSRAM is Unlawfully Uncertain and Unenforceable.

All Defendants argue that the DSRAM is an effective adaptive management program that provides the

agency the necessary remedial flexibility that makes the BiOp lawful. The BiOp describes the

DSRAM as follows:

The delta smelt risk assessment matrix (DSRAM) consists of month by month criteria

which, when exceeded will trigger a meeting of the Delta Smelt Working Group

(Working Group). The purpose of the DSRAM is to take actions to protect delta smelt in

a proactive manner prior to salvage events. . . . The DSRAM is an adaptive management

tool which may be further modified by the Working Group/WOMT as new information

becomes available, without undergoing formal reconsultation. . . . Data will be updated at

least weekly to determine the need for a meeting.

Should a triggering criterion be met or exceeded, Reclamation and/or DWR will inform

the members of the Working Group and the Working Group will determine the need to

meet. Any member of the Working Group may set up a meeting of the Working Group at

any time. A meeting of the Working Group may consist of an in-person meeting, a

conference call, or a discussion by email. If needed, the Working Group will meet prior

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to the weekly meetings of the DAT and the WOMT and information will be shared with

these groups.

Should a meeting of the Working Group prove necessary, the group will decide whether

to recommend a change in exports, change in south delta barrier operations, San

Joaquin River flows, or a change in delta cross channel operations, and the extent and

duration of the potential action. These potential actions are listed in the DSRAM by the

months wherein each of these tools generally become available. The group will

recommend actions which will be shared with the DAT and forwarded to the WOMT for

discussion and potential implementation. This recommendation will include a discussion

of the level of concern for delta smelt and will include who participated in the working

group discussions. All dissenting opinions and/or discussion points will also be

forwarded to the WOMT. The Working Group will meet at least weekly throughout the

period in which the triggering criteria are met or exceeded, to determine the need to

provide further recommendations to the WOMT.

Notes and findings of Working Group meeting will be submitted to the Service and

members of the WOMT for their records. The WOMT will respond to the Working

Group's recommendations and the actions taken by the WOMT will be summarized by

Reclamation and/or DWR annually and submitted to all WOMT agencies.

If an action is taken, the Working Group will follow up on the action to attempt to

ascertain its effectiveness. An assessment of effectiveness will be attached to the notes

from the Working Group's discussion concerning the action.

(AR 344-45 (emphasis added).)

The trigger criteria, which vary slightly from month to month, are, set forth in a table (or matrix) at

page 100 of the BiOp. (AR 346.) The criteria include: (1) the previous year's fall midwater trawl

recovery index; (2) the risk of smelt entrainment based upon the location of X2; (3) the estimated

duration of the smelt spawning period based upon water temperature; (4) the presence of spawning

female smelt; (5) the proximity of the smelt to the Project pumping facilities; and, (6) a salvage

trigger for adult smelt (calculated as the *352 ratio of adult smelt salvage to the FMWT index) and

juvenile smelt (set at zero for May and June, the months of the year during which salvage of smelt is

highest). (AR 346-49.)

Plaintiffs argue that the DSRAM is not "reasonably specific, certain to occur, and capable of

implementation" because: (1) the DSWG has complete discretion over whether to meet and whether

to recommend mitigation measures; (2) even if the DSWG meets and recommends mitigation

measures, the WOMT group is free to reject any recommendations; (3) there are no standards to

measure the effectiveness of actions taken; (4) reconsultation is not required should mitigation

measures prove ineffective; and (5) ultimately, no action is ever required.

DWR responds that implementation of the DSRAM process is "mandatory." For example, the

incidental take statement requires that the projects shall be implemented "as described" in the BiOp.

(AR 475.) Because the BiOp "describes" operation of the DSRAM, DWR asserts that its

implementation is made mandatory by the incidental take statement's command that the project shall

be implemented "as described;" if a DSRAM triggering criteria is met, the DSWG "will determine the

need to meet." (AR 344 (emphasis added).) If circumstances warrant action, the DSWG will

recommend fish protection actions and forward those recommendations to the WOMT. (Id.) The

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BiOp provides that the DSWG "will meet at least weekly throughout the period in which the

triggering criteria are met or exceeded, to determine the need to provide further recommendations to

the WOMT." (Id. at 345 (emphasis added).) The WOMT must then "respond" to DSWG's

recommendations. (Id.) If actions are taken, the DSWG will monitor the action to determine its

effectiveness. (Id.)

DWR correctly asserts that the DSRAM process must be followed; this does not address Plaintiffs'

argument: that the DSRAM process itself does not require any mitigation actions be taken. Nothing in

DSRAM requires the DSWG to make action recommendations, whatever the circumstances, and no

criteria prescribe when the WOMT must act to effect DSWG's recommendations.

DWR responds that as adaptive management, "DSRAM is intentionally flexible, taking into

consideration the uncertainties surrounding delta smelt population abundance and dynamics . . . [D]

elta smelt abundance has fluctuated widely, without a clear explanation why. While experts can

monitor trends in delta smelt populations, estimating overall population abundance presently is `not

possible,' nor are the sources of year-to-year variability in abundance well understood." (Doc. 246-1 at

12.) DWR suggests that "hard-wiring" the DSRAM to require specific actions be taken when

triggering criteria occur would impair the DSRAM's flexibility. For example, the trigger for salvage

of juvenile smelt is set at zero. This trigger was designed not to precipitate a meeting every time that

standard is exceeded, but to cause heightened awareness of conditions that might require protective

action. (Doc. 246-1, at 12, citing AR at 8217-18.)

The conflict between Defendants' choice of a flexible management approach and Plaintiffs' concern to

ensure enforceable protective actions are taken when necessary, highlights the extent to which overly

flexible adaptive management may be incompatible with the requirements of the ESA. Commentators

recognize that adaptive management schemes do not fit neatly within the ESA's existing regulatory

structure. See J.B. Ruhl, Taking Adaptive Management Seriously: A Case Study of the Endangered

Species Act, 52 *353 U. Kan. L.Rev. 1249, 1284 (2004) ("The [ESA] as a whole lacks a cohesive

adaptive management architecture. . . ."). H. Doremus, Adaptive Management, The Endangered

Species Act, and the Institutional Challenges of "New Age" Environmental Protection, 41 Washburn.

L.J. 50, 52 (2000) ("Adaptive Management . . . runs counter to human nature and the current structure

of our management institutions."); ("One key institutional challenge is to combine the flexibility

required by adaptive management with the long-term certainty we often seek through our legal and

political institutions.") 41 Washburn L.J. at 55.

The case law sheds little light on how to harmonize these competing objectives. The parties cite no

cases applying the "reasonably specific, certain to occur, and capable of implementation" concept (or

any closely related doctrine) to mitigation measures employed under an adaptive management

protocol. Most cases the parties cite are either wholly inapplicable or factually distinguishable.

For example, mitigation measures have been found unlawfully uncertain because their

implementation was not within the control of the relevant federal agencies. National Wildlife

Federation v. NMFS, 254 F.Supp.2d 1196, 1213 (D.Or.2003), invalidated a 2000 biological opinion

addressing the effects of the operation of the Federal Columbia River Power System ("FCRPS") on

several listed fish species. A 2000 biological opinion concluded that continued operation of the

FCRPS would jeopardize several of the species and adversely modify their critical habitat and adapted

mitigation measures to avoid jeopardy. The mitigation measures included a variety of short- and longterm state, regional, tribal, and private off-site mitigation actions. The plaintiffs argued that reliance

on such "uncertain and vaguely defined actions of third parties to protect and restore salmon habitat,"

violated the "reasonably certain to occur" standard. Id. at 1209. The district court agreed, concluding

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that the no jeopardy determination unlawfully relied on "non-federal off-site mitigation actions that

are not reasonably certain to occur." Id. at 1214. See also Sierra Club v. Marsh, 816 F.2d 1376, 1385

(9th Cir.1987) (invalidating biological opinion that relied on mitigation measure involving the transfer

of 188 acres of marshland from private ownership to a publicly owned wildlife refuge; land remained

under private control and subject to easements that rendered the land valueless for mitigation

purposes, and private owners and local government indicated intent to increase use of one of the

easements); Oregon Natural Desert Ass'n v. Lohn, 485 F.Supp.2d 1190 (D.Or.2007) (setting aside

biological opinion in part because it overly relied on the actions of private individuals who had a poor

past record of compliance with standards); Florida Key Deer v. Brown, 364 F.Supp.2d 1345, 1355-56

(S.D.Fla.2005) (setting aside biological opinion that relied on mitigation measures to be implemented

by private landowners; nothing compelled the landowners to act and "the record indicate[d] that some

landowners entirely disregarded [prior mitigation measures]").

Here, the BiOp's mitigation measures are largely under the control of the action agency (the Bureau),

which, operating in concert with the DWR, directly regulates water pumping and releases from

upstream reservoirs. Natural Resources Defense Council v. Rodgers, 381 F.Supp.2d 1212, 1241

(E.D.Cal.2005), does not provide guidance. In that case, plaintiffs contended a BiOp's mitigation

measures were not reasonably certain to occur because the action agency had a poor track record of

following through on prior commitments. The acknowledging that the agency's track record was

"discouraging" district court recognized that the agency had made some *354 progress toward

implementing its prior commitments, id., and declined to find that the new commitments were not

certain to occur. Id. However, the Rodgers plaintiffs did not attack the efficacy of the mitigation

measures themselves, only the likelihood that the agency would not satisfy its commitment to

implement them. Here, Plaintiffs challenge the inherent uncertainty and unenforceability of the

DSRAM and the other conservation measures.

Plaintiffs cite American Rivers v. U.S. Army Corps of Engineers, 271 F.Supp.2d 230, 252

(D.D.C.2003), where, despite the fact that a prior biological opinion required the Corps to implement

flow restrictions to mitigate impacts to listed species, the Corps "made it perfectly clear" to the district

court "that it ha[d] no intention of ensuring that its future operations will be consistent" with the

mitigation requirements. Id. at 253. A motion for preliminary injunction was granted: "Plaintiffs will

be likely to prove that the 2003 Supplemental BiOp violated the ESA and APA by improperly and

unreasonably relying on future actions by the Corps that are virtually certain not to occur." Id. at 254

(emphasis added). Here, in contrast, there is no such "smoking gun" evidence of the agency's intent to

disregard its mitigation responsibilities, just no definite, certain, or enforceable measures.

Center for Biological Diversity v. Rumsfeld, 198 F.Supp.2d 1139, 1151-53 (D.Ariz. 2002) addressed a

biological, opinion, that concluded the Army's continued operations at Fort Huachuca, Arizona would

not cause jeopardy to listed species that relied on flows from the Upper San Pedro River, even though

rapid development in the area and uncontrolled groundwater pumping at the Fort posed threats to the

species. The "no jeopardy" finding was premised on several required mitigation measures.

First, the Army had to develop and implement an on-base plan to protect and maintain populations of

listed species and habitats; id. at 1148, even though the onbase plan was not designed to address the

underlying problem of diminishing flows in the San Pedro River, see id. at 1153. Second, the Army

had to develop a regional water resources plan, sufficient to maintain flows in the San Pedro River to

sustain the protected species and their habitats. Id. at 1148. The biological opinion acknowledged, that

the Army had no authority over the implementation of the regional plan and was only required to

participate along with other stakeholders. Id. at 1153. Third, the Army had to monitor progress and

report on the implementation of the various projects. Id. at 1149. Fourth, the biological opinion

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assumed the operation of a water recharge facility designed to temporarily delay the impact of

groundwater overdraft, which the Rumsfeld court acknowledged was "subject to substantial

uncertainty." Id. at 1145.

Leaving it to the Army and other interested parties to develop a regional water management plan

"enables the Army to sidestep any direct responsibility for addressing deficit groundwater pumping,"

and was "an admission that what is currently on the table as far as mitigation measures is inadequate

to support the [] `no jeopardy' decision." 198 F.Supp.2d at 1153-54.[18]

*355 DWR distinguishes Rumsfeld, claiming it is like NWF v. NMFS, 254 F.Supp.2d 1196, where

mitigation measures were unlawful because they depended upon third parties without any guarantee

that those parties would implement the measures. Here, the DSRAM does not depend on actions by

outsiders. Rumsfeld further found that the Army's on-base mitigation measures were insufficient

because they did not require any measurable goals or an implementation schedule:

There are no requirements in the Final BO to reduce reliance on groundwater pumping

by any particular amount or to achieve any measurable goals with respect to water

recharge. There is no date certain implementation requirement. The MOA includes a

laundry list of possible mitigation measures related to water conservation and recharge

that the Army may implement, but it does not establish which projects have to be

undertaken, when, nor what the conservation objectives are for the respective projects.

Without such specificity, the mitigation measures in the Final BO are merely suggestions.

Id. at 1153 (emphasis added). Rumsfeld stands for the proposition that, at a minimum, a mitigation

strategy must have some form of measurable goals, action measures, and a certain implementation

schedule; i.e., that mitigation measures must incorporate some definite and certain requirements that

ensure needed mitigation measures will be implemented.

Here, the agency's BiOp admits that mitigation measures are essential. The no jeopardy finding is

conditioned on conservation measures and the DSRAM. (See AR 422.)

DWR's protestations that hard-wiring the DSRAM would cripple its effectiveness ignore the ESA's

requirements of reasonable certainty, timetables, and enforceability standards for mitigation measures.

The existing DSRAM process provides absolutely no certainty that any needed smelt protection

actions will be taken at any time by DSWG or WOMT. The DSRAM is in substance an

organizational flow chart that prescribes that certain administrative processes (meetings) will be held

whenever a trigger criteria is met or exceeded. Although mitigation measures are identified, no

defined mitigation goals are required, nor is any time for implementation prescribed. Incorporating

some ascertainable mitigation standards and enforceable mitigation measures is not inconsistent with

avoiding unduly restrictive "hard-wiring" of the DSRAM.

National Wildlife Federation v. Babbitt, 128 F.Supp.2d 1274 (E.D.Cal.2000) ("NWF v. Babbit"),

addresses an adaptive management approach that accommodated uncertainty by allowing regulators

to apply new information gathered through monitoring to adjust and employ well-defined mitigation

measures. There, a Habitat Conservation Plan ("HCP") called for a development fee to be collected on

all acreage developed in the Natomas Basin, north of Sacramento, home to a number of endangered

species. The HCP also incorporated adaptive management provisions designed *356 to allow the

mitigation fee to be modified if new information justified an adjustment:

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The [HCP] recognizes that the current state of knowledge as to the conservation needs of

protected species is imperfect, and that its assumptions as to the amount, location, and

pace of development in the Basin and as to the adequacy of the mitigation fee to

accommodate increased expenses may prove inaccurate. The Plan addresses these

uncertainties through its "adaptive management" provisions, which permit the Plan's

conservation strategy to be adjusted based on new information. The HCP's conservation

program can be modified under the adaptive management provisions if: (1) new

information results from ongoing research on the GGS or other covered species; (2)

recovery strategies under Fish and Wildlife Service recovery plans for the GGS or the

Swainson's hawk differ from the measures contemplated by the HCP; (3) certain of the

HCP's mitigation measures are shown through monitoring to require modification; or (4)

the HCP's required minimum block sizes for reserve lands are shown to require revision.

The Plan anticipates that the NBC will make discretionary decisions in future years based

upon new information. The NBC will decide, for example, which lands to purchase,

depending on a variety of future considerations difficult now to predict, and whether to

change the mix of in and out of Basin reserve lands and agricultural as opposed to marsh

reserve lands.

Id. at 1281-82.[19]

Here, the adaptive management process has no quantified objectives or required mitigation measures.

Although the process must be implemented by holding meetings and making recommendations,

nothing requires that any actions ever be taken.[20] The BiOp asks the court to trust the agency to

protect the species and its habitat. Notwithstanding any required deference to expertise, the ESA

requires more.

All parties agree that adaptive management can be beneficial and that flexibility is a necessary

incident of adaptive management. The law requires that a balance be struck between the dual needs of

flexibility and certainty. The DSRAM, as currently structured, does not provide the required

reasonable certainty to assure appropriate and necessary mitigation measures will be implemented.

The DSRAM does not provide reasonable assurance admitted adverse impacts of the 2004 OCAP will

be mitigated. This aspect of the BiOp is arbitrary and capricious and contrary to law. Plaintiffs'

motion for summary adjudication as to this claim is GRANTED. The agency has not provided a

reasonable explanation showing the DSRAM will satisfy ESA requirements to *357 assure survival

and recovery of the Delta smelt.

The Ninth Circuit's recent NWF v. NMFS decision suggests that mitigation measures that are not

reasonably certain to occur should be excluded from the agency's no jeopardy analysis. See 481 F.3d

1224, 1241 n. 16.[21] Because mitigation is insufficiently certain to occur under the DSRAM, the

DSRAM cannot cure other shortcomings of the BiOp.

3. Plaintiffs' Alternative Argument that the BiOp is Arbitrary and Capricious Because DSRAM

Depends Upon EWA, VAMP, CVPIA(b)(2) Water, Programs that are Uncertain in Terms of Funding

and Effectiveness.

Plaintiffs maintain that the DSRAM cannot feasibly be implemented without adequate water assets

from the EWA, CVPIA(b)(2), and VAMP programs. Plaintiffs allege that Defendants have not

demonstrated that adequate assets from these programs will be available during the 20 year term of

the BiOp. (See Doc. 306 at 17.)

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Plaintiffs correctly observe that the BiOp does not assure that adequate water assets from these

programs will be available for future use under DSRAM. The BiOp itself acknowledges that "[a]

lthough VAMP and [EWA] have helped to ameliorate these threats, it is unclear how effective these

will continue to be over time based on available funding and future demands for water." (AR 367-68.)

The BiOp recognizes that the "EWA Agencies envision implementation of a long-term EWA as part

of the operation of the Project." (AR 335.) However, the BiOp cannot and does not commit to

implement the EWA in the long run. (Id.)

The record reveals that the loss of EWA assets will "reduce the ability of the EWA agencies to

provide [] fish protections. . . ." (SAR 20.) Plaintiffs refer to statements made by FWS's D. Harlow

during an annual joint meeting of CALFED and the Bay-Delta Public Advisory Committee, that a

proposal to change CVPIA(b)(2) policy would "change fish protection envisioned in the Record of

Decision (ROD)." (Doc. 9 at 4.) At the same time, Mr. Harlow also noted that this would "not

necessarily diminish fish protection." (Id.) However, he opined that such a change would "necessitate

an increase in the size of the EWA." (Id.) National Oceanic and Atmospheric Administration

("NOAA") staff questioned FWS's reliance on the EWA in the BiOp, noting that EWA assets would

likely be used up for protective actions during the winter, before the peak months for Delta smelt

salvage (May and June). (AR 8574.)

Plaintiffs' claim rests in part on the assumption that the EWA, CVPIA(b)(2), and VAMP programs are

the only mechanisms by which DSRAM may be implemented. The record does not support this

assumption. Under the BiOp, the DSWG is tasked to make recommendations regarding fish

protection actions by selecting from a list of "tools for change," which include: (1) "export reduction

[s] at one or both facilities"; (2) "change[s] in barrier operations"; (3) "change[s] in San Joaquin River

flows"; and (4) "change[s] [in the] position of cross channel gates." (AR 346 and 348 n. 7.) No

mention is made of the EWA, CVPIA(b)(2), or VAMP in the DSRAM or its description of the "tools

for change." DWR rejoins that, regardless of whether these programs are fully funded and/or remain

functional mechanisms to provide water to the Delta, "the burden. *358 . . . falls on the Projects, not

the smelt." (Doc. 246 at 10.)

The EWA is simply a means by which the SWP and CVP can obtain water by purchasing it from

willing sellers. (AR 373.) EWA water may be used either to protect fish or to compensate project

water users for reduced exports at the project pumps. (Id.) If money is unavailable to fund the EWA,

Defendants are nonetheless required to prevent smelt take from exceeding permissible take limits.

The BiOp sets forth a three-tier process to supply water to protect the smelt:

Tier 1 (Regulatory Baseline). Tier 1 is baseline water and consists of currently existing

BOs, water right decisions and orders, CVPIA Section 3406(b)(2) water, and other

regulatory actions affecting operations of the CVP and SWP, Also included in Tier 1 are

other environmental statutory requirements such as Level 2 refuge water supplies.

Tier 2(EWA). Tier 2 is the EWA and provides fish protection actions supplemental to

the baseline level of protection (Tier 1). Tier 2 consists of EWA assets, which combined

with the benefits of CALFED's ERP, will allow water to be provided for fish actions

when needed without reducing deliveries to water users. EWA assets will include

purchased (fixed) assets, operational (variable) assets, and other water management tools

and agreements to provide for specified level of fish protection. Fixed assets are those

water supplies that are purchased by the EWA Agencies. These purchased quantities are

approximations and subject to some variability. Operational assets are those water

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supplies made available through CVP and SWP operational flexibility. Some examples

include the flexing of the export-to-inflow ratio standard required H for meeting Delta

water quality and flows, and ERP water resulting from upstream releases pumped at the

SWP Banks Pumping Plant. Water management tools provide the ability to convey, store,

and manage water that has been secured through other means. Examples include

dedicated pumping capacity, borrowing, banking, and entering into exchange agreements

with water contractors. Chapter 8 of this BA contains a more detailed description of

EWA operations, as characterized in the CASIM II modeling for the CVP OCAP.

Tier 3 (Additional Assets). In the event the EWA Agencies deem Tiers 1 and 2 levels of

protection insufficient to protect at-risk fish species in accordance with the Act, Tier 3

would be initiated. Tier 3 sets in motion a process based upon the commitment and ability

of the EWA Agencies to make additional water available, should it be needed. This Tier

may consist of additional purchased or operational assets, funding to secure additional

assets if needed, or project water if funding or assets are unavailable. It is unlikely that

protection beyond those described in Tiers 1 and 2 will be needed to meet requirements

of the Act.

(Id. at 336-37.) DWR emphasizes that, if all else fails, Tier 3 assets may be brought to bear, which

include "additional purchased or operational assets, funding to secure additional assets if needed, or

project water if funding or assets are unavailable." (Id. (emphasis added).)

There is a difference between the DSRAM's failure to require mitigation actions in response to trigger

events, designed to assure the commitment of necessary resources to smelt protection, and the duty to

have available or acquire those necessary resources. A court must leave to the agency the application

of its expertise and authority to manage the complex hydrologic, legal, financial, physical, and *359

logistical aspects of protecting the delta smelt. Plaintiffs motion for summary adjudication is DENIED

as to the issue of the insufficiency of the EWA, VAMP, and CVPIA (b)(2) programs.

C. Best Available Science.

The § 7 formal consultation process is designed to "insure" that any agency action "is not likely to

jeopardize the continued existence of any endangered species or threatened species or result in the

destruction or adverse modification of habitat of such species which is determined . . . to be critical. . .

." 16 U.S.C. 1536(a)(2). "In fulfilling the requirements of this paragraph each agency shall use the

best scientific and commercial data available." Id.

An agency has wide discretion to determine what is "the best scientific and commercial data

available." San Luis v. Badgley, 136 F.Supp.2d 1136, 1151 (E.D.Cal.2000). Yet, an agency must

make its decision about jeopardy based on the best science available at the time of the decision, and

may not defer that jeopardy analysis by promising future studies to assess whether jeopardy is

occurring. Rumsfeld, 198 F.Supp.2d at 1156. While uncertainty is not necessarily fatal to an agency

decision, e.g., Greenpeace Action v. Franklin, 14 F.3d 1324, 1337 (9th Cir. 1992) ("Greenpeace I")

(upholding agency decision even though there was uncertainty about the effectiveness of management

measures because agency premised its decision on a reasonable evaluation of all available data), an

agency may not entirely fail to develop appropriate projections where data "was available but [was]

simply not analyzed," Greenpeace v. NMFS, 80 F.Supp.2d 1137, 1149-50 (W.D.Wash.2000)

("Greenpeace II") (where agency totally failed to develop any projections regarding population

viability, it could not use as an excuse the fact that relevant data had not been analyzed). Here, EWS

maintains the necessary data cannot be obtained.

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1. Does a "Benefit of the Doubt to the Species" Presumption Apply?

The parties debate at length whether the best available scientific information principle includes a

requirement that the agency "give the benefit of the doubt to the species." This language has its

origins in the legislative history of the ESA, H.R. Conf. Rep. No. 96-697, 96th Cong., 1st Sess. 12,

reprinted in 1979 U.S.C.C.A.N. 2572, 2576:

Section 7(b) of the act requires the fish and wildlife service and the national marine

fisheries service to render biological opinions which advise whether or not proposed

agency actions would violate section 7(a)(2). Courts have given substantial weight to

these biological opinions as evidence of an agency's compliance with section 7(a). The

amendment would not alter this state of the law or lessen in any way an agency's

obligation under section 7(a)(2).

As currently written, however, the law could be interpreted to force the fish and wildlife

service and the national marine fisheries service to issue negative biological opinions

whenever the action agency cannot guarantee with certainty that the agency action will

not jeopardize the continued existence of the listed species or adversely modify its critical

habitat. The amendment will permit the wildlife agencies to frame their section 7(b)

opinions on the best evidence that is available or can be developed during consultation. If

the biological opinion is rendered on the basis of inadequate information then the federal

agency has a continuing obligation to make a reasonable effort to develop that

information. *360 This language continues to give the benefit of the doubt to the species,

and it would continue to place the burden on the action agency to demonstrate to the

consulting agency that its action will not violate section 7(a)(2). Furthermore, the

language will not absolve federal agencies from the responsibility of cooperating with the

wildlife agencies in developing adequate information upon which to base a biological

opinion. If a federal agency proceeds with the action in the face of inadequate knowledge

or information, the agency does so with the risk that it has not satisfied the standard of

section 7(a)(2) and that new information might reveal that the agency has not satisfied the

standard of section 7(a)(2).

(emphasis added).

In Conner v. Burford, 848 F.2d 1441, 1454 (9th Cir.1988), the Ninth Circuit applied this "benefit of

the doubt" language to hold that FWS violated the ESA by "failing to use the best information

available to prepare comprehensive biological opinions considering all stages of the agency action. . .

." At dispute in Conner was a biological opinion reviewing the proposed sale of oil and gas leases on

National Forest land. The biological opinion analyzed the impact of the "initial lease phase," but

failed to address the potential impact of post leasing activities, such as oil and gas development. FWS

reasoned that there was "insufficient information available to render a comprehensive biological

opinion beyond the initial lease phase," relying instead on "incremental-step consultation." Id. at

1452. The Ninth Circuit recognized that "the precise location and extent of future oil and gas activities

were unknown at the time," but, "extensive information about the behavior and habitat of the species

in the areas covered by the leases was available." Id. at 1453. With this information, "FWS could have

determined whether post-leasing activities in particular areas were fundamentally incompatible with

the continued existence of the species." Id. at 1454.

In light of the ESA requirement that the agencies use the best scientific and commercial

data available to insure that protected species are not jeopardized, 16 U.S.C. § 1536(a)(2),

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the FWS cannot ignore available biological information or fail to develop projections of

oil and gas activities which may indicate potential conflicts between development and the

preservation of protected species. We hold that the FWS violated the ESA by failing to

use the best information available to prepare comprehensive biological opinions

considering all stages of the agency action, and thus failing to adequately assess whether

the agency action was likely to jeopardize the continued existence of any threatened or

endangered species, as required by section 7(a)(2). To hold otherwise would eviscerate

Congress' intent to "give the benefit of the doubt to the species."

Id. (emphasis added). Conner does not directly support the broader interpretation urged by Plaintiffs,

that the agency should err on the side of the species when evaluating uncertain evidence. Conner

stands for the proposition that an agency cannot abdicate its responsibility to evaluate the impacts of

an action on a species by labeling available information "uncertain," because doing so violates

Congress' intent that the agencies "give the benefit of the doubt to the species."

Center for Biological Diversity v. Lohn, 296 F.Supp.2d 1223, 1239 (W.D.Wash.2003) (rev'd on other

grounds, 483 F.3d 984 (9th Cir.2007)), applied the Conner holding in conformity with Plaintiffs'

interpretation. Lohn addressed the listing under the ESA of a population of orca whales. Despite

considerable record evidence suggesting the Orca whales should be considered a *361 separate

species, the Orca population had not yet been identified as a separate taxon. NMFS decided not to list

the species based on the scientific uncertainty that existed in the field of taxonomy, relying on the fact

that the new taxon had not yet been designated. The district court ruled this decision was arbitrary and

capricious:

Given the considerable morphological, behavioral, and genetic evidence that the global

Orcinus orca taxon is inaccurate and that residents and transients do not belong to the

same taxon, the decision not to list the Southern Residents cannot be based upon a lack of

consensus in the field of taxonomy regarding the precise, formal taxonomic redefinition

of killer whales, particularly when that lack of agreement is compounded by the extreme

difficulty in gathering evidence to achieve consensus. The best available science

standard gives "the benefit of the doubt to the species." Conner v. Burford, 848 F.2d

1441, 1454 (9th Cir.1988) (observing one of the purposes of the best available science

standard in review of whether agency action may result in destruction or adverse

modification of listed species' habitat pursuant to 16 U.S.C. § 1536(a)(2)). To deny listing

of a species simply because one scientific field has not caught up with the knowledge in

other fields does not give the benefit of the doubt to the species and fails to meet the best

available science requirement.

Id. at 1239 (emphasis added).[22]

In response, Defendant Intervenors cite Oceana, Inc. v. Evans, 384 F.Supp.2d 203 (D.D.C.2005), a

challenge to NMFS's choice between two estimates of how much take a particular type of fishing gear

would cause. The agency chose the lower estimate, reasoning that it was the "best estimate possible."

The plaintiff argued that this estimate failed to give the "benefit of the doubt" to the species. Id. at

228. Although the lower estimate was uncertain, the district court reasoned that "the ESA does not

require the agency to reject the `best estimate possible' in favor of a more `conservative' estimate that,

according to the scientists, would be lacking in support." Id.

Lohn and Oceana appear irreconcilable, but, they can be harmonized. Lohn rejected an agency's

decision to follow the taxonomy in the face of significant and compelling scientific evidence favoring

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a different *362 conclusion. To side with the agency under such circumstances would "not give the

benefit of the doubt to the species. . . ." Id. at 1239. In contrast, Oceana, concerned an agency's choice

of the "best estimate possible" over a more "conservative" estimate that lacked scientific support. The

Oceana court refused to ignore the general rule that an agency must choose the best available science,

simply because the ESA commands that the agency give the "benefit of the doubt" to the species.

Both cases stand for the proposition that the agency must carefully examine the available scientific

data and models and rationally choose the most reliable.

2. The BiOp's Failure to Address the 2004 Fall Midwater Trawl Data.

Plaintiffs assert that "one of the most egregious errors in the [BiOp] is its failure to consider available

fall 2004 Delta smelt abundance data, which evoked grave concern among agencies involved in smelt

management."[23] (Doc. 232 at 5.) On February 9, 2005, FWS and other CALFED members met to

discuss Delta smelt abundance. Among other things, participants discussed data from the 2004 fall

midwater trawl ("FMWT") survey, which revealed that "estimates of Delta smelt appear to be their

lowest since 1964." (Doc. 11 at 5; AR 9199-9200, 9202; Doc. 12.) The February 16, 2005, BiOp,

contained no mention of the 2004 FMWT data.

Plaintiffs assert that FWS acted arbitrarily, capriciously and unlawfully by "ignoring" the 2004

FMWT data and relying instead on the more favorable abundance data from earlier abundance

surveys. (AR 366-67 (noting that the 2003 FMWT results were more favorable than those from 2002,

while simultaneously acknowledging that the 2003 summer townet index (1.6) was "well below the

pre-decline average of 20.4 in (1959).").) Despite the receipt of the new, even less favorable 2004

FMWT data, FWS made no substantive changes to its jeopardy analysis in the biological opinion and

did not use or address the new data in any way, not even to explain why the data was not discussed.

At oral argument, the agency maintained that ESA analysis cannot go on forever, that there must be a

cutoff.

Plaintiffs note that the low population numbers revealed by the FMWT data were "not unexpected,"

as smelt abundance had been on a downward trend for at least two years prior. (AR 370-71; 9199-

9200, 9202.) One prominent smelt biologist warned at a June 2003 OCAP symposium that managers

should expect very low smelt abundance data in the near future and that water exports were a key

factor in the population decline, noting that the "cumulative proportion of the population lost to

exports relative to abundance" could be as high as 30 percent. (AR 5069.)

Federal Defendants suggest that Plaintiffs' entire argument should be rejected as internally

inconsistent. (Doc. 242 at 26-27.) Plaintiffs contend that FWS should have revised the BiOp in light

of the 2004 FMWT data and that additional evidence of a downward trend was "not unexpected."

These contentions are consistent with the central premise of Plaintiffs' position that the 2004 FMWT

data reflected a record low abundance (the data showed "estimates of Delta smelt appear to be at their

lowest since 1964" (Doc. 11 at 5)); so low that the data should have been addressed in the BiOp, even

if the agency already knew that smelt abundance was trending downward.

*363 The State Water Contractors suggest that Plaintiffs' acknowledgment that the downward trend

was "not unexpected," establishes that the BiOp fully recognizes the dire situation of the smelt. (Doc.

241 at 4.) The BiOp reflects that FWS had knowledge that smelt population levels were at extremely

low levels, "[s]ince 1983, the delta smelt population has exhibited more low FMWT abundance

indices, for more consecutive years, than previously recorded." (AR 367.)

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The results of seven surveys conducted by the Interagency Ecological Program (IEP)

corroborate the dramatic decline in delta smelt. . . . According to seven abundance indices

designed to record trends in the status of the delta smelt, this species was consistently at

low population levels during the last ten years (Stevens et al.1990). These same indices

also show a pronounced decline from historical levels of abundance (Stevens et al.1990).

(AR at 370.) The State Water Contractors' argument ignores that the 2004 FM-WT data evidences

record low (the lowest) smelt abundance. Plaintiffs maintain that FWS' acknowledgment of a

downward trend is inadequate as it does not address or analyze in survival and recovery terms, that

smelt abundance levels had reached the lowest ever recorded.

The State Water Contractors argue that, although the BiOp admits the fact of the smelt's declining

population, it does not and cannot explain the cause of the decline, because there is no scientific

consensus as to causation. (Doc. 241 at 5.) "Contributing to [this] uncertainty," "is the fact that SWP

and CVP operations have been ongoing for decades a period during which Delta smelt abundance has

increased as well as declined." (Id. at 6.) The State Water Contractors assert that the DSRAM was

adopted in part to protect the smelt while further monitoring and research is carried out to resolve

these uncertainties. They conclude that even if the 2004 FMWT data had been addressed in the BiOp,

the ultimate opinion reached would not have differed; i.e., that operation of the projects under the

2004 OCAP BiOp would not jeopardize the smelt because, among other things, take will remain at or

below historic levels and the DSRAM will protect smelt from salvage at project facilities.[24] But, this

is post hoc argument; neither the agency or the biological opinion addressed the 2004 FMWT data

and available scientific information opined that Project operations contributed to the decline of the

smelt.

The cases the parties cite do not answer whether FWS did not have to analyze most recent data

because it would not have altered the ultimate conclusion. Some cases suggest that FWS must use all

available information to ensure that a biological opinion analyzes the threats to a species in a

comprehensive manner. Plaintiffs refer to Greenpeace II, 80 F.Supp.2d at 1149-50, for the proposition

that failure to analyze and incorporate available data is fatal to a biological opinion.. In that case,

NMFS concluded in a biological opinion that the total groundfish catch authorized in the Bering Sea

and Gulf of Alaska in a single fishing season (1999) would not jeopardize the endangered Stellar sea

lion. NMFS limited the scope of the biological opinion to that single year of fisheries management

activities. The district court ruled that the agency should have broadened the scope of the biological

opinion to consider the overall fishery management regime, including relevant regulations and

specifications. Id. at 1146-47. This failure to produce a comprehensive biological opinion *364

permeated all other aspects of the agency's decision. The district court found fault with the BiOp's

superficial analysis, emphasizing the agency's failure to address the overall effects of the fisheries

upon the sea lion:

As far as the Court can ascertain, the focus of BiOp2 is limited to analyzing whether the

fisheries compete with the sea lion for prey. In particular, BiOp2 focuses on the potential

for localized depletions of prey caused by the fisheries. BiOp2 at 90, 112. Even with

respect to this limited topic of discussion, meaningful analysis is virtually non-existent.

NMFS itself repeatedly concludes in BiOp2 that it simply lacks the information to make

any determination one way or the other. See BiOp2 at 111-118. Thus, NMFS's analysis is

admittedly incomplete and its conclusions inconclusive. Although inconclusive data does

not necessarily render a particular scientific conclusion invalid, the limited scope and

quality of analysis that is contained in BiOp2 serves to highlight its overall inadequacy.

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For example, NMFS relies substantially on its conclusion that many of the target

groundfish species are not important sea lion prey, despite uncertain evidence. BiOp2 at

114. That many of the target species may not individually constitute a major prey source,

however, does not mean the cumulative impact of these fisheries is insignificant. In other

words, limited analysis which suggests the fisheries do not jeopardize the sea lion does

not obviate the requirement that NMFS address the full scope of the FMPs in order to

ascertain their overall effects. In sum, BiOp2 is limited in scope, heavy on general

background information, and deficient in focused and meaningful discussion and analysis

of how these large fisheries, and the complex management measures which regulate

them, affect endangered Steller sea lions. That NMFS now finds it necessary to undertake

yet another "comprehensive consultation" is a final indication to this Court that BiOp2 is

not the broad and in-depth consultation it was purported to be by NMFS, much less

coextensive in scope with the FMPs as required under the ESA.

A biological opinion which is not coextensive in scope with the identified agency action

necessarily fails to consider important aspects of the problem and is, therefore, arbitrary

and capricious. Here, BiOp2 not only fails to consider important aspects of the problem,

the analysis it does contain is simply not adequate. Although an agency need not rely on

conclusive scientific proof in a biological opinion, its conclusions must be based on "the

best scientific and commercial data available." 16 U.S.C. § 1536(a)(2). Thus, an agency

"cannot ignore available biological information or fail to develop projections" which

may indicate potential conflicts between the proposed action and the preservation of

endangered species. Conner, 848 F.2d at 1454.

Id. at 1149-50 (emphasis added).

In Greenpeace NMFS admitted that the information it needed to perform a more comprehensive

review was available, but argued that it "could not have been analyzed in the time allowed." Id. at

1150. The district court rejected this argument:

A federal agency . . . is not "excused from [fulfilling the dictates of the ESA] if, in its

judgment, there is insufficient information available to complete a comprehensive

opinion and it takes upon itself [a more limited analysis]." Conner, 848 F.2d at 1455. This

is not a situation where NMFS fully addressed the problem based on uncertain scientific

data. See Greenpeace Action v. Franklin, 14 F.3d 1324, 1337 (9th Cir. *365 1992).

Rather, NMFS entirely ignored relevant factors and admittedly failed to analyze and

develop projections based on information that was available.

Id. at 1150 (emphasis added); see also Conner, 848 F.2d at 1454 (biological opinion invalidated

because agency failed to "use best information available to prepare comprehensive biological opinions

considering all stages of agency action").

Plaintiffs analogize this case to Greenpeace II, because the agency has ignored available biological

information. Here, Plaintiffs complain that FWS failed to incorporate into existing models and

analyses that already reflected concern over an overall declining trend in smelt, the most recent survey

information, evidencing a more pronounced decline in smelt populations than ever before recorded. In

Greenpeace II, the agency entirely failed to perform a comprehensive review of threats to the sea lion.

The difference in degree is not significant.

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Federal Defendants cite Oceana, 384 F.Supp.2d 203, where NMFS concluded that an amendment to

the Atlantic Sea Scallop Fishery Management Plan would not jeopardize the protected loggerhead sea

turtle, based on a population model that involved a degree of uncertainty, but that the agency

determined was the "most reliable method." Id. at 215. The Oceana plaintiffs did not dispute that the

model represented the "best available science," instead arguing that the model was "so illsuited to the

purpose for which it was used, and so fraught with uncertainties," that the agency could not rationally

reach its no jeopardy conclusion. Id. at 218. The district court upheld the agency's use of the model,

reasoning "[t]ime and again courts have upheld agency action based on the `best available' science,

recognizing that some degree of speculation and uncertainty is inherent in agency decisionmaking,

even in the precautionary context of the ESA." Id. at 219. Though the ESA should not be

implemented "haphazardly, on the basis of speculation", id. at 219, the model "bears a rational

relationship to the reality it purports to represent" and no other alternative model was available, id. at

221.

The circumstances here are not analogous to those in Oceana, where the plaintiffs admitted that the

challenged model was the best, albeit uncertain, available science. Here, Plaintiffs maintain the

agency's failure to analyze the most recent smelt population information prevented consideration of

the best available, consequential scientific information.

Federal Defendants also rely on Greenpeace I, 14 F.3d at 1337, an earlier challenge to a Stellar sea

lion biological opinion. The Greenpeace I plaintiffs argued that the agency acted arbitrarily and

capriciously by approving certain fishery management measures despite uncertainty about the effects

of the measures on the sea lion. The Ninth Circuit concluded that the presence of some uncertainty did

not violate the best available science requirement in part because that BiOp analyzed all the available

data:

We hold that the Service has fulfilled its substantive duties as well. Despite Greenpeace's

assertions to the contrary, the Service supported its conclusions with ample data and

analysis. The June biological opinion indicates that the Service, the Alaska Fisheries

Science Center, and the National Marine Mammal Laboratory "analyzed all the available

data on the pollock fishery and Steller sea lions" in the Gulf of Alaska. The Service also

sought the recommendations of the Steller Sea Lion Recovery Team. The opinion

demonstrates that the Service evaluated the spatial and temporal distribution of

commercial fishing across the Gulf of Alaska. It *366 then addressed not only the total

biomass of pollock in the Gulf and the effects of fishery removals on that biomass, but

also the spatial and temporal distribution of pollock across the Gulf. And despite

Greenpeace's claims to the contrary, the Service did not ignore hydroacoustic surveys of

pollock biomass, but considered and compared them to bottom trawl surveys. Finally,

while the Service has repeatedly conceded that it was uncertain about the effectiveness of

its management measures, it premised these measures on a reasonable evaluation of

available data, not on pure speculation.

The biological opinions indicate that the Service, an expert agency, consulted with other

teams of experts to consider all relevant factors pertaining to the effects of the Gulf

fishery on the Steller sea lion. And they indicate that the Service did not ignore data, as

Greenpeace suggests. The Service's decision to go ahead with the 1991 fishery under the

proposed restrictions, despite some uncertainty about the effects of commercial pollock

fishing on the Steller sea lion, was not a clear error of judgment.

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(Emphasis added.) Id. at 1337. Here, unlike Greenpeace FWS failed to analyze all of the available

data on the Delta smelt, as the 2004 FMWT data is not mentioned in the BiOp. Nor has FWS resolved

uncertainties about the identified causes of the serious decline in Delta smelt abundance by adopting

unenforceable management measures.

"Although a decision of less than ideal clarity may be upheld if the agency's path may reasonably be

discerned, [a court] 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." Pacific Coast Fed'n of

Fishermen's Ass'ns v. United States Bureau of Reclamation, 426 F.3d 1082, 1091 (9th Cir.2005)

(internal citations and quotations omitted). "[W]hen reviewing a biological opinion, [a court may] rely

only `on what the agency actually said'. . . ." Id. (quoting Gifford Pinchot Task Force, 378 F.3d at

1072 & n. 9). Had FWS examined the FMWT 2004 data in the BiOp, the weight it gave to that data

would have been entitled to deference. The agency's silence cannot be afforded deference.

a. The timing of the 2004 FMWT Data relative to the issuance of the BiOp.

Federal Defendants complain the timing of the release of the 2004 FMWT data did not leave enough

time to address the data before issuance of the biological opinion. The record shows at the very latest,

the 2004 FMWT data was presented to FWS and other CALFED members on February 9, 2005, less

than a week before the February 16, 2005, issuance of the biological opinion. Federal Defendants

assert they were not required to rewrite the BiOp at the "eleventh hour." (Doc. 242 at 27).

Although the record shows the 2004 FMWT data was presented at the February 9, 2005 CALFED

meeting, it is unclear when FWS first saw this data. Plaintiffs' claim that the data was available in

December 2004, is not supported.[25] However, even assuming FWS was not aware of the 2004

FMWT data until February 9, 2005, the agency was not operating under a deadline. As in Greenpeace

II, where the agency's statutory duty was not excused because the data could not be *367 "analyzed in

the time allowed," 80 F.Supp.2d at 1150, here, FWS could have delayed releasing the biological

opinion until it had reviewed and analyzed the new abundance data, which was especially significant

as it showed Delta smelt abundance at its nadir.

Defendants and Defendant-Intervenors rejoin that the failure of the BiOp to directly address the 2004

FM-WT is harmless, because one of the DSRAM's trigger criteria is an index based upon the previous

years' FMWT results, calling for any new abundance data to be incorporated into the adaptive

management process. However, even if the data were considered later in the DSRAM process, no

designated protective actions are required to be taken in response to any of the triggering criteria.[26]

Federal Defendants raise a legitimate concern about having to prolong completion of the BiOp on the

eve of its release. In theory, new scientific information could arrive on FWS's doorstep on a daily

basis. If FWS was required to consider and address every new piece of information it received prior to

publication of its decision, it would be effectively impossible for the agency to complete a biological

opinion. But, this is not such a case. The FMWT is a credible and reliable Delta smelt population

abundance survey, regularly compiled on an annual basis, and relied upon by the agency in the past.

There is no rational reason to ignore such important data. The BiOp places great weight on the

FMWT as "the second longest running survey." (AR 366, 370). The agency does not suggest the time

of receipt of the 2004 FMWT data was unexpected. The agency's failure to acknowledge and analyze

the record low abundance levels revealed by the 2004 FMWT is unreasonable and violated its duty to

use the best available scientific information. 16 U.S.C. § 1536(a)(2).

Plaintiffs' motion for summary adjudication is GRANTED as to this claim.

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3. Global Climate Change Evidence.

Plaintiffs next argue that the BiOp ignored data about Global Climate Change that will adversely

affect the Delta smelt and its habitat. (Doc. 232 at 7.) This is potentially significant because the

BiOp's conclusions are based in part on the assumption that the hydrology of the water bodies affected

by the OCAP will follow historical patterns for the next 20 years. (AR 375 (explaining that CALSIM

II modeling involved making "adjustments to historic water supplies . . . by imposing future level land

use on historical meteorological and hydrologic conditions").)

In a July 28, 2004 comment letter, Plaintiff NRDC directed FWS's attention to several studies on the

potential effects of climate change on water supply reliability, urging that the issue be considered in

the BiOp. (AR 8552-56.) The comment letter stated:

The best scientific data available today establishes that global climate change is occurring

and will affect western hydrology. At least half a dozen models predict warming in the

western United States of several degrees Celsius over the next 100 years (Redmond,

2003). Such sophisticated regional climate models must be considered as part of the *368

FWS' consideration of the best available scientific data.8:43 AM 6/5/2007 Unfortunately,

the Biological Assessment provided by the Bureau to FWS entirely ignores global

climate change and existing climate change models. Instead, the BA projects future

project impacts in explicit reliance on seventy-two years of historical records. In effect,

the Biological Assessment assumes that neither climate nor hydrology will change. This

assumption is not supportable.

In California, a significant percentage of annual precipitation falls as snow in the high

Sierra Nevada mountains. Snowpack acts as a form of water storage by melting to release

water later in the spring and early summer months (Minton, 2001). The effects of global

climate change are expected to have a profound effect on this dynamic. Among other

things, more precipitation will occur as rain rather than snow, less water will be released

slowly from snowpack "storage" during spring and summer months, and flooding is

expected to increase (Wilkinson, 2002; Dettinger, 2003). These developments will make it

more difficult to fill the large reservoirs in most years, reducing reservoir yields and will

magnify the effect of CVP operations on downstream fishes (Roos, 2001). These

developments will also dramatically increase the cost of surface storage relative to other

water supply options, such as conservation.

While the precise magnitude of these changes remains uncertain, judgments about the

likely range of impacts can and' have been made. See e.g., U.S. Global Climate Action

Report-2002; Third National Communication of the United States Under the United

Nations Framework Convention on Climate Change at 82, 101 (2002).[FN3]. The Service

can and must evaluate how that range of likely impacts would affect CVP operations and

impacts, including the Bureau's ability to provide water to contractors while complying

with environmental standards. We therefore request that the Service review and consider

the work cited above, as well as the background and Dettinger presentation at a recent

climate change conference held in Sacramento, June 9-11, 2004 [citation omitted] and

climate change reports [citation omitted].

(AR at 8554-55 (emphasis added).)

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A second presentation by Michael Dettinger at a December 8-9, 2004 CALFED meeting, attended by

FWS staff, concluded that "warming is already underway . . ."; that this would result in earlier flows,

more floods, and drier summers; and that "California water supplies/ecosystems are likely to

experience changes earliest and most intensely." (Doc. 10 at 18.) Following Dettinger's presentation,

members of CALFED noted "the need to reevaluate water storage policies and ERP [Ecosystem

Recovery Program] recovery strategies, all of which would be affected by projected climate

changes." (Doc. 9 at 3.) The record reflects that extreme water temperatures can have dramatic

impacts upon smelt abundance. (AR 8979-80.)

In addition to the specific studies and data cited by NRDC, FWS scientists recognized the issue of

climate change warranted further consideration. At a June 2003 symposium entitled "Framing the

issues for Environmental and Ecological Effects of Proposed Changes in Water Operations: Science

Symposium on the State of Knowledge," a number of questions regarding climate change were raised,

including: "How does the proposed operations plan account for the potential effects of climate change

(e.g., El Nino or La Nina, long term changes in precipitation and runoff patters, or increases in water

temperature)?" (AR at 4839.)

*369 Plaintiffs argue that, despite this evidence that climate change could seriously impact the smelt

by changing Delta hydrology and temperature, the BiOp "did not so much as mention the probable

effects of climate change on the delta smelt, its habitat, or the magnitude of impacts that could be

expected from the 2004 OCAP operations, much less analyze those effects." (Doc. 232 at 8.)

Defendants and Defendant-Intervenors respond by arguing (1) that the evidence before FWS at the

time the BiOp was issued was inconclusive about the impacts of climate change; and (2) that, far from

ignoring climate change, the issue is built into the BiOp's analysis through the use of X2 as a proxy

for the location and distribution of Delta smelt.

a. Inconclusive Nature of Available Information Regarding the Impacts of Global Climate Change on

Precipitation.

Federal Defendants and the State Water Contractors characterize Mr. Dettinger's presentation, as

reflecting "a great deal of uncertainty that climate change will impact future precipitation." The

presentation is entitled "Climate Change Uncertainties and CALFED Planning." (Doc. 10 at 1.)

Dettinger acknowledges that, although current climate models "yield condence sistent warming

scenarios for California" (id. at 6), there is no similar consensus regarding the impact of warming on

future precipitation (id. at 7). Federal Defendants suggest that FWS "responsibly refused to engage in

sheer guesswork, and properly declined to speculate as to how global warming might affect delta

smelt." (Doc. 242 at 23.) But, the NRDC letter cited a number of studies in addition to Mr. Dettinger's

presentations, all of which predict that anticipated climate change will adversely impact future water

availability in the Western United States.

At the very least, these studies suggest that climate change will be an "important aspect of the

problem" meriting analysis in the BiOp. Pacific Coast Fed'n, 265 F.3d at 1034. However, as with the

2004 FMWT data, the climate change issue was not meaningfully discussed in the biological opinion,

making it impossible to determine whether the information was rationally discounted because of its

inconclusive nature, or arbitrarily ignored.[27]

b. X2 as a Proxy for Climate Change.

The State Water Contractors argue that the approaches taken in the DSRAM are "more than adequate

to deal with the projected impacts of climate change assuming *370 they occur." (Doc. 241 at 8.) For

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example, Plaintiffs' suggestion that climate change will produce earlier flows, more floods, and drier

summers is addressed by the DSRAM's X2 trigger. Flow level changes will be reflected in the

position of X2. If climate change alters water temperatures, DSRAM also includes a temperature

trigger, that monitors the temperature range within which successful Delta smelt spawning occurs.

The DSRAM offers no assurance that any mitigating fish protection actions will be implemented if

the X2 criteria is triggered. That X2 indirectly monitors climate change does not assuage Plaintiffs'

concerns that the BiOp has not adequately analyzed the potential impact of climate change on the

smelt.

The BiOp does not gauge the potential effect of various climate change scenarios on Delta hydrology.

Assuming, arguendo, a lawful adaptive management approach, there is no discussion when and how

climate change impacts will be addressed, whether existing take limits will remain, and the probable

impacts on CVP-SWP operations.

FWS acted arbitrarily and capriciously by failing to address the issue of climate change in the BiOp.

This absence of any discussion in the BiOp of how to deal with any climate change is a failure to

analyze a potentially "important aspect of the problem."[28]

Plaintiffs' motion for summary adjudication is GRANTED as to this claim.

D. There is No Rational Connection Between the No Jeopardy Finding and the Status of the Species.

Plaintiffs next allege that there is no rational connection between the record evidence and the BiOp's

"no jeopardy" conclusion. Plaintiffs first argue that the BiOp's approach to setting take limits is

arbitrary and capricious because FWS failed to consider defined take limits in the context of current

smelt abundance. Plaintiffs complain that the BiOp does not explain how its no jeopardy conclusion

can be justified in light of the admitted adverse effects of the project, along with indirect and

cumulative effects on the species.

In a formal consultation, the ESA requires FWS to "[f]ormulate its biological opinion as to whether

the action, taken together with cumulative effects, is likely to jeopardize the continued existence of a

listed species or result in the destruction or adverse modification of critical habitat." 50 C.F.R. §

402.14; see also 16 U.S.C. § 1536(a)(2). The phrase "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 C.F.R. § 402.02.

Agency action may be overturned if the agency has "relied on factors which Congress has not

intended it to consider, entirely failed to consider an important aspect of the problem, offered an

explanation for its decision that runs counter to the evidence before the agency, or is so implausible

that it could not be ascribed to a difference in view or the product of agency expertise." Pacific Coast

Fed'n, 265 F.3d at 1034. A court must ask "whether the agency considered the relevant factors and

articulated a rational connection between the facts found and the choice made." Id. The agency must

"examine *371 the relevant data and articulate a satisfactory explanation for its action including a

rational connection between the facts found and the choice made." Motor Vehicle Mfrs. Ass'n v. State

Farm Mutual Ins., 463 U.S. 29, 43, 103 S.Ct. 2856, 77 L.Ed.2d 443 (1983).

1. Plaintiffs' Argument that Salvage Underestimates Project Impacts on the Smelt.

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Plaintiffs assert that the BiOp's reliance on salvage is arbitrary and capricious because salvage is not a

reliable basis for setting Project take limits. Plaintiffs cite record evidence, including statements made

by smelt biologists and FWS employees, that salvage does not accurately estimate incidental take of

young Delta smelt. (See AR 8403, 7578.) The BiOp admits that salvages does not fully account for all

smelt losses. (AR 419 ("It should be noted that although salvage is used to index delta smelt take, it

does not reliably index delta smelt entrainment. Furthermore, delta smelt salvage is highly variable at

all time scales. . . . ).") Plaintiffs have not shown that a better measure of smelt take could have been

generated from available data. The agency is entitled to rely on this approach as it appears to be the

"best estimate possible," no party has suggested an alternative. See Oceana, 384 F.Supp.2d at 228.

This objection standing alone is insufficient to justify summary adjudication.

2. The BiOp's Approach to Estimating Future Take Without Considering the Smelt's Current

Abundance Is Arbitrary and Capricious.

The take limits are based on historic sampling from "salvage density" (number of fish taken per unit

of water), which data is adjusted using CALSIM II modeling to reflect water flows anticipated under

the circumstances of the final consultation. FWS's no jeopardy determination is based in part on flow

modeling for the final consultation scenario that predicted lower than historic salvage levels during

critical times. (AR 474) (finding that the level of anticipated take "is not likely to result in jeopardy to

the smelt because this level of take is at or below historical levels of take.")

A close examination of the administrative record reveals that this conclusion relies upon an

unsupported irrational assumption not justified by the record, i.e., that maintaining salvage at or below

historic salvage levels will ensure that the 2004 OCAP is not likely to jeopardize the continued

existence of the Delta smelt. First, by focusing only on how proposed operations will either increase

or decrease smelt take, FWS effectively limited its analysis to determining whether the magnitude of

the OCAP's impact upon the smelt would be different from the Projects' impact under the regulatory

historical baseline. FWS did not analyze how the absolute number of smelt taken during any given

period of Project operations will impact overall smelt abundance at the time of the 2005 BiOp or in

the future. Nor does the finding the smelt "still persists," even at the lowest recorded abundance

levels, have any meaning if the smelt's "persistence" is at a level at or near extinction. Evaluating

"persistence" instead of smelt population abundance is irrational, arbitrary, and runs counter to the

evidence before the agency.

The Ninth Circuit, in NWF v. NMFS, 481 F.3d 1224, 1235-36, invalidated a biological opinion in part

because it failed to view the agency action "in the present and future human and natural contexts."

Here, the BiOp similarly fails to provide a scientific explanation for why it is appropriate to set

incidental take without considering the most current smelt population data. This methodology fails to

take most *372 recent available natural conditions (i.e., the smelt's current and/or future population

abundance) into consideration. For example, if the smelt's population is currently 600,000, it might be

justifiable to permit a monthly take of over 30,000. However, if the smelt's current population is only

60,000, allowing 30,000 to be entrained in the pumps in a single Month would represent a 50%

reduction in smelt population. Even if the 30,000 figure was significantly lower than historic take,

Defendant-Intervenors agree "that salvage impacts cannot be accurately identified without a

population estimate." (Doc. 247 at 9 n. 13.)

DWR asserts that, in setting the take limits, the BiOp took into consideration concerns expressed by

experts that using historic information alone would not create an appropriate take limit. (See AR

4880, 5532, 5543). The first of the citations offered by DWR, an email sent by FWS's Wim Kimmerer

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to several individuals at DWR, EPA and elsewhere, states that there was some discussion at FWS

about "getting away from take as the principle criterion governing management and recovery of delta

smelt." (AR 4880.) The next page of this email goes on to admit that "determining what level of

mortality is acceptable or `safe' is going to be difficult . . . Ultimately . . . this should be done through

some sort of population model or viability analysis." (AR 4881 (emphasis added).) The other cited

communications express similar concerns. (See AR 5532, 5543.) It is time to do it, yet FWS continues

to profess the smelt population cannot be reliably measured.

DWR argues. that, together, the take limits and the DSRAM address these concerns by moving the

focus of management away from salvage. However, there is no way to know when or what measures

will be taken under the DSRAM, which leaves the existing take limits as the only enforceable

measures in the BiOp,[29] while the species heads toward extinction. Using flawed take limits and

refusing to quantify smelt population and recent viability trends create substantial doubt about the

reliability of the BiOp.

Defendants and Defendant-Intervenors suggest that sufficient information was simply not available to

accurately determine smelt abundance.[30] Plaintiffs rejoin by referring to an email sent by Zachary

Hymanson to Ryan Olah at FWS, with copies to others at concerned federal and state agencies. Mr.

Hymanson opined: "I think we are at the point where we should report and use quantified estimates of

the total number of individuals at the various life stages monitories. Quantified population and life

stage estimates of fishes around the world are routinely made with A LOT less data than we have for

delta smelt." (AR 7542 (emphasis in original).)

*373 The viability of Delta smelt has been under scrutiny for over ten years. No party has shown that

producing a reliable population estimate is scientifically unfeasible. Information does not have to be

perfect or infallible for the agency to be required to use it to create a population estimate. See

Greenpeace II, 80 F.Supp.2d at 1149-50 (finding it unlawful for agency to entirely ignore relevant

factor and fail to analyze and develop projections regarding that factor based on information that was

available); see also Conner, 848 F.2d at 1454 (biological opinion invalidated because agency failed to

"use best information available to prepare comprehensive biological opinions considering all stages of

agency action."). Without population estimates, it is arbitrary for the agency to conclude that project

operations will not result in jeopardy simply because the projects will take relatively fewer smelt than

they did in the past, in the face of the undisputed fact that the smelt population has been declining

steadily in recent years. Failing to incorporate any information about smelt population abundance into

the setting of the take limits is a fundamental failure rendering the BiOp arbitrary and capricious.

The San Luis Parties' rationalization of FWS's approach, setting the incidental take limits using a

model that does not take current abundance data into consideration, is that historic records reveal

"either no, or perhaps a very weak relationship, between juvenile abundance measured by the TNS

and adult abundance measured by the FMWT." (Doc. 247 at 5.) This "lack of [a] linear relationship

between the two indices, shows that events after the TNS, in late summer and early fall, are probably

affecting the number of juveniles that mature into spawners." (Doc. 247 at 6.) From the lack of a

linear relationship, San Luis infers that something other than salvage (i.e. entrainment in the pumps) is

causing the smelt's decline[31]

The BiOp interprets the data differently: In a near-annual fish like delta smelt, a strong

relationship would. be expected between number of spawners present in one year and

number of recruits to the population the following year. Instead, the stock-recruit

relationship for delta smelt is weak, accounting for about a quarter of the variability in

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recruitment (Sweetnam and Stevens 1993). This relationship does indicate, however, that

factors affecting numbers of spawning adults (e.g., entrainment, toxics, and predation)

can have an effect on delta smelt numbers the following year.

(AR at 364 (emphasis added).)[32] Plaintiffs refer to other record evidence creating *374 doubt that

salvage is not a statistically reliable indicator of smelt abundance, including high entrainment events

in the early 1980s and other "extreme events," including the El Mho of 1982-83, which caused

significant declines in smelt abundance. (AR 8979.)

The BiOp acknowledges that salvage can have an impact on smelt abundance (although the statistical

relationship is nonlinear). It is arbitrary and capricious for FWS to base take limits on a projection of

future salvage calculated without considering the most current or future smelt abundance and without

reliable smelt population estimate.

Plaintiffs' motion for summary adjudication is GRANTED as to this issue. The BiOp's approach to

setting incidental take limits is arbitrary and capricious because it fails to incorporate reliable smelt

population data and the most recent information regarding smelt abundance.

3. Plaintiffs' Argument That the Biop Fails to Explain How its No Jeopardy Conclusion Can Be

Justified in Light of the Identified Adverse Effects of the Project, along with Indirect and Cumulative

Effects.

In formulating a biological opinion, the ESA requires FWS to determine "whether the action, taken

together with cumulative effects, is likely to jeopardize the continued existence of listed species or

result in the destruction or adverse modification of critical habitat." 50 C.F.R. § 402.14 (emphasis

added). "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 C.F.R. § 402.02 (emphasis added).

The BiOp concludes that the 2004 OCAP will have numerous direct and indirect impacts apart from

salvage, including habitat loss, increased vulnerability of Delta smelt to predation, and increased

vulnerability to adverse temperature effects. (See AR 399, 443-44.) Plaintiffs allege that, although the

BiOp lists indirect impacts, it fails to explain how they relate to the potential for jeopardy.

Federal Defendants respond to this allegation with a single paragraph, asserting generally that "the

biological opinion considers the effects of dozens of project components, each with a multi-layered

analysis," and indicating how many times the topics of predation (18), temperature changes (180

references), life cycle impacts (75 references to the term "juveniles") are discussed in the BiOp. (Doc.

242 at 30.) What Federal Defendants do not do is point to those portions of the BiOp which analyze

these issues in a way that demonstrates why these indirect impacts will not cause jeopardy or how

they relate to survival and recovery of the smelt. A review of the BiOp does not reveal such an

analysis.

The State Water Contractors suggest that the DSRAM trigger criteria were designed to address all of

the potential impacts identified in the BiOp. (Doc. 241 at 8.) This leaves for future consideration and

speculation the impacts events activating DSRAM triggers will have.

a. Cumulative Impacts.

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Plaintiffs also argue that the BiOp fails to meaningfully address cumulative impacts, "those effects of

future State or private activities, not involving Federal activities, *375 that are reasonably certain to

occur within the action area of the Federal action subject to consultation." 50 C.F.R. § 402.02. The

BiOp highlights a number of predicted cumulative effects:

Any continuing or future non-Federal diversions of water that may entrain adult or larval

fish would have cumulative effects to the smelt. Water diversions through intakes serving

numerous small, private agricultural lands contribute to these cumulative effects. These

diversions also include municipal and industrial uses. State or local levee maintenance

may also destroy or adversely modify spawning or rearing habitat and interfere with

natural long term habitatmaintaining processes.

Additional cumulative effects result from the impacts of point and non-point source

chemical contaminant discharges. These contaminants include but are not limited to

selenium and numerous pesticides and herbicides as well as oil and gasoline products

associated with discharges related to agricultural and urban activities. Implicated as

potential sources of mortality for smelt, these contaminants may adversely affect fish

reproductive success and survival rates. Spawning habitat may also be affected if

submersed aquatic plants, used a[s] substrates for adhesive egg attachment, are lost due to

toxic substances.

Other cumulative effects could include: the dumping of domestic and industrial garbage

may present hazards to the fish because they could become trapped in the debris, injure

themselves, or ingest the debris; golf courses reduce habitat and introduce pesticides and

herbicides into the environment; oil and gas development and production remove habitat

and may introduce pollutants into the water; agricultural uses on levees reduce riparian

and wetland habitats; and grazing activities may degrade or reduce suitable habitat, which

could reduce vegetation in or near waterways.

(AR 468.) There is no quantitative and qualitative analysis of the potential impact of these cumulative

effects on the smelt and its habitat, except to identify the causes, the BiOp concludes without

explanation, "[t]he cumulative effects of the proposed action [are] not expected to alter the magnitude

of cumulative effects on the above described actions upon the critical habitat's conservation function

for the smelt." (Id.)

The San Luis Parties argue that FWS's no jeopardy conclusion and impacts analysis is "rationally

based on its determination that the proposed future changes will not significantly increase the

magnitude of the ongoing Project's potential impacts." (Doc. 247 at 9.) This conclusion is the kind of

analysis recently rejected by the Ninth Circuit in NWF v. NMFS:

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. *376

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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 background conditions place a species in jeopardy. To

leopardize" 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 agency may not "cause

[a species] to be or to become" in a state of jeopardy or "subject [a species] to" jeopardy.

American 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' preaction 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

survival 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.

Our approach does not require NMFS to include the entire environmental baseline in the

"agency action" subject to review. It simply requires that NMFS appropriately consider

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 challenge) that "[t]he 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." Pac. Coast Fed'n, 426 F.3d at 1093 (emphasis added).

481 F.3d at 1234-36 (emphasis added) (footnote omitted).

Here, the BiOp does not consider the cumulative effects of any future DSRAM actions, which it relies

on to avoid jeopardy, nor does it meaningfully relate the most current abundance of the species to

future OCAP operations to assess jeopardy. The BiOp unlawfully fails to adequately analyze indirect

and cumulative impacts of the 2004 OCAP. Summary adjudication on this issue is appropriate.

E. Did the BiOp Fail to Adequately Consider Impacts to Critical Habitat?

Plaintiffs allege that the BiOp fails to adequately consider critical habitat in two respects. First, by

failing to analyze the impacts of the 2004 OCAP on the value of critical habitat for the recovery as

opposed to just the survival of the smelt. Second, failure to consider impacts to all of the Delta smelt's

critical habitat because it focuses only on X2.

1. Did the BiOp Fail to Consider Whether 2004 OCAP Would Diminish Value of Critical Habitat for

Recovery?

The ESA requires FWS to determine whether the 2004 OCAP will destroy or adversely affect Delta

smelt critical habitat. 16 U.S.C. 1536(a)(2). "Destruction or adverse modification of critical *377

habitat" means "a direct or indirect alteration that appreciably diminishes the value of critical habitat

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for both the survival and recovery of a listed species. Such alterations include, but are not limited to,

alterations adversely modifying any of those physical or biological features that were the basis for

determining the habitat to be critical." 50 C.F.R. § 402.02

Initially, the critical habitat analysis was conducted pursuant to agency regulations that defined

adverse modification as:

[A] direct or indirect alteration that appreciably diminishes the value of critical habitat for

both survival and recovery of a listed species. Such alterations include, but are not

limited to, alterations adversely modifying any of those physical or biological features

that were the basis for determining the habitat to be critical.

50 C.F.R. § 402.02 (emphasis added).

Following the issuance of the 2004 BiOp, the Ninth Circuit invalidated the adverse modification

regulation, based on its own interpretation of the regulation's language, "alteration that appreciably

diminish the value of critical habitat for both the survival and recovery of a listed species," "reads the

`recovery' goal out of the adverse modification inquiry." Gifford Pinchot, 378 F.3d at 1069-70.

The Bureau requested that FWS reinitiate consultation on the 2004 OCAP to ensure compliance with

Gifford Pinchot. The result was the disputed 2005 BiOp, which expressly states that it does not rely

on the invalidated regulation. (AR 248.) Rather, the BiOp "relied on the statutory provisions of the

ESA to complete the analysis with respect to critical habitat." (Id.) The ESA defines critical habitat as

including "the specific areas . . . occupied by the species . . . which are . . . essential to the

conservation of the species" and the "specific areas outside the geographical area occupied by the

species . . . that . . . are essential for the conservation of the species. . . ." 16 U.S.C. § 1532(5)(A). This

statutory reference to "conservation" was the premise for the Ninth Circuit's Gifford Pinchot

reasoning:

"Conservation" is a much broader concept than mere survival. The ESA's definition of

"conservation" speaks to the recovery of a threatened or endangered species. Indeed, in a

different section of the ESA, the statute distinguishes between "conservation" and

"survival." Requiring consultation only where an action affects the value of critical

habitat to both the recovery and survival of a species imposes a higher threshold than the

statutory language permits

378 F.3d at 1070 (internal citation omitted).

The 2005 BiOp uses the term "conservation," rather than "survival" and/or "recovery," several times

in connection with its critical habitat analysis. In the "Critical Habitat Effects" section, the BiOp states

that the "primary constituent elements essential to conservation of the species will not be affected by

the proposed project." (AR 423.) In addition, after discussing critical habitat, including those areas

essential to spawning, transport, rearing and migration, the BiOp acknowledges impacts, but explains

that after the proposed diversions in the OCAP are implemented "the primary constituent elements [of

critical habitat] essential to the conservation of the species still function." (Id. at 371.)[33]*378 What

specific effects any DSRAM measures will have on the smelt are not described, nor is there

discussion of how the survival and recovery of the smelt will be accomplished.

The Ninth circuit explained in NWF v. NFMS, that the agency must conduct a "full analysis" of risks

to recovery.

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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

conduct 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,

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. The only reasonable interpretation of the

jeopardy regulation requires NMFS to consider recovery impacts as well as survival.

481 F.3d at 1236-39 (emphasis added).[34]

Plaintiffs claim that although the BiOp includes generic promises to consider recovery of the smelt, it

does not competently analyze nor provide for recovery. Federal Defendants and Defendant

Intervenors respond that the BiOp's discussion of critical habitat effects, in conjunction with the

BiOp's conclusion that "the smelt's primary constituent elements essential to the conservation of the

species [will] still function" (AR 371) under the 2004 OCAP, is `a sufficient analysis of the impacts

on recovery.

The BiOp's overarching conclusion is that "the smelt's primary constituent elements essential to the

conservation of the species [will] still function." In designating critical habitat for a listed species,

FWS must "consider those physical and biological features that are essential to the conservation of

[the] species and that may require special management considerations or protection." 50 C.F.R. §

424.12. The features that must be considered include, but are not limited to, the following:

1. Space for individual and population growth, and for normal behavior;

2. Food, water, air, light, minerals, or other nutritional or physiological requirements;

3. Cover or shelter;

4. Sites for breeding, reproduction, rearing of offspring, germination, or seed dispersal;

and

5 Habitats that are protected from disturbance or are representative of the historic

geographical and ecological distributions of a species.

Id. The BiOp explained that, in designating critical habitat for the Delta smelt, FWS identified the

following primary constituent elements "essential to the conservation of the species":

*379 Physical habitat, water, river flow, and salinity concentrations required to maintain

delta smelt habitat for spawning, larval and juvenile transport, rearing, and adult

migration.

* * * * * *

Specific areas that have been identified as important delta smelt spawning habitat include

Barker, Lindsey, Cache, Prospect, Georgiana, Beaver, Hog, and Sycamore sloughs and

the Sacramento River in the Delta, and tributaries of northern Suisun Bay.

Larval and juvenile transport. Adequate river flow is necessary to allow larvae from

upstream spawning areas to move to rearing habitat in Suisun Bay and to ensure that

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rearing habitat is maintained in Suisun Bay. To ensure this, X2 must be located westward

of the confluence of the Sacramento-San Joaquin Rivers, located near Collinsville

(Confluence), during the period when larvae or juveniles are being transported, according

to historical salinity conditions. X2 is important because the "entrapment zone" or zone

where particles, nutrients, and plankton are "trapped," leading to an area of high

productivity, is associated with its location. Habitat conditions suitable for transport of

larvae and juveniles may be needed by the species as early as February 1 and as late as

August 31, because the spawning season varies from year to year and may start as early

as December and extend until July.

Rearing habitat. An area extending eastward from Carquinez Strait, including Suisun,

Grizzly, and Honker bays, Montezuma Slough and its tributary sloughs, up the

Sacramento River to its confluence with Three Mile Slough, and south along the San

Joaquin River including Big Break, defines the specific geographic area critical to the

maintenance of suitable rearing habitat. Three Mile Slough represents the approximate

location of the most upstream extent of historical tidal incursion. Rearing habitat is

vulnerable to impacts of export pumping and salinity intrusion from the beginning of

February to the end of August.

Adult migration. Adequate flow and suitable water quality is needed to attract migrating

adults in the Sacramento and San Joaquin river channels and their associated tributaries,

including Cache and Montezuma sloughs and their tributaries. These areas are vulnerable

to physical disturbance and flow disruption during migratory periods.

(AR 368-69.)

The BiOp acknowledges that this Delta smelt critical habitat has been adversely affected by numerous

activities, but indicates that the 1994 and 1995 OCAP BiOps "provide a substantial part of the

necessary riverine flows and estuarine outflows that allow smelt larvae to move downstream to

suitable rearing habitat . . . outside the influence of marinas, agricultural diversions, and Federal and

State pumping plant." (AR 371.) The BiOp also explains that increasing demands for surface water

"would likely result in lower delta outflows and increased entrainment," but that the impacts of these

demands "have not altered critical habitat's conservation function for the delta smelt, and the smelt's

primary constituent elements essential to the conservation of the species still function." (Id.) Finally,

the BiOp concludes:

In evaluating the Status of the Species for critical habitat and the Environmental Baseline,

while there are current actions that result in adverse effects to delta smelt critical habitat,

the primary constituent elements continue to remain functional for the smelt. In the

effects section, the Service determined that the primary constituent elements of delta

*380 smelt critical habitat would not be affected by the proposed project since there will

not be a loss of physical habitat in the delta, river flows will continue to provide habitat,

salinity will not be affected by the proposed project, and no breeding habitat will be

affected and the sustainability of the food base will not be affected. In the cumulative

effects section, we determined that the cumulative effects of the proposed action are not

expected to alter the magnitude of future actions' effects on critical habitat's conservation

function for the smelt. Based on the analysis in these four areas, it is our conclusion that

Critical habitat is not likely to be adversely modified or destroyed as a result of

implementing the proposed project.

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(AR 469 (emphasis added).)

These conclusions are not supported by most recent smelt data to corroborate that the primary

constituent elements of Delta smelt habitat will still function in a manner consistent with conservation

(i.e.recovery). The functions and their locations are identified, but impacts upon breeding habitat are

not analyzed. Second, although "there will still be water in the Delta. . . . whether the water will be of

adequate quality and quantity to allow the delta smelt to recover is an entirely different

question." (Doc. 306 at 25.) The BiOp does not analyze the water supply, temperature, and quality

under variable conditions with results that demonstrate the impact on smelt, nor is such an analysis

found elsewhere in the administrative record.[35]

The analysis of the predicted movement of X2 is more specific. When X2 is located upstream of

Chipps Island, smelt are vulnerable to entrainment and are located in an area that is not ideal for

feeding or protection. (See AR 424.) FWS opines that smelt reproduce better when X2 remains in a

specific area, west of the confluence of the Sacramento and San Joaquin Rivers. That smelt

reproduction is increased and the fish may be located where there are better sources of food does not

assure that the smelt are on a path to recovery. The DSRAM is to provide the means by which FWS

will maintain X2 in the most beneficial location. As the DSRAM is uncertain, speculative, and

lacking enforceable action measures, there is no reasonable assurance that X2 will be maintained in

the necessary protective location.

DSRAM utilizes other trigger criteria, arguably aimed at the recovery of the smelt. (Doc. 241 at 13-

14.) One criteria is the "recovery index trigger," derived from the September and October FMWT

sampling. (AR 347; Sommer Decl. at 119a.) The number used to trigger the DSWG is 74, the median

value of the recovery index for the 1980-2002 period. Whenever the recovery index falls below this

median, the DSWG convenes to decide whether to recommend actions. (AR 346-47.) Use of the term

"recovery" in the title of the trigger index, suggests that this index will serve to monitor the potential

for the smelt population to recover. This title is inaccurate. All that this trigger criteria monitors is

whether the abundance of smelt drops below the 1980-2002 median abundance. As smelt have been in

decline throughout the period to February 2005, the opinion that maintaining abundance slightly

above this median leads to recovery of the smelt is unjustified.

The temperature trigger criterion of 12-18° C, the range within which the most *381 smelt spawning

occurs, is more arguably focused on recovery. (AR 347.) If the number of days falling within the

temperature range is 39 days or less by April 15, or 50 days or less by May 1, DSWG is triggered.

This trigger is arguably related to the recovery of smelt, because it focuses on spawning. However, no

action except a group meeting is required in response to the trigger. Moreover, maximizing the

potential for smelt to spawn is only one aspect of recovery. If Project operations and/or other impacts

kill more smelt than are produced during spawning, recovery does not occur. The existence of this

trigger, alone, does not establish that recovery of smelt was adequately considered or addressed.[36]

2. The Biop Does Not Adequately Assess Impacts to All Areas of Critical Habitat.

Plaintiffs also allege that the BiOp arbitrarily ignores impacts to certain areas of critical habitat

because it focuses on X2 as a proxy for Delta smelt habitat. Plaintiffs argue that the focus on X2

ignores other areas of designated critical habitat.

The BiOp focuses on the impact project operations have had and will have on the position of X2.

Defendants and Defendant-Intervenors argue that critical habitat will be protected, because any

impacts to the position of X2 will be addressed by the DSRAM. The State Water Contractors contend

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that protecting critical habitat outside X2 "makes no sense if they are not the areas in which the fish

resides." (Doc. 241 at 17.)

Plaintiffs do not dispute the notion that X2 directly relates to where most smelt are located. Rather,

Plaintiffs maintain that critical habitat is not coextensive with X2. The BiOp identifies numerous

areas in which smelt occur (AR 362) and acknowledges that X2 "does not necessarily regulate smelt

distribution in all years." (Id.) Delta smelt critical habitat is defined by physical boundaries:

California Areas of all water and all submerged lands below ordinary high water and the

entire water column bounded by and contained in Suisun Bay (including the contiguous

Grizzly and Honker Bays); the length of Montezuma Slough; and the existing contiguous

waters contained within the Delta, as defined by section 12220, of the State of

California's Water Code of 1969 (a complex of bays, dead-end sloughs, channels

typically less than 4 meters deep, marshlands, etc.) as follows:

Bounded by a line beginning at the Carquinez Bridge which crosses the Carquinez Strait;

thence, northeasterly along the western and northern shoreline of Suisun Bay, including

Goodyear, Suisun, Cutoff, First Mallard (Spring Branch), and Montezuma Sloughs;

thence, upstream to the intersection of Montezuma Slough with the western boundary of

the Delta as delineated in section 12220 of the State of California's Water Code of 1969;

thence, following the boundary and including all contiguous water bodies contained

within the statutory definition of the Delta, to its intersection with the San Joaquin River

at its confluence with Suisun Bay; thence, westerly along the south shore of Suisun Bay

to the Carquinez Bridge.

59 Fed.Reg. 65,256, 65,277 (Dec. 19, 1994).

Federal Defendants respond that "the agencies have developed an operating *382 and adaptive

management system that adequately protects the existing critical habitat, that reasonably uses X2 as

an evaluation tool, and that also ensures that `additional measures' will be taken in accordance with

the DSRAM to affirmatively and proactively manage habitat, as needed." (Doc. 242 at 26.) But, apart

from the X2 analyses, Federal Defendants identify no other record evidence that reflects the agency

analyzed impacts to critical habitat or that any "additional measures" will be required under DSRAM,

as the DSRAM does not require any measure be implemented.

Defendant Intervenors assert that it is unnecessarily costly to accommodate impacts to all of the

geographically designated critical habitats because the smelt are not located in the entirety of their

critical habitat range all of the time. They argue the focus must be on protecting the habitat occupied

by the smelt. Even if more sensible, the law requires that the agency analyze whether project

operations will directly or indirectly alter critical habitat in a way that "appreciably diminishes the

value of critical habitat for both the survival and recovery of a listed species." 50 C.F.R. § 402.02.

"Such alterations include, but are not limited to, alterations adversely modifying any of those physical

or biological features that were the basis for determining the habitat to be critical." Id. The statute

defines critical habitat to include both "the specific areas within the geographical area occupied by the

species . . . on which are found those physical or biological features . . . essential to the conservation

of the species" and "specific areas outside the geographical area occupied by the species . . . upon a

determination by the Secretary that such areas are essential for the conservation of the species." 16

U.S.C. § 1532(5)(A). The definition of critical habitat is broader than the specific areas of occupation.

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Here, the agency defined critical habitat to have a geographic scope. Absent any alterations to the

critical habitat designation, the agency must address in the BiOp the full extent of impacts to the

currently designated critical habitat,[37] which excluded "already degraded areas." Alternatively, the

Delta smelt's critical habitat should be redefined to reflect the actual location of the smelt, if such

redesignation would be consistent with law.

This has not been done. Plaintiffs motion for summary adjudication is GRANTED as to this issue.

F. Did the BiOp Fail to Address the Impacts of the Whole Project?

1. Plaintiffs' Argument That the Biop Should Have Analyzed the Effects of Constructing the SDIP,

Intertie, and FRWP.

Plaintiffs complain that the BiOp's scope is unlawfully narrow because it fails to consider all planned

actions. The BiOp includes within its formal consultation, "delivery of CVP water, to the proposed

Freeport Regional Water Project (FRWP)" as well as the "operation of the SWP-CVP intertie." The

BiOp designates as an early consultation issue "operations *383 of components of the South Delta

Improvement Program (SDIP)," which include "permanent barrier operations in the South

Delta." (AR 248.) The effects of constructing the FRWP, the Intertie, and the permanent barriers are

to be covered in separate formal consultations. (AR 256, 339, 341, 421.)

The ESA requires FWS to address impacts associated with the entire agency action. See Conner, 848

F.2d at 1453-54 (holding that agency violated ESA by choosing not to analyze the effects of all stages

of oil and gas activity on federal lands). According to ESA regulations, the effects of an agency action

include "direct and indirect effects of an action on the species or critical habitat, together with the

effects of other activities that are interrelated or interdependent with that action, that will be added to

the environmental baseline." 50 C.F.R. § 402.02. "The meaning of `agency action' is determined as a

matter of law by the Court, not by the agency." Greenpeace II, 80 F.Supp.2d at 1146 (citing Pacific

Rivers Council v. Thomas, 30 F.3d 1050, 1054 (9th Cir. 1994).)

The BiOp explains -its approach to scope as follows:

The proposed action is to continue to operate the CVP and SWP in a coordinated manner.

In addition to current day operations, several future actions are to be included in this

consultation. These actions are: (1) increased flows in the Trinity River, (2) 8500 Banks,

(3) permanent barriers operated in the South Delta, (4) an intertie between the California

Aqueduct (CA) and the Delta-Mendota Canal (DMC), (5) a long-term EWA, (6) delivery

of CVP water to the FRWP, and (7) various operational changes that are identified in this

project description. Some of these items will be part of early consultation including 8500

Banks, permanent barriers and the long-term EWA. These proposed actions will come

online at various times in the future. Thus, the proposed action is continued operation of

the Project without these actions, and operations as they come online.

The actions listed in the preceding paragraph are not being implemented at present;

however, they are part of the future proposed action on which Reclamation is consulting.

Only the operations associated with the proposed activities are addressed in this

consultation; i.e., the activities do not include construction of any facilities to implement

the actions. All site specific/localized activities of the actions such as

construction/screening and any other site specific effects will be addressed in separate

action specific section 7 consultations.

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(AR at 256 (emphasis added).) In sum, only those aspects of the 2004 OCAP that will be

implemented without further approval were the subject of formal consultation. However, certain other

changes that will be effectuated in the future were the subject of early consultation. With respect to

future operational changes, including some subject to formal consultation, full implementation will

require the construction of specified facilities. The impact of the construction activities themselves

will be the subject of separate § 7 consultation.

Plaintiffs argue that the BiOp should have addressed the full impacts of construction of the Intertie,

Freport diversion, and the SDIP because those projects are within the scope of the agency action as a

whole and are "interrelated and interdependent" with the 2004 OCAP.[38]

*384 In response, Federal Defendants cite the Endangered Species Consultation Handbook, which

explains, in a hypothetical example, that operation of an existing dam project need not be considered

an interrelated or interdependent activity, where the agency action being evaluated in a biological

opinion was the addition of a new turbine to an existing dam.[39] (Handbook at 4-25 to 4-29.)

Although not cited by the Federal Defendants for this purpose, the Handbook also describes a general

approach FWS should use when determining whether certain actions are "interrelated or

interdependent," so as to be considered part of the action:

Interrelated and interdependent actions: Effects of the action under consultation are

analyzed together with the effects of other activities that are interrelated to, or

interdependent with, that action. An interrelated activity is an activity that is part of the

proposed action and depends on the proposed action for its justification. An

interdependent activity is an activity that has no independent utility apart from the action

under consultation. (Note: the regulations refer to the action under consultation as the

"larger action" [50 CFR § 402.02] ). . . .

As a practical matter, the analysis of whether other activities are interrelated to, or

interdependent with, the proposed action under consultation should be conducted by

applying a "but for" test. The biologist should ask whether another activity in question

would occur "but for" the proposed action under consultation. If the answer is "no," that

the activity in question would not occur but for the proposed action, then the activity is

interrelated or interdependent and should be analyzed with the effects of the action. If the

answer is "yes," that the activity in question would occur regardless of the proposed

action under consultation, then the activity is not interdependent or interrelated and

would not be analyzed with the effects of the action under consultation. There will be

times when the answer to this question will not be apparent on its face. The biologist

should ask follow-up questions to the relevant parties to determine the relationship of the

activity to the proposed action under consultation. It is important to remember that

interrelated or interdependent activities are measured against the proposed action. That is,

the relevant inquiry is whether the activity in question should be analyzed with the effects

of the action under consultation because it is interrelated to, or interdependent with, the

proposed action. Be careful not to reverse the analysis *385 by analyzing the relationship

of the proposed action against the other activity. For example, as cited below, if the

proposed action is the addition of a second turbine to an existing dam, the question is

whether the dam (the other activity) is interrelated to or interdependent with the proposed

action (the addition of the turbine), not the reverse.

Section 7 Handbook at 4-26.

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Here, applying the Handbook test, the question is whether the other activities (construction and

operation of SDIP, Freeport, and the Intertie) are interrelated to or interdependent with the proposed

actions subject to formal consultation? The formal consultation, as described in the BiOp, covers

. . . the proposed 2020 operations of the CVP including the Trinity River Mainstem ROD

(Trinity ROD) flows on the Trinity River, the increased water demands on the American

River, the delivery of CVP water to the proposed Freeport Regional Water Project

(FRWP), water transfers, the long term Environmental Water Account (EWA), the

operation of the Tracy Fish Facility, and the operation of the SWP-CVP intertie. The

effects of operations of the SWP are also included in this opinion and include the

operations of the North Bay Aqueduct, the Suisun Marsh Salinity Control Gates, the

Skinner Fish Facility and water transfers.

(AR 248 (emphasis added).) The formal consultation admittedly covers delivery of CVP water to the

proposed FRWP and operation of the Intertie. But, the BiOp expressly excludes the impacts of

construction associated with FRWP or the Intertie:

The actions listed in the preceding paragraph [including permanent barriers in the South

Delta, an intertie, and the FRWPI are not being implemented at present; however, they

are part of the future proposed action on which Reclamation is consulting. Only the

operations associated with the proposed activities are addressed in this consultation; i.e.,

the activities do not include construction of any facilities to implement the actions. All

site specific/localized activities of the actions such as construction/screening and any

other site specific effects will be addressed in separate action specific section 7

consultations.

(AR 256 (emphasis added).)

Is there a "but-for" relationship between the 2004 OCAP and the new projects? The FRWP and the

Intertie are designed to more effectively distribute CVP and SWP waters. There is no evidence in the

record indicating that construction of either project is tied in any way to the preapproval of delivery of

water to the projects. Flow operations could be approved after or simultaneously with the approval of

new construction. Under the Handbook test, the construction projects are not considered

interdependent and interrelated. These projects may be consulted upon separately. By approving a

flow regime before the construction, the Bureau may plan for the possibility that the FRWP will be

constructed in the future. The entire OCAP BiOp would not need to be revised should the projects be

constructed. This is a reasonable approach.

With respect to the SDIP, the BiOp currently excludes both its operation and related construction

coverage under the formal consultation. Plaintiffs allege that both should have been covered by the

BiOp because they are interrelated with or interdependent on the agency action. Applying the

Handbook analysis, the operation and construction of the SDIP (which includes increased pumping at

Banks and operation of permanent barriers) will not occur "but for" the approval of the 2004 OCAP

for CVP-SWP operations? Each action is independent of the 2004 OCAP. *386 The SDIP is a

separate addition that may or may not be constructed. Project operations under the 2004 OCAP in no

way depend upon the SDIP. There is no prohibition to addressing the future operation, if and when

the construction of the SDIP will occur, in a separate consultation.

Plaintiffs' motion for summary adjudication is DENIED as to the future projects issue.

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2. Plaintiffs' Argument that the BiOp Failed to Analyze the Impact of Full Contract Deliveries.

A biological opinion must consider the effects of the entire agency action, meaning "all activities or

programs of any kind authorized, funded, or carried out," including "the granting of . . . contracts." 50

C.F.R. § 402.02. One of the primary purposes of the 2004 OCAP is to "deliver water supplies to

affected water rights holders as well as project contractors." (AR 259.) The Bureau delivers water to

numerous parties pursuant to long-term contracts ("CVP Contracts"), some of which were renewed

shortly after the BiOp was issued. (AR 4732, 4796, 4855.)

The CALSIM II model incorporated water deliveries into its various flow scenarios, but only

performed its analysis based on the effects of delivering between 11 and 89 percent of the full CVP

Contract allocations. (See AR 1067; see also Doc. 242 at 31 (acknowledging that the agency "did not

evaluate the impacts of 100% percent delivery of all contracted waters").) This range of delivery

scenarios is based on historic average water deliveries.

Plaintiffs allege that, by failing to evaluate the impact of delivering full amount (100%) of contracted

water, the BiOp violates the requirement that the it evaluate the entire agency action. Plaintiffs cite

Rodgers, 381 F.Supp.2d at 1237-40, which examined a biological opinion approving long term water

contracts in the Friant, Buchanan, and Hidden water units of the CVP. The BiOp only examined the

impacts of the amount of historical water deliveries, which amounted to less than half of the water

deliveries authorized under the long term water service contracts. Id. at 1237-28.

The Friant long-term contracts cumulatively authorized the Bureau to deliver more than

2.1 million acre-feet of water per year, for twenty-five years. Rather than analyzing the

effects of 2.1 million acre-feet of water delivery, FWS explained that its "effects analysis

is conducted under the expectation that water will be delivered to CVP service

contractors in quantities that approximate historic deliveries (1988 through 1997), as

given in Appendix D of the November 21, 2000 programmatic long-term CVP contracts

consultation." This assumption was made, the BiOp explained, because "delivery of full

contract quantities is unrealistic."

Id. at 1238. Rodgers rejected FWS's approach, reasoning that the "ESA requires that all impacts of

agency action-both present and future effects-be addressed in the consultation's jeopardy analysis."

The fact that it was thought by FWS that "delivery of full contract quantities is

unrealistic" and that "deliveries continue to be impacted by existing climate, hydrology,

actions and statutes, . . . socio-economic factors" does not excuse consulting on the

"entire agency action," which was the authorized delivery of over 2.1 million acre-feet of

water, and nothing less than that.

Id. at 1239.

Federal defendants assert that the Rodgers decision was wrong, arguing that "[a]bsent alternative

information that the agency failed to consider, and given the fact that the agency did use the best

available information, the Rodgers court should *387 have deferred to the agency." (Doc. 242 at 32.)

It is not the province of another district court to decide whether Rodgers is "wrong." Rodgers is

distinguishable as it specifically addressed the government authorization of CVP water users' longterm water service contracts. Those contracts authorized 2.1 MAF of water deliveries in total.

Rodgers found unlawful the biological opinion's limitation in its scope to approximate historic

deliveries, instead of the full contract allocations. Here, however, the agency action subject to

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consultation is not the authorization or merits of the water service contracts, rather, it is the operation

of the CVP and SWP under the OCAP and whether those projected operations will cause jeopardy to

the survival and recovery of smelt or smelt habitat. The government is entitled to make reasonable

assumptions about the operational volume of water flows, water levels, temperature, and quality based

on the historical and projected data in the administrative record. The BiOp explains that the delivery

of full water service contract entitlements is expected only when excess water conditions exist, i.e., in

a wet water year when sufficient water is available to meet all beneficial needs. (AR 259.) Plaintiffs

do not suggest that this assumption is factually impossible. (Nor would it be unreasonable for FWS to

model a full (100%) water contract delivery scenario, even if it has not happened in the past fifteen

years.) The agency model for the worst case scenario is indispensable. Analysis of a "best of the best"

case in a wet water year is not indispensable, as such "wet" water year conditions do not present any

reasonable likelihood of jeopardy, absent an additional showing. However, because such a scenario

could eventuate, it is not unlawful for the agency to analyze the effects on the smelt of 100% water

contract deliveries. However, the 100% delivery analysis is not required. This is a matter committed

to the agency's expertise and discretion.

Plaintiffs motion for summary adjudication is DENIED as to this issue.

VIII. CONCLUSION

As the history of the many CVP water cases decided in this court evidences, the duty to defer to the

agency's expertise is well recognized and honored, when the agency has acted reasonably and

lawfully to discharge its statutory responsibilities. The disputed BiOp depends in material measure for

its no jeopardy finding on the DSRAM, which is legally insufficient. The agency's recognition the

Delta smelt is increasingly in jeopardy; that its operative BiOp is inadequate, as evidenced by its

second initiation of reconsultation for the 2004 OCAP, now pending, and its insistence that it will

nonetheless operate the Projects under the challenged BiOp is unreasonable. The agency could have,

but did not, offer a viable protective alternative. Adaptive management is within the agency's

discretion to choose and employ, however, the absence of any definite, certain, or enforceable criteria

or standards make its use arbitrary and capricious under the totality of the circumstances.

The agency's failure to reasonably estimate the Delta smelt population and to analyze most recent

smelt abundance data make the take limits based on historical data unreliable and unreasonable. The

Delta smelt is undisputedly in jeopardy as to its survival and recovery. The 2005 BiOp's no jeopardy

finding is arbitrary, capricious, and contrary to law.

For all the reasons set forth above, the 2005 OCAP BiOp is unlawful and inadequate on the following

grounds:

(1) The DSRAM, as currently structured, does not provide a reasonable degree of

certainty that mitigation actions will take place, even if the *388 agency retains the

discretion to draw upon numerous sources of water, not just the EWA, CVPIA(b)(2), and

VAMP programs, to support fish protection.

(2) The agency failed to utilize the best available scientific information by not addressing

the 2004 FMWT data and the issue of climate change.

(3) The BiOp's historical approach to setting take limits fails to consider take in the

context of most recent overall species abundance and jeopardy.

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(4) The BiOp did not adequately consider impacts to critical habitat by (a) failing to

analyze how project operations will impact the value of critical habitat for the recovery of

the smelt and (b) failing to consider impacts upon the entire extent of known smelt

critical habitat.

The Plaintiffs' motions for summary judgment are GRANTED IN PART AND DENIED IN PART, as

delineated above.

Based on the legally flawed BiOp, an appropriate interim remedy must be implemented. All parties

agree that it is not prudent to impose a remedy without further input from the parties. A separate

remedies hearing will be scheduled within thirty days at the parties' mutual convenience.[40] During

oral argument, Federal Defendants and Defendant-Intervenors jointly requested a stay of any order

finding the BiOp unlawful to avoid the draconian consequences of operating the CVSWP without a

lawful take limit. Affording all parties the opportunity to participate in a remedies hearing will not

jeopardize the species or the public interest during interim operation of the projects. Plaintiffs did not

object to such an approach.

A Scheduling Conference is set for May 30, 2007, at 8:45 a.m. in Courtroom' 3 to afford the parties

time for discussions to set a remedies hearing, and to consider the entry of a stay, if necessary.

Plaintiffs shall submit a form of order on the motions for summary judgment consistent with this

decision within five (5) days following service of this decision.

IT IS SO ORDERED.

NOTES

[1] The Delta smelt was listed as a threatened species under the ESA, March 5, 1992, 58 Fed.Reg.

12863.

[2] The biological opinion was first issued in July 2004. Then, after reconsultation, was reissued in

February 2005.

[3] All "AR" references are to the administrative record provided by the U.S. Fish and Wildlife

Service..

[4] Whether the 2004 OCAP is a "final agency action" for the purposes of the National Environmental

Policy Act is at issue in a related lawsuit, Pacific Coast Federation of Fishermen's Associations v.

Gutierrez, 1:06-cv-00245 OWW (TAG) ("PCFFA"). This overview of the OCAP does not prejudge

the merits of the pending motion to dismiss in PCFFA.

[5] The OCAP itself does not plan for increased pumping or the construction or operation of any new

facilities, nor does it describe or model flow regimes under any, of these future plans. These planned

operational changes are set forth in the BA and the BiOp. (See AR 381-423) (describing the effects of

those actions included in formal consultation, including re-operation of the Trinity River, increased

demands on the American River, operation of the Freeport Regional Water Project ("FRWP"), and

operation of an intertie between the Delta-Mendota Canal and the California Aqueduct); AR 357-61

(describing the "items for early consultation," including operation of components of the South Delta

Improvement Project, which calls for pumping at Banks to increase to 8500 cfs, operation of

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permanent barriers in various places within the Delta, the operation of a long term EWA, the use of

CVP/SWP capacity to facilitate expanded water transfers, and further integration of CVP/ SWP

operations.)

[6] The first step in the consultation process is usually the preparation of a Biological Assessment

("BA") by the action agency (in this case, the Bureau), the purpose of which is to "evaluate the

potential effects of the action on listed [] species and designated [] critical habitat and determine

whether any such species or habitat are likely to be adversely affected by the action. . . ." 50 C.F.R. §

402.12(a). In this case, the Bureau issued its BA regarding the "Long-Term Central Valley Project and

State Water Project Operations and Criteria Plan" on June 30, 2004. (AR 729.) The BA describes the

project on which consultation is being held, both early and formal, in much the same terms as are used

in the BiOp.

[7] Prior to 2004, the OCAP operated under Biological Opinions issued in 1993 and 1995.

[8] Pelagic fish live in open water, generally away from vegetation or the bottom. (AR 365.) A

significant amount of the smelt's habitat are the Delta waters and waters of surrounding areas.

[9] The BiOp contradictorily acknowledges that "although salvage is used to index delta smelt take, it

does not reliably index delta smelt entrainment." (AR 419.)

[10] These "hard" take limits, as the Defendants and Defendant Intervenors referred to them during

oral argument are different from a separate take trigger that is part of the DSRAM process described

below.

[11] DWR insisted during oral argument that the data used to run the CALSIM II models was not

"salvage" data but was rather "density data." The BiOp is explicit that the models were run using a

"salvage density" estimate generated from periodic samplings of salvaged fish.

[12] The information contained in these tables was derived by the court from the BiOp but was not

presented in this form in the BiOp.

[13] The tables at pages 414 and 419 of the AR do not list the absolute number of smelt estimated to

be taken in any given month under the 1995 regulatory base case (Study No. 1). However, the

incidental take limits (set forth in the Table 3 below) were based on the absolute numbers of smelt

that are projected to be taken under Study No. 5a. For example, the take limit for the month of May in

a Critically Dry year, set at 30,500, under the CALSIM II results in a reduction of the 30,500 to

18,921 (representing 11,652 reduction in CVP salvage plus 7,269 reduction in SWP salvage) lower

than the 1995 regulatory base case.

[14] The DSRAM also includes a chart illustrating when during the year each of these actions will be

available. (AR 346.)

[15] In a footnote at the end of Plaintiffs' motion to strike the Sommer Declaration, Plaintiffs also

challenge Federal Defendants' reliance on the declaration of Ann Lubas-Williams, which Federal

Defendants filed with their response to Plaintiffs' motion for summary judgment/cross motion to

dismiss. (See Doc. 242-4.) The Lubas-Williams declaration concerns the implementation of DSRAM

and the sources from which DWR plans to obtain water to protect Delta smelt in the near future.

Federal defendants relied on her declaration primarily to support their motion to dismiss or for

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voluntary remand. No party has relied upon this declaration in the context of the pending motions; it

was not considered by the court. It is unnecessary to rule on this motion to strike.

[16] Federal Defendants also cite Pension Benefit Guar. Corp. v. LTV Corp., 496 U.S. 633, 654-655,

110 S.Ct. 2668, 110 L.Ed.2d 579 (1990), in which the Supreme Court reasoned: "Here, unlike in

Overton Park, the Court of Appeals did not suggest that the administrative record was inadequate to

enable the court to fulfill its duties under § 706."

Federal Defendants quote Pension Benefit entirely out of context. The quoted language is drawn from

a part of the opinion addressing the Second Circuit's ruling about the adequacy of procedures used by

the defendant agency. Specifically, that court ruled that the agency acted arbitrarily and capriciously

because it failed to apprise the plaintiff of the material on which it was to base its decision, never gave

plaintiff an adequate opportunity to offer contrary evidence, failed to proceed according to

ascertainable standards, and failed to provide plaintiff a statement showing its reasoning. Id. at 653,

110 S.Ct. 2668. One party claimed that Overton Park validated a court's order that an agency

undertakes additional procedures. Id. The Supreme Court rejected this argument, reasoning that, at

most, Overton Park "imposes a general `procedural' requirement of sorts by mandating that an agency

take whatever steps it needs to provide an explanation that will enable the court to evaluate the

agency's rationale at the time of decision." Id. at 654, 110 S.Ct. 2668. The Supreme Court then

distinguished Overton Park, reasoning that "[h]ere, unlike in Overton Park, the Court of Appeals did

not suggest that the administrative record was inadequate to enable the court to fulfill its duties under

§ 706." Id. at 655, 110 S.Ct. 2668. This was a specific reference to language in Overton Park which

criticized the lower courts for relying only on the litigation affidavits, rather than the whole

administrative record. Pension Benefit sheds absolutely no light on the admissibility of extra-record

evidence.

[17] At least one district court has followed the holding in American Rivers. See NRDC v. Rodgers,

381 F.Supp.2d 1212, 1230 (E.D.Cal. 2005).

[18] Rumsfeld also found fault with the biological opinion's monitoring plan, characterizing it as a

means of delaying the implementation of necessary mitigation measures:

The Army may Dot delay identifying the measures necessary to mitigate the effects of its ten-year plan

based on the monitoring provisions in the Final BO. . . .

The Final BO's monitoring requirements do not measure the success or failure of the on-base and/or

regional mitigation measures to reduce the groundwater deficit. It only requires the Army to develop

monitoring program designed to assess progress," and requires an annual review of the AWRMP, as

to which projects have been implemented the past year and which are to be implemented in the

coming year. Especially since the Final BO and the AWRMP fail to quantify the remedial value of the

proposed projects, simply reporting project implementation is not a meaningful assessment of the

success or failure of the mitigation measures in protecting the water umbel, willow flycatcher, and

critical habitat from adverse impact. Such an assessment would require systematic monitoring of

either San Pedro baseflows or the groundwater aquifer.

198 F.Supp.2d at 1154 (internal record citations omitted). No such failure is alleged here. Plaintiffs do

not suggest that the monitoring called for by the DSRAM is flawed.

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[19] In NWF v. Babbit, the district court expressly approved the design of the HCP as a whole, but

invalidated the permit issued in connection with the plan on grounds wholly independent from the

design of the HCP and/or the adaptive management plan. See 128 F.Supp.2d at 1298-99.

[20] The only clearly enforceable standard or benchmark in the BiOp is compliance with the BiOp's

"hard" take exceedence limits. But, the existence of enforceable take limits does not shield the

DSRAM from scrutiny. There is no provision to allow the "hard" take exceedence limits to be

adjusted to reflect new information about the species. Moreover, the BiOp expressly recognizes that

the take limits alone are not enough to prevent jeopardy, requiring, among other things,

implementation of the DSRAM as a reasonable and prudent measure. (See AR 475) ("The Project

shall be implemented as described.") This is exactly the reason why the DSRAM must be made more

certain and enforceable.

[21] As of the date of oral argument, the man date has not yet issued in NWF v. NMFS.

[22] Plaintiffs cite another district court decision that applied the benefit of the doubt language: "To

the extent that there is any uncertainty as to what constitutes the best scientific information, Congress

intended for the agency to `give the benefit of the doubt to the species.'" Ctr. for Biological Diversity

v. Bureau of Land Mgmt., 422 F.Supp.2d 1115, 1127 (N.D.Cal.2006) (citing Conner, 848 F.2d at

1454). However, that district court did not apply the "benefit of the doubt" concept in its analysis in

any way, let alone as a presumption governing the agency's analysis of scientific information.

Another case Plaintiffs cite, Rock Creek Alliance v. U.S. Fish & Wildlife Service, 390 F.Supp.2d 993,

1003 (D.Mont.2005), does not support imposing a "benefit of the doubt" presumption to uncertain

scientific evidence:

Though the agency has discretion to make decisions based in its expertise, the ESA expresses a

legislative mandate "to require agencies to afford first priority to the declared national policy of

saving endangered species. . . . Congress has spoken in the plainest of words, making it abundantly

clear that the balance has been struck in favor of affording endangered species the highest of

priorities, thereby adopting a policy which it described as `institutionalized caution.'"

Id. (quoting Tennessee Valley Authority v. Hill, 437 U.S. 153, 185, 98 S.Ct. 2279, 57 L.Ed.2d 117

(1978)). However, as in Center for Biological Diversity, this language was part of a general

discussion of the legal framework; the Rock Creek court never applied a benefit of the doubt

presumption in the manner Plaintiffs suggest it should be applied here.

[23] Defendants and Defendant-Intervenors dispute whether the data "evoked grave concern." The

degree of concern is irrelevant to the inquiry, as it is undisputed that the 2004 FMWT data showed the

lowest smelt abundance on record.

[24] The State Water Contractors maintain that CVP/SWP operations have been on-going for decades,

during which time Delta smelt abundance has fluctuated greatly.

[25] Plaintiffs' record citations, AR 9199-9202, are print-outs of the FMWT data which post date the

issuance of the BiOp.

[26] Abundance data is relevant to aspects of the BiOp that are independent of the DSRAM process.

For example, the agency's conclusion that the level of anticipated take "is not likely to result in

jeopardy to the smelt because this level of take is at or below historical levels of take" (AR 474), is

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irrational because no consideration is given to the current decline in smelt abundance nor any

explanation provided how the further decline of the smelt does not exacerbate jeopardy to the species'

survival and recovery.

[27] Plaintiffs argue that "Hegardless of the uncertainty involved in predicting the consequences of

climate change, FWS had an obligation under the ESA to address the probable effects on Delta

smelt." (Doc. 232 at 7.) In response, the State Water Contractors quote the following passage from

Bennett v. Spear, 520 U.S. 154, 176-177, 117 S.Ct. 1154, 137 L.Ed.2d 281 (1997), in support of the

proposition that the ESA intended to preclude exactly this kind of argument:

The obvious purpose of the requirement that each agency "use the best scientific and commercial data

available" is to ensure that the ESA not be implemented haphazardly, on the basis of speculation or

surmise. While this no doubt serves to advance the ESA's overall goal of species preservation, we

think it readily apparent that another objective (if not indeed the primary one) is to avoid needless

economic dislocation produced by agency officials zealously but unintelligently pursuing their

environmental objectives.

But, this passage from Bennet was part of a broader discussion holding that persons who are

economically burdened by a decision made under the ESA fall within the zone of interests the statute

protects for the purposes of standing. Bennet sheds little light on the current inquiry whether and to

what extent the data that was before the FWS regarding climate change should have been considered

and addressed in the BiOp.

[28] There is no basis to determine what weight FWS should ultimately give the climate change issue

in its analysis.

[29] There is no recognized mechanism for introducing any population viability data, collected

through the adaptive management process, into the setting of the take limits.

[30] The San Luis Parties mischaracterize Plaintiffs argument as a request for FWS to undertake

additional research projects. (Doc. 247.) Defendant Intervenors are correct that FWS Is not required to

undertake new research, Greenpeace Action v. Franklin, 14 F.3d 1324, 1335 (9th Cir.1992) (agency

may proceed despite uncertainty about accuracy of modeling effort); Southwest Ctr for Biological

Diversity, 215 F.3d 58, 60 (D.C.Cir.2000) (agency could rely on inconclusive data to make decision;

not obligated to conduct new independent studies). Plaintiffs do point out that FWS acknowledges in

the AR that an accurate determination of non-jeopardy would require knowledge of how many smelt

existed, what proportion would be lost due to the projects, and what level of loss would be

sustainable. (Doc. 232 at 23 (citing AR 8221).) However, the crux of Plaintiffs' concern is that FWS

has not developed such population data and ignored important existing data on abundance in setting

the take limits.

[31] The Administrative Record reflects various explanations for the lack of a linear relationship

between the TNS and the FMWT. (AR 1025-26.) One possible explanation for why the number of

spawning age smelt (indexed by the FMWT) seems to be a poor predictor of subsequent offspring

(indexed by the TNS) is that there is some environmental factor (not directly related to entrainment at

The projects) limiting survivability, inferring that there is a carrying capacity for the population. (Id.)

Alternatively, some scientists question whether it is proper to try to draw statistical conclusions from

the entire 1969-2002 data pool, given that the smelt experienced a precipitous decline in 1981. These

scientists have postulated that the data "may reflect two different relationships from two time periods

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with different delta smelt carrying capacities." (Id. at 1026.) One study cited in the AR indicates that

food supply may be the limiting factor during this time period. (AR 8976.)

[32] The San Luis Parties raise numerous questions regarding FWS's conclusion that there is a

statistical relationship between the numbers of spawning adults and Delta smelt abundance the

following year, criticizing the statistical analyses referenced in the BiOp. (Doc. 247 at 5.) It is

unnecessary to adjudicate these issues, as the San Luis Parties have not separately challenged the

conclusions reached in the BiOp on this ground nor have they moved for summary judgment on any

issue in this case.

[33] Defendant-Intervenors argue that, because of these mentions of "conservation," FWS is entitled

to a "presumption of regularity," and the court must assume that agency considered recovery. (Doc.

247 at 12.) In Gifford Pinchot, after invalidating the destruction and adverse modification regulation,

the Ninth Circuit considered whether it should presume that the agency followed its own regulation

that was valid at the time the biological opinion was issued. The Ninth Circuit concluded that, because

the agencies must be afforded a "presumption of regularity," a court must assume that the agency

followed the then applicable regulation. Id. at 1072. Applying this presumption here, given that the

agency specifically applied the statute, not the invalid regulation, there is no evidence the agency

applied an invalid regulation. However, Defendant-Intervenors' suggestion that the presumption

should be applied to validate the BiOp's analysis of recovery is misplaced. The agency still has an

obligation to thoroughly consider the issue of recovery and to reach a reasoned conclusion based on

the evidence in the administrative record.

[34] Although this portion of NWF v. NMFS concerned analysis of recovery in the context of the "no

jeopardy" determination, as opposed to the "destruction or adverse modification of critical habitat"

analysis, the holding is equally applicable to habitat jeopardy.

[35] There is also merit to Plaintiffs' argument that "[G]iven that the very same sorts of impacts to

critical habitat have contributed to the species decline, one might expect FWS to examine carefully

how the continuance and magnification of these kinds of impacts could allow for the survival of the

species, much less its recovery." (Doc. 306 at 5.)

[36] The San Luis Parties correctly note that the CALSIM II models indicate that increased pumping

capacity and operational flexibility may actually increase the smelt's prospects vis-a-vis the regulatory

baseline. However, that the species will fare better than in the past does not assure that the totality of

OCAP operations are consistent with the smelt's recovery.

[37] Plaintiffs raise an additional contention why the critical habitat analysis is insufficient; i.e., that

the BiOp unlawfully "writes off' areas of critical habitat because they have already been degraded. For

example, the BiOp concludes that "[a]n upstream movement of X2 of 0.5 km would not be significant

when [X2] is located upstream of the [Sacramento-San Joaquin River] confluence because smelt

habitat is already poor and the upstream movement does not result in any substantial additional loss

of habitat or increase in adverse effects." (AR 443.) This issue need not be reached, as the critical

habitat analysis is insufficient on other grounds. Federal Defendants are already revising the BiOp to

reflect new information and new law.

[38] The San Luis Parties cite Gifford Pinchot in support of the proposition that this is a properly

"tiered" biological opinion. In Gifford Pinchot, the Ninth Circuit approved for the the tiering of a

biological opinion for timber harvests in specified forest areas. The no jeopardy conclusion contained

in that biological opinion relied on compliance with a very thorough, overarching forest management

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plan that was previously approved by the court. 378 F.3d at 1067-68. Gifford Pinchot allowed the

agency to tier its BiOp of a timber harvest with a programmatic forest management plan that provided

guidelines regarding the harvesting of timber. Rodgers, 381 F.Supp.2d at 1228 n. 27, interpreted the

holding narrowly to apply tiering only to cases in which the programmatic opinion was particularly

thorough. Tiering of future construction projects is not appropriate here, because the BiOp provides

no programmatic guidelines regarding construction activities. However, just because the later projects

cannot be "tiered" off the current BiOp does not mean they must be included in the current BiOp. The

relevant inquiry is whether the construction projects are interrelated to and/or interdependent upon the

BiOp and the 2004 OCAP.

[39] Federal Defendants correctly point out that the FWS uses as a guidance document the ESA

Section 7 Consultation Handbook (March 1998), available at "http:/ /www.fws.

gov/endangered/consultations/s7hndbk/s7

hndbk.htm" (last visited Apr. 27, 2006). See e.g., Oregon Natural Res. Council v. Allen, 476 F.3d

1031, 1039 n. 7 (9th Cir.2007); Ariz. Cattle Growers' Ass'n v. U.S. Fish & Wildlife, 273 F.3d 1229

(9th Cir.2001).

[40] The parties stated that they may be able to reach an agreement as to interim remedies, avoiding

the need for a remedies hearing.

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