Full opinion text
MEMORANDUM DECISION RE CROSS MOTIONS FOR SUMMARY JUDGMENT (DOCS. 548, 549, 550, 658, & 661) OLIVER W. WANGER, District Judge. TABLE OF CONTENTS I. INTRODUCTION........................................................863 II. PROCEDURAL HISTORY................................................863 III. STATUS OF THE SPECIES..............................................866 IV. SUMMARY OF MOTION.................................................867 A. Plaintiffs’ Motion.....................................................867 B. DWR’s Motion.......................................................867 Y. STANDARD OF DECISION..............................................868 VI. BASIC LEGAL FRAMEWORK ...........................................868 A. Review under the APA................................................868 (1) Record Review ...................................................868 (2) Deference to Agency Expertise.....................................869 (3) General Obligations Under the ESA.................................870 (4) Best Available Science.............................................870 (5) Best Available Science Standards and the Application of Analytical/Statistical Methodologies ...............................873 VII. ANALYSIS..............................................................874 A. Challenges to the Effects Analysis & Related Challenges to the RPA Actions............................................................874 (1) Legal Requirements for a Project Effects Analysis....................874 (2) Best Available Science Challenges to the Effects Analysis and Related Challenges to the Justification Provided for the RPA Actions........................................................875 a. The BiOp’s General Conclusion that Entrainment by Project Operations Adversely Affects Smelt Survival & Recovery is Supported by the Record.....................................876 b. Population Level Analysis/Life-Cycle Modeling....................881 e. FWS’ Use of Raw Salvage Numbers .............................885 (1) Federal Defendants’ Argument that the Flow Prescriptions in Actions 1 and 2 are Otherwise Justified...................890 (2) Use of Raw Salvage Analyses in Justification for Action 3.....895 d. FWS’s Comparison of CALSIM II Data to DAYFLOW Data........896 (1) Was FWS’s Decision to Compare Calsim II to Dayflow Model Runs a Violation of the Best Available Science Requirement? ...........................................903 (2) Does the Use of Dayflow to Represent the Baseline in the Project Effects Analysis Improperly Attribute Past Effects to the Projects?...................................909 (3) Use of Comparisons Between CALSIM and DAYFLOW Model Outputs to Justify Imposition of Component 3 (Action 4), the Fall X2 Action..............................910 (3) Other Challenges to the Fall X2 Action ..............................913 a. Plaintiffs’ Argument that Action 4 is an “Untested Hypothesis.”.....913 b. FWS’ Reliance on the Feyrer Papers.............................913 c. Do the Studies Cited in the BiOp Support FWS’s Conclusion that Fall X2 Determines the Extent of Suitable Smelt Habitat?....................................................915 (1) Feyrer (2007)..............................................915 (2) The Feyrer (2008) Paper....................................917 (3) The Bennett (2005) Article..................................918 d. Does the Best Available Science Support the Assumption that X2 Is a Surrogate for Smelt Habitat?...........................918 a. Are Delta Smelt Habitat Limited? ...............................919 b. FWS’ Use of a Linear Model Instead of a Multiplicative Stock-Recruit Model...............................................920 c. DWR’s Challenge to the BiOp’s Choice of X2 Location..............922 (4) Challenges to Turbidity Trigger.....................................923 (5) Challenges to the Incidental Take Limit/Selective Use of Data..........924 a. FWS’s Exclusion of Certain Data Points When Analyzing Entrainment................................................924 b. FWS’s Use of Data to Examine the Relationship Between OMR Flows and Salvage and Exclusion of that Data from the Incidental Take Limit Analysis................................925 e. DWR’s Additional Challenges the ITS............................928 (6) Challenges to the BiOp’s Analysis of the Hydrodynamic Effects of the Projects....................................................929 a. Project Operations as a Driver of Hydrodynamic Conditions in the Delta...................................................930 b. Treatment of Other Stressors ...................................932 (1) Predation Analysis.........................................934 (2) Aquatic Macrophytes.......................................934 (3) Microcystis................................................936 (7) Indirect Effects Analysis...........................................936 a. Effect of Project Operations on Delta Smelt Food Supplies..........937 b. Pollution and Contaminants.....................................940 (8) Critical Habitat as Independent Basis for RPA........................943 a. Identification of a Threshold For Adverse Modification/ Explanation of How Any Alleged Alteration To Critical Habitat Would Exceed that Threshold..........................944 b. Reliance On Assumptions Of Indirect Effects Without Providing Evidence That These Indirect Effects Are Reasonably Certain To Occur............................................946 c. Reliance on Analysis Of Entrainment and X2 in Support of the Adverse Modification Determination............................947 (9) Discretionary v. Nondiseretionary Actions............................947 B. Application of the RPA Regulations.....................................948 (1) FWS Did Not Explicitly Analyze Any of the Four Factors in the BiOp..........................................................948 (2) Compliance with § 402.02 ..........................................949 a. Jeopardy Factor (Fourth Factor)................................949 b. Non-Jeopardy Factors (Factors One Through Three) ..............949 c. There is no Procedural Requirement that FWS Accept, Consider, and/or Address Comments Regarding the BiOp or its RPA.....957 C. Stewart & Jasper Orchards’ Argument Re: Reasonable and Prudent Measures..........................................................957 D. Stewart & Jasper, et al.’s, Argument that FWS Illegally Arrogated Authority to Itself Over Bureau of Reclamation and California Department of Water Resources Operations ...........................958 E. Information Quality Act Claim.........................................959 (1) Legal Framework of the IQA.......................................959 (2) Right to Judicial Review Under the APA.............................960 a. APA § 701(a)(2)’s Exception for Agency Action “Committed to Agency Discretion by Law” Bars Judicial Review in this Case.....961 (3) To the Extent FFA Bases Any of its Claims against Reclamation on the ESA, Such Claims are Subject to the ESA’s Pre-Filing Requirements ..................................................964 F. Renewed Claim That FWS Violated NEPA..............................964 G. Reclamation’s Liability under the ESA..................................966 VIII. CONCLUSION 967 I. INTRODUCTION These consolidated cases arise out of the continuing war over protection of the delta smelt (Hypomesus transpacificus), an ESA-threatened species, and associated impacts to the water supply for more than half of the State of California. Plaintiffs, San Luis & Delta Mendota Water Authority (“SLDMWD”) and Westlands Water District, Metropolitan Water District of Southern California, State Water Contractors (“SWC”), Coalition for a Sustainable Delta and Kern County Water Agency, Stewart & Jasper Orchards, Arroyo Farms, LLC, and King Pistacho Grove, and Family Farm Alliance, move for summary judgment on their numerous remaining claims against the United States Fish and Wildlife Service’s (“FWS”) December 15, 2008 Biological Opinion addressing the impacts of the coordinated operations of the federal Central Valley Project (“CVP”) and State Water Project (“SWP”) on the threatened delta smelt (Hypomesus transpacificus). Doc. 550. Plaintiff-in-Intervention, the California Department of Water Resources (“DWR”) filed a separate motion for summary judgment on narrower grounds. Docs. 548 & 549. Federal Defendants, the United States Department of the Interior, FWS, and the United States Bureau of Reclamation (“Reclamation”), and Defendant Intervenors, Natural Resources Defense Council and The Bay Institute, oppose and cross move for summary judgment on all remaining claims. Docs. 658 & 661. Plaintiffs and DWR replied. Docs. 697 & 695. The motion came on for hearing on July 8 & 9, 2010. After oral argument, the parties submitted supplemental briefing on a limited set of issues. Docs. 746-49. II. PROCEDURAL HISTORY FWS’s 2005 biological opinion (“2005 Smelt BiOp”) found that the proposed coordinated operations of the SWP and CVP will have no adverse effect on the continued existence and recovery of the Delta Smelt and its critical habitat. The 2005 BiOp was remanded to FWS as arbitrary and capricious. Order, NRDC v. Kempthorne, 506 F.Supp.2d 322 (E.D.Cal. 2007), Doc. 323. Following an extensive evidentiary hearing, the Court issued an interim remedial order and Findings of Fact and Conclusions of Law (“Findings”), which covered, among other things, the effects on delta smelt of negative flows in Old and Middle Rivers (“OMR”), two dis-tributary channels of the San Joaquin River. See Interim Remedial Order Following Summary Judgment and Evidentiary Hearing (“Int. Rem. Order”), NRDC v. Kempthorne, Doc. 560, 2007 WL 4462391 (Dec. 14, 2007); Findings re: Delta Smelt ESA Remand and Reconsultation (“Int. Rem. Findings”), NRDC v. Kempthorne, Doc. 561, 2007 WL 4462395 (Dec. 14, 2007). Reclamation and DWR were ordered, among other things, to implement a winter “pulse flow” in OMR of no more negative than -2,000 cubic feet per second (“cfs”), and to “operate the CVP and SWP to achieve a daily average net upstream (reverse) flow in the OMR not to exceed 5,000 cfs on a seven-day running average” during a defined period in the spring. Int. Rem. Order at 5-7; see also Int. Rem. Findings at 15-20. FWS issued a new delta smelt biological opinion on December 15, 2008 (“2008 Smelt BiOp” or “BiOp”). See Administrative Record (“AR”) at 00001-00411. This BiOp concluded that proposed CVP and SWP operations are “likely to jeopardize the continued existence of’ the delta smelt and “adversely modify” its critical habitat. BiOp at 276-79. The BiOp includes a required Reasonable and Prudent Alternative (“RPA”) designed to allow the projects’ continued operations without causing jeopardy to the species or adverse modification to its critical habitat. Id. at 279-85. The RPA includes operational components designed to reduce entrainment of smelt during critical times of the year by controlling (limiting) water exports from the Delta by the Projects. Id. at 279-85. Component 1, to protect of the adult delta smelt life stage, consists of two Actions related to OMR flows. • Action 1, to protect upmigrating delta smelt, is triggered during low and high entrainment risk periods based on physical and biological monitoring. Action 1 requires OMR flows to be no more negative than -2,000 cfs on a 14-day average and no more negative than -2,500 cfs for a 5-day running average. Id. at 280-82, 329-51. • Action 2, to protect adult delta smelt that have migrated upstream and are present in the Delta prior to spawning. Action 2 is triggered immediately after Action 1 concludes or if recommended by the Smelt Working Group (“SWG”). Flows under Action 2 can be set within a range from -5,000 to -1,250 cfs, depending on a complex set of biological and environmental parameters. Id. at 281-82, 352-56. Component 2 (Action 3), to protect larval and juvenile delta smelt, requires OMR flows to be kept between -1,250 and -5,000 cfs, after Component 1 is completed, when Delta water temperatures reach 12° Celcius (“C”), or when a spent female smelt is detected in trawls or at salvage facilities. Id. at 282, 357-58. Component 2 continues until June 30 or when the Clifton Court Forebay water temperature reaches 25 ° C. Id. at 282, 368. Component 3 (Action 4), to improve habitat for delta smelt growth and rearing, requires sufficient Delta outflow to maintain average mixing point locations of Delta outflow and estuarine water inflow (“X2” ) from September to December, depending on water year type, in accordance with a specifically described “adaptive management process” overseen by FWS. Id. at 282-83, 369. Component I (Action 6) (Habitat Restoration), requires DWR to create or restore 8,000 acres of intertidal and subtidal habitat in the Delta and Suisun Marsh within 10 years. Id. at 283-84, 379. Component 5 (Monitoring and Reporting), requires Reclamation and DWR to gather and report information to ensure proper implementation of the RPA actions, achievement of physical results, and evaluation of the effectiveness of the actions on the targeted life stages of delta smelt, so that the actions can be refined, if needed. Id. at 284-85, 328, 375. The first of the six consolidated challenges to the BiOp was filed on March 3, 2009. Doc. 1. Plaintiffs moved for a preliminary injunction on April 24, 2009 to prevent Reclamation from implementing Component 2 of the RPA, alleging that FWS violated the National Environmental Policy Act (“NEPA”) and the ESA. See Doc. 31. On May 22, 2009, the Court granted that motion in part, finding that Plaintiffs were likely to succeed on the merits of their NEPA claim and requiring FWS to make specific written findings to justify OMR flow restrictions. See Doc. 84; see also Doc. 94, Findings re Mot. for Prelim. Inj. (May 29, 2009). Defendants complied with that Order, submitting weekly notices of FWS’s OMR flow decisions. See, e.g., Doc. Ill, Notice of OMR Flow Decision (June 11, 2009). The Court’s May 2009 preliminary injunction ruling was not based on Plaintiffs’ ESA claims. Doc. 94 at 43. Plaintiffs amended their Complaint, joined and added claims against Reclamation, see Doc. 292, and moved for summary judgment on their NEPA claim, see Doc. 245. A November 13, 2009, 686 F.Supp.2d 1026 (E.D.Cal.2009) ruling granted summary adjudication in part, based on Reclamation’s failure to prepare an environmental impact statement before provisionally accepting and implementing the BiOp and its RPA Actions. Doc. 399. Summary judgment for Defendants was granted on: (1) Stewart and Jasper Orchards’ Commerce Clause claim that the ESA did not apply to protect delta smelt, a purely intra-state species, Doc. 339; and (2) claims that the BiOp violated regulations governing formulation of the RPA by not including required information in the BiOp text, Doc. 354. Plaintiffs then filed three temporary restraining order motions over a six week period—all of which were denied. See Docs. 555 & 583; see also 3/16/10 Hrg. Tr. at 86-88. Plaintiffs next sought a preliminary injunction against implementation of RPA Component 3. An evidentiary hearing was held from April 2, 2010 through April 7, 2010. Docs. 644, 652-54. Findings Re Plaintiffs’ Request for Preliminary Injunction issued May 27, 2010 (“PI Decision”), 717 F.Supp.2d 1021 (E.D.Cal.2010). Doc. 704. The PI Decision confirmed Plaintiffs had succeeded on their NEPA claim and found Plaintiffs were likely to succeed on the merits of their ESA claim: Although the premise underlying Component 2—that the species may be jeopardized by increased negative flows occasioned by export pumping—has record support, FWS has failed to adequately justify by generally recognized scientific principles the precise flow prescriptions imposed by Component 2. The exact restrictions imposed, which are inflicting material harm to humans and the human environment, are not supported by the record, making it impossible to determine whether RPA Component 2 [is] overly protective. Judicial deference is not owed to arbitrary, capricious, and scientifically unreasonable agency action. Id. at 1070. Plaintiffs presented evidence under NEPA on the balance of the hardships that social dislocation, unemployment, and other threats to human health and safety were caused by interdiction of Plaintiffs’ water supply. See id. at 1070. Countervailing irreparable harm was found, because “the species and its critical habitat[] are entitled to protection under the ESA.” Id. at 1070. Acknowledging the existence of legal and equitable grounds for injunctive relief, further evidence was requested on the “status of the species to assure that altered operations will not deepen jeopardy to the affected species or otherwise violate other laws.” Id. at 1071. Specifically, to establish “that Plaintiffs’ proposed remedy of a flat -5,600 efs ceiling on negative OMR flows will not jeopardize the continued existence of the species and/or adversely modify its critical habitat.” Id. A May 28, 2010 status conference sought to determine whether a mutually-agreeable interim operational plan could be implemented. Doc. 706. On June 22, 2010, the parties stipulated to a joint operational plan to maintain OMR flows so as not to be more negative than -5,000 cfs, unless certain, defined salvage triggers required a further reduction in OMR flows. Doc. 724. After these dispositive motions were filed, the National Academy of Sciences, completed a comprehensive review of the BiOp, and concluded that the BiOp and the RPA Actions were “scientifically justified.” See National Academy of Sciences, National Research Council, A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California’s Bay Delta at 3. Doc. 635. This post-decisional document is not part of the Administrative Record (“AR”) and no legal justification exists to supplement the AR to include it. Additionally, a scientific peer review panel was convened by the private consulting firm, Post Buckley Shuh and Jernigan (“PBS & J”), at the request of Plaintiff Family Farm Alliance (“FFA”) in connection with FFA’s administrative petition under the Information Quality Act (“IQA”). See Family Farm Alliance v. Salazar, 09-cv-1201 OWW-DLB (E.D.Cal.), Doc. 27, Ex. A. This document is part of the administrative record in the Family Farm Alliance IQA case, not the smelt AR. There is no basis to consider this document for non-IQA claims. III. STATUS OF THE SPECIES The delta smelt was listed as a threatened species under the ESA on March 5, 1993. 58 Fed. Reg. 12,854 (March 5, 1993). Critical habitat was designated for the delta smelt on December 19, 1994. 59 Fed.Reg. 65,256 (Dec. 19, 1994). Once an abundant species in the Bay-Delta ecosystem as recently as thirty years ago, the delta smelt is now in imminent danger of extinction. PI Decision, Finding of Fact ¶ 10. All the evidence shows a significant decline in smelt abundance since 2000, recently up to three orders of magnitude below historic lows. Id. The latest fall mid-water trawl (“FMWT”) abundance index for the species was 17, the lowest level ever recorded. Id. On April 7, 2010, FWS announced that reclassifying the delta smelt from a threatened to an endangered species was warranted, but precluded by higher priority listing actions. 75 Fed.Reg. 17,667 (Apr. 7, 2010). The direct mortality of delta smelt by entrainment at the CVP-SWP pumps, as well as the destruction and adverse modification of its habitat in the Delta caused by water exports, were important factors in this determination. Id. at 17,669, 17,671 (“The operation of State and Federal export facilities constitute a significant and ongoing threat to delta smelt through direct mortality by entrainment”). As a result of the “immediate and high magnitude threats” confronting the species, the delta smelt was assigned a listing priority number of 2. Id. at 17,675. IV. SUMMARY OF MOTION A. Plaintiffs’Motion. Plaintiffs’ motion advances the following grounds and contentions: (1) FWS failed to rely on the “best available science” by making fundamental scientific errors in its analysis of the impacts of Project Operations on the species by: (a) Relying on raw salvage numbers in quantitative impact analyses; (b) Failing to conduct a life cycle analysis; (c) Comparing the results of two entirely different, incompatible flow and salinity models; and (d) Selectively excluding certain data for one purpose, but then unjustifiably using it for another; (2) The BiOp’s Project Effects Analysis is arbitrary and capricious because FWS: (a) Assumed that Project operations drive hydrological conditions in the Delta and did not explain or justify this attribution; (b) Evaluated the impacts of other (i.e., non-Project) stressors erroneously and inconsistently; and (c) Improperly characterized summer food supply suppression, invasive species, and pollution and contaminants as indirect effects of Project Operations; (3) The BiOp is arbitrary and capricious because it does not distinguish between discretionary and nondiscretionary actions, improperly inflating the alleged effects of Project Operations; (4) The BiOp’s RPA is unlawful because FWS did not conduct the specific analyses required by the ESA and FWS’ own RPA regulation, 50 C.F.R. § 402.02, because neither the BiOp nor the AR demonstrate that FWS analyzed or applied the first three (of four) § 402.02 factors; (5) FWS illegally arrogated to itself Project operating authority in derogation of Reclamation and DWR; (6) FWS acted arbitrarily and capriciously by disregarding the Information Quality Act (“IQA”) when preparing and issuing the BiOp; (7) FWS violated NEPA by not considering the environmental impacts of issuing the BiOp and RPA. (8) Reclamation violated its legal duties by accepting FWS’ inherently flawed BiOp. B. DWR’s Motion. DWR’s attacks three aspects of the BiOp: (1) By relying on a comparison of CALSIM II model runs with what the BiOp terms “historic” data (which was actually generated by the Day-flow model), the BiOp’s analysis of the effects of the proposed action on smelt habitat does not yield meaningful information and violates the ESA’s best available science requirement. This analysis further violates the APA because FWS did not adequately articulate any rational connection between the facts found based on these comparisons, and its conclusions regarding the Projects’ effects on the smelt. (2) Component 3 of the RPA, also referred to in the BiOp as Action 4, is intended to mitigate the effects of the proposed action on smelt habitat, by requiring the Projects to maintain X2 in specified locations, depending on the type of water year. The BiOp, however, lacks sufficient explanation as to the basis for the specific prescriptions imposed by this Component, in violation of the APA. Moreover, to the extent that the record reveals that these prescriptions are based, even in part, on the methods used in the effects analysis, they violate the ESA’s “best available science” mandate. (3) The Incidental Take Statement (“ITS”) is defective. First, its estimates are based on the average take from water years 2006 through 2008, which predicts the ITS will likely be exceeded in half of all years. Second, FWS erroneously misapplied its own data with the result that the BiOp claims that the ITS was only exceeded in five of the previous sixteen years, rather than accurately stating that it was exceeded in eleven of the sixteen years. Third, the ITS take estimate is based on a data sample that is too small to provide a reasonable prediction of take under the RPA. These defects violate the ESA’s “best available science” requirement, the ESA’s ITS requirements, and the APA. V. STANDARD OF DECISION Summary judgment is appropriate when the pleadings and the record demonstrate that “there is no genuine dispute as to any material fact and that the moving party is entitled to judgment as a matter of law.” Fed.R.Civ.P. 56(c). The claims in this case involve FWS’s issuance of a biological opinion, which is a final agency action subject to judicial review under the APA, 5 U.S.C. § 702. Nat'l Wildlife Fed’n v. Nat’l Marine Fisheries Serv., 524 F.3d 917, 925 (9th Cir.2008) (“NWF v. NMFS II”). A court conducting judicial review under the APA may not resolve factual questions, but instead determines “whether or not as a matter of law the evidence in the administrative record permitted the agency to make the decision it did.” Sierra Club v. Mainella, 459 F.Supp.2d 76, 90 (D.D.C.2006) (quoting Occidental Eng’g Co. v. INS, 753 F.2d 766, 769 (9th Cir.1985)). “[I]n a case involving review of a final agency action under the [APA] ... the standard set forth in Rule 56(c) does not apply because of the limited role of a court in reviewing the administrative record.” Id. at 89. In this context, summary judgment becomes the “mechanism for deciding, as a matter of law, whether the agency action is supported by the administrative record and otherwise consistent with the APA standard of review.” Id. at 90. VI. BASIC LEGAL FRAMEWORK A. Review under the APA. Administrative Procedure Act (“APA”) invalidation of a biological opinion requires Plaintiffs to prove that FWS’s action was “arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law.” 5 U.S.C. § 706(2)(A). (1) Record Review. APA review of a biological opinion is “based upon the evidence contained in the administrative record.” Arizona Cattle Growers’ Ass’n v. FWS, 273 F.3d 1229, 1245 (9th Cir.2001). Judicial review under the APA must focus on the administrative record already in existence, not some new record made initially in a reviewing court. Parties may not use “post-decision information as a new rationalization either for sustaining or attacking the agency’s decision.” Ass’n of Pac. Fisheries v. EPA, 615 F.2d 794, 811-12 (9th Cir.1980). Exceptions to administrative record review for technical information or expert explanation make such evidence admissible only for limited purposes, and those exceptions are narrowly construed and applied. Lands Council v. Powell, 395 F.3d 1019, 1030 (9th Cir.2005). Here, as evidentiary rulings explained, see, e.g., Docs. 387, 392 (10/19/09 Hrg. Tr.), 406, 407, 462, 740 (7/8/10 Hrg.), 750, expert testimony has been considered only for explanation of technical terms and complex scientific subject matter beyond the Court’s knowledge; and to understand the agency’s explanations, or lack thereof, and the parties’ arguments. (2) Deference to Agency Expertise. A Court must defer to the agency on matters within the agency’s expertise, unless the agency completely failed to address some factor, consideration of which was essential to making an informed decision. Nat’l Wildlife Fed’n v. Nat’l Marine Fisheries Serv., 422 F.3d 782, 798 (9th Cir.2005) (“NWF v. NMFS I”). A court “may not substitute its judgment for that of the agency concerning the wisdom or prudence of the agency’s action.” River Runners for Wilderness v. Martin, 593 F.3d 1064, 1070 (9th Cir.2010): In conducting an APA review, the court must determine whether the agency’s decision is “founded on a rational connection between the facts found and the choices made ... and whether [the agency] has committed a clear error of judgment.” Ariz. Cattle Growers’ Ass’n v. U.S. Fish & Wildlife, 273 F.3d 1229, 1243 (9th Cir.2001). “The [agency’s] action ... need be only a reasonable, not the best or most reasonable, decision.” Nat’l Wildlife Fed. v. Burford, 871 F.2d 849, 855 (9th Cir.1989). Id. Although deferential, judicial review under the APA is designed to “ensure that the agency considered all of the relevant factors and that its decision contained no clear error of judgment.” Arizona v. Thomas, 824 F.2d 745, 748 (9th Cir.1987) (internal citations omitted). “The deference accorded an agency’s scientific or technical expertise is not unlimited.” Brower v. Evans, 257 F.3d 1058, 1067 (9th Cir.2001) (internal citations omitted). [An agency’s decision is] arbitrary and capricious if [it] 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. Motor Vehicle Mfrs. Ass’n of U.S. v. State Farm Mut. Auto. Ins. Co., 463 U.S. 29, 43, 103 S.Ct. 2856, 77 L.Ed.2d 443 (1983); see also Citizens to Preserve Overton Park, Inc. v. Volpe, 401 U.S. 402, 416, 91 S.Ct. 814, 28 L.Ed.2d 136 (1971) (reviewing court may overturn an agency’s action as arbitrary and capricious if the agency failed to consider relevant factors, failed to base its decision on those factors, and/or made a “clear error of judgment”), overruled on other grounds by Califano v. Sanders, 430 U.S. 99, 105, 97 S.Ct. 980, 51 L.Ed.2d 192 (1977). More generally, “[u]nder the APA ‘the agency must examine the relevant data and articulate a satisfactory explanation for its action including a rational connection between the facts found and the choice made.’ ” Humane Soc. of U.S. v. Locke, 626 F.3d 1040, 1048 (9th Cir.2010) (quoting Motor Vehicle Mfrs. Ass’n, 463 U.S. at 43, 103 S.Ct. 2856). “The reviewing court should not attempt itself to make up for an agency’s deficiencies: We may not supply a reasoned basis for the agency’s action that the agency itself has not given.” Id. (3) General Obligations Under the ESA. ESA Section 7(a)(2) prohibits agency action that is “likely to jeopardize the continued existence” of any endangered or threatened species or “result in the destruction or adverse modification” of its critical habitat. 16 U.S.C. § 1536(a)(2). 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 C.F.R. § 402.02; see also NWF v. NMFS II, 524 F.3d 917 (rejecting agency interpretation of 50 C.F.R. § 402.02 that in effect limited jeopardy analysis to survival and did not realistically evaluate recovery, thereby avoiding an interpretation that reads the provision “and recovery” entirely out of the text). An action is “jeopardizing” if it keeps recovery “far out of reach,” even if the species is able to cling to survival. NWF v. NMFS II, 524 F.3d at 931. “[A]n 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.” Id. at 930. To satisfy this obligation, the federal agency undertaking the action (the “action agency”) must prepare a “biological assessment” that evaluates the action’s potential impacts on species and species’ habitat. 16 U.S.C. § 1536(c); 50 C.F.R. § 402.12(a). If the proposed action “is likely to adversely affect” a threatened or endangered species or adversely modify its designated critical habitat, the action agency must engage in “formal consultation” with FWS to obtain its biological opinion as to the impacts of the proposed action on the listed species. See 16 U.S.C. § 1536(a)(2), (b)(3); see also 50 C.F.R. § 402.14(a), (g). Once the consultation process has been completed, FWS must give the action agency a written biological opinion “setting forth [FWS’s] opinion, and a summary of the information on which the opinion is based, detailing how the agency action affects the species or its critical habitat.” 16 U.S.C. § 1536(b)(3)(A); see also 50 C.F.R. § 402.14(h). If FWS determines that jeopardy or destruction or adverse modification of critical habitat is likely, FWS “shall suggest those reasonable and prudent alternatives which [it] believes would not violate subsection (a)(2) of this section and can be taken by the Federal agency or applicant in implementing the agency action.” 16 U.S.C. § 1536(b)(3)(A). “Following the issuance of a ‘jeopardy’ opinion, the agency must either terminate the action, implement the proposed alternative, or seek an exemption from the Cabinet-level Endangered Species Committee pursuant to 16 U.S.C. § 1536(e).” Nat’l Ass’n of Home Builders v. Defenders of Wildlife, 551 U.S. 644, 652, 127 S.Ct. 2518, 168 L.Ed.2d 467 (2007). (4) Best Available Science. Under the ESA, an agency’s actions must be based on “the best scientific and commercial data available.” 16 U.S.C. § 1536(a)(2); 50 C.F.R. § 402.14(g)(8) (“In formulating its Biological Opinion, any reasonable and prudent alternatives, and any reasonable and prudent measures, the Service will use the best scientific and commercial data available.... ”). A failure by the agency to utilize the best available science is arbitrary and capricious. See Pac. Coast Fed’n of Fishermen’s Assns. v. Gutierrez, 606 F.Supp.2d 1122, 1144 (E.D.Cal.2008). “The obvious purpose of the [best available science requirement] is to ensure that the ESA not be implemented haphazardly, on the basis of speculation or surmise.” Bennett v. Spear, 520 U.S. 154, 176, 117 S.Ct. 1154, 137 L.Ed.2d 281 (1997). While this no doubt serves to advance the ESA’s overall goal of species preservation, we think it readily apparent that another objective [of the best available science requirement] (if not indeed the primary one) is to avoid needless economic dislocation produced by agency officials zealously but unintelligently pursuing their environmental objectives. That economic consequences are an explicit concern of the ESA is evidenced by § 1536(h), which provides exemption from § 1536(a)(2)’s no-jeopardy mandate where there are no reasonable and prudent alternatives to the agency action and the benefits of the agency action clearly outweigh the benefits of any alternatives. We believe the “best scientific and commercial data” provision is similarly intended, at least in part, to prevent uneconomic (because erroneous) jeopardy determinations. Id. at 176-77, 117 S.Ct. 1154. A decision about jeopardy must be made based on the best science available at the time of the decision; the agency cannot wait for or promise future studies. See Ctr. for Biological Diversity v. Rumsfeld, 198 F.Supp.2d 1139, 1156 (D.Ariz.2002). The “best available science” mandate of the ESA sets a basic standard that “prohibits the [agency] from disregarding available scientific evidence that is in some way better than the evidence [it] relies on.” Am. Wildlands v. Kempthorne, 530 F.3d 991, 998 (D.C.Cir. 2008) (citation omitted). What constitutes the “best” available science implicates core agency judgment and expertise to which Congress requires the courts to defer; a court should be especially wary of overturning such a determination on review. Baltimore Gas & Flee. Co. v. Natural Res. Defense Council, 462 U.S. 87, 103, 103 S.Ct. 2246, 76 L.Ed.2d 437 (1983) (a court must be “at its most deferential” when an agency is “making predictions within its area of special expertise, at the frontiers of science”). As explained in the en banc decision in Lands Council, 537 F.3d at 993, courts may not “impose on the agency their own notion of which procedures are best or most likely to further some vague, undefined public good.” In particular, an agency’s “scientific methodology is owed substantial deference.” Gifford Pinchot Task Force v. U.S. Fish & Wildlife Serv., 378 F.3d 1059, 1066 (9th Cir.2004). “When specialists express conflicting views, an agency must have discretion to rely on the reasonable opinions of its own qualified experts even if, as an original matter, a court might find contrary views more persuasive.” Lands Council, 537 F.3d at 1000 (quoting Marsh v. Oregon Natural Res. Council, 490 U.S. 360, 378, 109 S.Ct. 1851, 104 L.Ed.2d 377 (1989)). Mere uncertainty, or the fact that evidence may be “weak,” is not fatal to an agency decision. Greenpeace Action v. Franklin, 14 F.3d 1324, 1337 (9th Cir.1992) (upholding biological opinion, despite uncertainty about the effectiveness of management measures, because decision was based on a reasonable evaluation of all available data); Natl Wildlife Fed’n v. Babbitt, 128 F.Supp.2d 1274, 1300 (E.D.Cal.2000) (holding that the “most reasonable” reading of the best scientific data available standard is that it “permits the [FWS] to take action based on imperfect data, so long as the data is the best available”). FWS “must utilize the ‘best scientific ... data available,’ not the best scientific data possible.” Building Indus. Ass’n v. Norton, 247 F.3d 1241, 1246 (D.C.Cir.2001), cited with approval in Kern County Farm Bureau v. Allen, 450 F.3d 1072, 1080-81 (9th Cir. 2006) (“Absent superior data occasional imperfections do not violate” the ESA best available data standard); see also Defenders of Wildlife v. Babbitt, 958 F.Supp. 670, 680 (D.D.C.1997) (best available science standard does not require “conclusive evidence,” only that agency use best science available and not ignore contrary evidence). The deference afforded under the best available science standard is not unlimited. For example, Tucson Herpetological Society v. Salazar, 566 F.3d 870, 879 (9th Cir.2009), held that an agency may not rely on “ambiguous studies as evidence” to support findings made under the ESA. Because the studies did not lead to the conclusion reached by FWS, the Ninth Circuit held that these studies provided inadequate support in the administrative record for the determination made by FWS. Id.; see also Rock Creek Alliance v. U.S. Fish & Wildlife Service, 390 F.Supp.2d 993, 1008 (D.Mont.2005) (rejecting FWS’s reliance on a disputed scientific report, which explicitly stated its analysis was not applicable to the small populations addressed in the challenged opinion). Alternatively, the presumption of agency expertise may be rebutted if the agency’s decisions, although based on scientific expertise, are not reasoned, Greenpeace v. NMFS, 80 F.Supp.2d 1137, 1147 (W.D.Wash.2000), or if the agency disregards available scientific evidence better than the evidence on which it relies, Kern County Farm Bureau, 450 F.3d at 1080. Courts routinely perform substantive reviews of record evidence to evaluate the agency’s treatment of best available science. The judicial review process is not one of blind acceptance. See, e.g., Kern County, 450 F.3d at 1078-79 (thoroughly reviewing three post-comment studies and FWS’s treatment of those studies to determine whether they “provide[d] the sole, essential support for” or “merely supplemented” the data used to support a listing decision); Home Builders Ass’n of N. Cal. v. U.S. Fish and Wildlife Serv., 529 F.Supp.2d 1110, 1120 (N.D.Cal.2007) (examining substance of challenge to FWS’s determination that certain data should be disregarded); Trout Unlimited v. Lohn, 645 F.Supp.2d 929 (D.Or.2007) (finding best available science standard had been violated after thorough examination of rationale for NMFS’s decision to withdraw its proposal to list Oregon Coast Coho salmon); Oceana, Inc. v. Evans, 384 F.Supp.2d 203, 217-18 (D.D.C.2005) (carefully considering scientific underpinnings of challenge to FWS’s use of a particular model, including post decision evidence presented by an expert to help the court understand the complex model, applying one of several record review exceptions articulated in Esch v. Yeutter, 876 F.2d 976, 991 (D.C.Cir.1989), which are similar to those articulated by the Ninth Circuit). Courts are not required to defer to an agency conclusion that runs counter to that of other agencies or individuals with specialized expertise in a particular technical area. See, e.g., Am. Tunaboat Ass’n v. Baldrige, 738 F.2d 1013, 1016-17 (9th Cir.1984) (NMFS’s decision under the Marine Mammal Protection Act was not supported by substantial evidence because agency ignored data that was product of “many years’ effort by trained research personnel”); Sierra Club v. U.S. Army Corps of Eng’rs, 701 F.2d 1011, 1030 (2d Cir.1983) (“court may properly be skeptical as to whether an EIS’s conclusions have a substantial basis in fact if the responsible agency has apparently ignored the conflicting views of other agencies having pertinent experience! ]”) (internal citations omitted). A court should “reject conelusory assertions of agency ‘expertise’ where the agency spurns unrebutted expert opinions without itself offering a credible alternative explanation.” N. Spotted Owl v. Hodel, 716 F.Supp. 479, 483 (W.D.Wash.1988) (citing Am. Tunaboat Ass’n, 738 F.2d at 1016). In Conner v. Burford, 848 F.2d 1441, 1453-54 (9th Cir.1988), the agency attempted to defend its biological opinions by arguing that there was a lack of sufficient information to perform additional analysis. In rejecting this defense, the Ninth Circuit held that “incomplete information ... does not excuse the failure to comply with the statutory requirement of a comprehensive biological opinion using the best information available,” and noted that FWS could have completed more analysis with the information that was available. Id. at 1454. In light of the ESA requirement that the agencies use the best scientific and commercial data available ... the FWS cannot ignore available biological info or fail to develop projections of ... 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. Id. (emphasis added). (5) Best Available Science Standards and the Application of Analytical/Statistical Methodologies. The above-described standards apply with equal force to the use and interpretation of statistical methodologies. As the D.C. Circuit in Appalachian Power Co. v. EPA, 135 F.3d 791 (D.C.Cir.1998), explained in reviewing a challenge to a decision of the Environmental Protection Agency (“EPA”) under the “arbitrary and capricious” standard of review: Statistical analysis is perhaps the prime example of those areas of technical wilderness into which judicial expeditions are best limited to ascertaining the lay of the land. Although computer models are “a useful and often essential tool for performing the Herculean labors Congress imposed on EPA in the Clean Air Act,” [citation] their scientific nature does not easily lend itself to judicial review. Our consideration of EPA’s use of a regression analysis in this case must therefore comport with the deference traditionally given to an agency when reviewing a scientific analysis within its area of expertise without abdicating our duty to ensure that the application of this model was not arbitrary. Id. at 802. The model must fit the available data. See Nat'l Wildlife Fed’n v. EPA, 286 F.3d 554, 565 (D.C.Cir.2002) (“NWF v. EPA ”) (a court will only reject the choice of a model “when the model bears no rational relationship to the characteristics of the data to which it was applied”). For example, Oceana, 384 F.Supp.2d at 220, rejected a challenge to NMFS’s use of a particular analytical model that used data drawn from existing literature, even though experts “suggested that reliable take limits cannot be established without quantitative data gathered from ‘in-water’ surveys.” Although NMFS conceded “a thorough quantitative analysis based on empirical estimates of population size would be a superior way to analyze the impact [ ] on [the species],” it was undisputed that “given the paucity of information on sea turtles and the difficulties of using the data that does exist, ‘[a] different or more complex model [than that used by NMFS] was not available and could not even be constructed.’ ” Id. Likewise, “the fact that a given model has some imperfections does not prevent it from constituting the ‘best scientific information available.’ ” Oceana v. Evans, 2005 WL 555416, *16-*17 (D.D.C. Mar. 9, 2005) (citing 16 U.S.C. § 1851(a)(2)) (approving NMFS’s use of a model despite known limitations, where it was the only model available and the agency supplemented its analysis with other sources to address areas where the model was unable to make accurate predictions). VII. ANALYSIS A. Challenges to the Effects Analysis & Related Challenges to the RPA Actions. (1) Legal Requirements for a Project Effects Analysis. Under section 7(a)(2) of the ESA and the Joint Consultation Regulations, FWS must “[e]valuate the effects of the action and cumulative effects on the listed species or critical habitat.” 50 C.F.R. § 402.14(g)(3). FWS must then “[f]ormulate its biological opinion as to 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.” § 402.14(g)(4). The effects of the action are defined as: the 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. § 402.02. The environmental baseline includes: the past and present impacts of all Federal, State, or private actions and other human activities in the action area, the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section 7 consultation, and the impact of State or private actions which are contemporaneous with the consultation in process. Id. The baseline is described in FWS and NMFS’s Joint Consultation Handbook as: an analysis of the effects of past and ongoing human and natural factors leading to the current status of the species, its habitat (including designated critical habitat), and ecosystem, within the action area. The environmental baseline is a “snapshot” of a species’ health at a specified point in time. It does not include the effects of the action under review in the consultation. Consultation Handbook 4-22. Once the baseline, the “direct and indirect effects” of the action, and the “effects of other activities that are interrelated or interdependent with that action” are determined, 50 C.F.R. § 402.02, FWS then is required to consider whether, in light of the environmental baseline, the effects of the action, taken together with cumulative effects, are likely to jeopardize the continued existence of the listed species, 50 C.F.R. § 402.14(g). [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. .... [The agency must] appropriately consider the effects of its actions “within the context of other existing human activities that impact the listed species.” ALCOA [v. Administrator, Bonneville Power Admin.], 175 F.3d [1156,] 1162 n. 6 [(9th Cir.1999) ] (citing 50 C.F.R. § 402.02’s definition of the environmental baseline). This approach is consistent with our instruction ... 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.” [PCFFA v. U.S. Bureau of Reclamation], 426 F.3d [1082,] 1093 [ (9th Cir.2005) ] (emphasis added). NWF v. NMFS II, 524 F.3d at 930 (emphasis in original). To jeopardize 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.” 50 C.F.R. § 402.02. The Consultation Handbook further provides that to “appreciably diminish the value: [means] to considerably reduce the capability of designated [critical habitat].” Consultation Handbook at 4-36. A related case found: interpretation of “appreciably” to mean any “perceptible” effect would lead to irrational results, making any agency action that had any effects on a listed species a “jeopardizing” action. This is not the law, as such an interpretation conflicts with other provisions of the ESA that permit incidental take of listed species. PCFFA v. Gutierrez, 606 F.Supp.2d 1195, 1208 (E.D.Cal.2008) (citing 16 U.S.C. 1536(b)(4), 1539(1)(B)). (2) Best Available Science Challenges to the Effects Analysis and Related Challenges to the Justification Provided for the RPA Actions. Plaintiffs argue that the project effects analysis is predicated upon scientific errors that render the BiOp and its conclusion that project operations jeopardize the delta smelt arbitrary, capricious and an abuse of discretion: The Project Effects Analysis is the heart of the section 7 consultation process, providing the basis for FWS’ jeopardy and adverse modification determinations and for formulating the RPA. In this case, FWS began the Project Effects Analysis of the 2008 Smelt BiOp with a remarkable assumption: “The following analysis assumes that the proposed CVP/SWP operations affect delta smelt throughout the year either directly through entrainment or indirectly through influences on its food supply and habitat suitability.” BiOp at 203 (AR 000218.) This assumption plainly violates the “best available science” required by the ESA. The science, including the reports that FWS purports to rely on, shows that OMR flows and entrainment do not have any statistically significant effect on the delta smelt’s population growth rate. Restricting flows has no effect on the delta smelt population’s survival-such restrictions are a costly, but meaningless gesture. The same is true for [restrictions designed to control the position of] X2 [in the Fall]. Doc. 551 at 8. Plaintiffs maintain that the best available science does not support FWS’ “assumption” that “CVP/SWP operations affect delta smelt throughout the year either directly through entrainment or indirectly through influences on its food supply and habitat suitability.” BiOp at 203. Plaintiffs maintain that the science demonstrates: (a) OMR flows have no statistically significant effect on the delta smelt population growth rate; (b) With respect to the adult population, only OMR flows more negative than - 6,100 cfs will correlate to an increase in entrainment; (c) The location of Fall X2 does not determine the extent and quality of suitable smelt habitat-as with OMR flows, Fall X2 has no statistically significant effect on the population growth rate; and, (d) The CVP/SWP projects do not indirectly govern abiotic and biotic factors in the Delta that affect delta smelt abundance. Doc. 551 at 11. Plaintiffs also maintain that there is no scientific support for the BiOp’s assumption that the Projects control hydrodynamic conditions in the Delta, or for the BiOp’s classification of non-Project causes of harm as “indirect effects” of Project Operations. Id. a. The BiOp’s General Conclusion that Entrainment by Project Operations Adversely Affects Smelt Survival & Recovery is Supported by the Record. The magnitude of diversions at the CVP and SWP pumping facilities influences flows throughout the Delta, including in the Old and Middle Rivers (“OMR”). BiOp at 160. When the level of diversion at the pumps is high, Old and Middle Rivers may flow backwards (in the opposite direction than they would under natural hydrological conditions) and toward the CVP and SWP natural conditions (called “negative” flows). Id. Negative OMR flows draw delta smelt present in the central and south Delta toward the pumps, and high negative flows increase the risk that they will be entrained at the pumps. Id. at 163, 253 (Figure E-7). Unlike larger fish species, entrainment is lethal for weak-swimming delta smelt. Id. at 145. Relying on estimates of proportional entrainment presented by Dr. Wim Kimmerer in a 2008 paper entitled “Losses of Sacramento River Chinook Salmon and Delta Smelt to Entrainment in Water Diversions in the Sacramento-San Joaquin Delta,” published in the journal, San Francisco Estuary & Watershed Science (“Kimmerer (2008)”), the BiOp concludes that “[t]otal annual entrainment of the delta smelt population (adults and their progeny combined) ranged from approximately 10 percent to 60 percent per year from 2002-2006.” Id. at 210. In years when low flows and high exports coincide with a spawning distribution of the delta smelt that includes the San Joaquin River, the loss of larval delta smelt due to entrainment can exceed 50% of the population. Id. at 164-65. Such losses do not occur every year, but FWS concluded the effect of these large larval loss events is “substantial when it does,” particularly in light of the fact that the delta smelt is an annual fish. Id. at 165. Even one year where its spawning occurs “within the footprint of entrainment by the pumps” can lead to “a [severe] reduction in that year’s production.” Id. The BiOp’s Effects Analysis concludes that Project pumping operations have a “sporadically significant” adverse effect on smelt abundance: The population-level effects of delta smelt entrainment vary; delta smelt entrainment can best be characterized as a sporadically significant influence on population dynamics. Kimmerer (2008) estimated that annual entrainment of the delta smelt population (adults and their progeny combined) ranged from approximately 10 percent to 60 percent per year from 2002-2006. Major population declines during the early 1980s (Moyle et al. 1992) and during the recent POD years (Sommer et al. 2007) were both associated with hydrodynamic conditions that greatly increased delta smelt entrainment losses as indexed by numbers of fish salvaged. However, currently published analyses of long-term associations between delta smelt salvage and subsequent abundance do not support the hypothesis that entrainment is driving population dynamics year in and year out (Bennett 2005; Manly and Chotkowski 2006; Kimmerer 2008). BiOp at 210 (emphasis added). This passage was based in large part on Kimmerer (2008), which states: Delta smelt may suffer substantial losses to export pumping both as prespawning adults and as larvae and early juveniles. In contrast to the situation for salmon, pre-salvage mortality has been constrained in the calculations for adult Delta smelt, and its effects eliminated from the calculations for larval/juvenile Delta smelt. Combining the results for both life stages, losses may be on the order of zero to 40 percent of the population throughout winter and spring. The estimates have large confidence limits, which could be reduced by additional sampling, particularly to estimate 0 in Equation 18. If there is interest in improving these estimates further, some attempts should be made to examine the assumptions not fully tested above, particularly those used in extrapolating larval abundance to hatch dates. AR 018877. Plaintiffs argue that the BiOp misinterprets and misapplies Kimmerer’s work. Dr. Bryan Manly, Plaintiffs’ expert in the fields of biostatistics and population survey design, addressed the BiOp’s statement that “delta smelt entrainment can best be characterized as a sporadically significant influence on population dynamics.” Manly Decl., Doc. 897, at ¶ 7. Manly opines that “[t]his statement is unclear and confusing,” and explains: If the Service meant only that abundance at a point in time during a single year may vary depending upon entrainment, then Kimmerer’s estimates support that statement. But if, as appears more likely, the Service was relying upon Kimmerer’s estimates to support a conclusion that entrainment sometimes causes abundance to vary significantly later in the same year or in following years, then the statement in the BiOp has no scientific basis. Id. Kimmerer (2008) only estimated percentage losses of delta smelt within single year classes, and did not conclude that such losses reduce population abundance from one year to the next. Id. at ¶ 8. In fact, Kimmerer (2008) contains a number of disclaimers, including the caveat that “export effects” on smelt are small relative to other factors affecting survival: Although the upper bound of [the 0-40% loss] range represents a substantial loss, the effect of this loss is complicated by subsequent variability in survival (Figure 17). If this variability is uncorrelated with entrainment losses, then these losses will contribute little to the variability in fall abundance index. The simplest way to evaluate this is by regression of fall midwater trawl index on winter-spring export flow, but this relationship is contaminated by the downward step change in abundance in approximately 1981-1982, together with the long-term upward trend in export flow (mainly up to the mid-1970s, see Kimmerer 2004). Including this step in a regression model eliminates the effect of export flow on the fall midwater trawl index (coefficient = -1.5 ± 2.4, 95% CL, 36 df). It seems unlikely that the downward step change was due to the earlier increase in export flow; furthermore, despite substantial variability in export flow in years since 1982, no effect of export flow on subsequent mid-water trawl abundance is evident. This is not to dismiss the rather large proportional losses of delta smelt that occur in some years; rather, it suggests that these losses have effects that are episodic and that therefore their effects should be calculated rather than inferred from correlative analyses. In the absence of density dependence, using means in Figure 15 with natural mortality, fall abundance should have been reduced by ~ 10% during 1995-2005. This would have an equivalent effect of reducing the summer-fall survival index by 10%. This would have made little difference to fall abundance in the context of the approximately 50-fold variation in summer-fall survival (Figure 17), and would be difficult to detect through correlation. Although summer-fall survival appears to dominate variability in abundance of delta smelt in fall (Figure 17), this does not imply that control of export effects would be fruitless, as these effects can be considerable during dry years. Management of delta smelt should incorporate any opportunities that arise to improve habitat or food supply and to reduce any negative impacts of predation or toxic contamination. However, current evidence does not provide a clear path toward improving the status of delta smelt using these factors. Manipulating export flow (and, to some extent, inflow) is the only means to influence the abundance of delta smelt that is both feasible and supported by the current body of evidence, even though export effects are relatively small. The results presented here can be used to suggest when, and under what conditions, control of export effects would be most helpful. AR 018878. Kimmerer (2008) concludes that even though correlative analysis revealed “no effect of export flow on subsequent midwater trawl abundance,” there is reason to be concerned about episodic effects caused by “large proportional losses of delta smelt that occur in some years.” Id. As a result, according to Kimmerer (2008), population level effects should be calculated, rather than inferred from correlative analysis. Id. After performing such a calculation, Kimmerer (2008) concluded that entrainment reduced “the summer-fall survival index by 10%” during 1995-2005. Id. Although this 10% figure was small in the context of the 50-fold variation in summer-fall survival, Kimmerer (2008) nonetheless recommended controlling