Full opinion text
MEMORANDUM DECISION RE CROSS MOTIONS FOR SUMMARY JUDGMENT (DOCS. 430, 435, 446, 474, 477) OLIVER W. WANGER, District Judge. TABLE OF CONTENTS I. INTRODUCTION.............................................................812 II. BACKGROUND .............................................................813 A. The Listed Species........................................................813 1. Sacramento River Winter-Run Chinook Salmon..........................813 2. Spring Run Chinook..................................................814 3. Central Valley Steelhead..............................................815 4. Green Sturgeon......................................................816 5. Southern Resident Killer Whale .'.......................................816 B. The 2009 Salmonid BiOp and RPA..........................................816 III. STANDARD OF DECISION .................................................818 IV. BASIC LEGAL FRAMEWORK...............................................819 A. Review under the APA....................................................819 1. Record Review.......................................................819 2. Deference to Agency Expertise........................................819 B. General Obligations Under the ESA.........................................820 1. Best Available Science................................................821 2. Best Available Science Standards and the Application of Analytical/ Statistical Methodologies.................................. 824 V. EXPORT PLAINTIFFS’ & DWR’S CLAIMS....................................824 A. Alleged Clear Scientific Errors Pertaining to Delta Operations..................824 1. Challenged Statistical Methodologies ...................................825 2. Failure to Perform a Population-Level Quantitative Analysis ..............834 B. Baseline Analysis Challenges...............................................845 1. Failure to Distinguish Between Discretionary and Nondiscretionary Actions ...........................................................845 2. Treatment of Available Data on Ocean Harvest and Ocean Conditions.....852 C. Effects Analysis Challenges................................................858 1. Use of a 100-Year Timeframe..........................................858 2. Winter-Run Viability Analysis.........................................861 3. . Orea Analysis........................................................864 4. Interior Delta Mortality as an Indirect Effect............................866 D. Critical Habitat Analysis...................................................871 1. There Is No Requirement that NMFS Identify a Numerical Threshold for Adverse Modification............................................871 2. Significance of Impacts to Critical Habitat...............................872 E. Use of Surrogates..........................................................880 F. Challenges to the Reasonable and Prudent Alternative.........................882 1. RPA Action IV.2.1....................................................882 2. RPA Action IV.2.3....................................................898 3. Action IV.3..........................................................909 G. Compliance with 50 C.F.R. § 402.02 .........................................911 1. Consistency with Purposes of the Action ................................914 2. Consistency with the Action Agency’s Legal Authority and Jurisdiction.....917 3. Economic and Technical Feasibility.....................................919 4. Avoidance Jeopardy and/or Adverse Modification.........................922 5. DWR’s Feasibility Challenges to Action IV.4.2...........................922 VI. STANISLAUS RIVER PLAINTIFFS’ CLAIMS ................................928 A. Relevant Factual Background..............................................928 1. The New Melones Project.............................................928 2. The Stanislaus River Plaintiffs.........................................928 3. The Status of Steelhead in the Stanislaus River..........................928 B. Inclusion of the New Melones Unit in the Proposed Action Subject to Consultation ...........................................................930 C. Effects Analysis Challenges................................................931 1. New Melones Operations v. Baseline Effects.............................931 2. Challenge to Critical Habitat Adverse Modification Finding................934 D. Stanislaus River RPA Challenges...........................................937 1. Challenge to the Assumptions Used to Model New Melones Project Operations........................................................937 2. Do Actions III.1.2, III.1.3, and IV.1.2 Improperly Require Reclamation to Infringe Upon OID and SSJID’s Prior Right to Stanislaus River Water in violation of 50 C.F.R. § 402.02?..............................938 3. Use of the San Joaquin River Temperature Model........................941 4. Exceptions Built into Action III.1.2.....................................947 5. Does the Record Support the Finding that Action III.1.3 Will Avoid Jeopardy to or Adverse Modification of CV Steelhead or Critical Habitat?..........................................................948 6. DFG Salmon Population Model ........................................950 7. SR Plaintiffs’ “Impermissible Major Changes” Argument..................951 8. Challenges to the BiOp’s Feasibility Analyses?...........................951 9. Are Actions III.1.3, III.2.2 Consistent with the Purposes of the Project?.....952 10. Waste and Unreasonable Use of Water (California Constitution Article X, Section 2).......................................................953 VII. RECLAMATION’S LIABILITY UNDER THE ESA............................954 VIII. CONCLUSION............................................................955 I. INTRODUCTION These consolidated cases arise out of continuing efforts to protect several species listed under the Endangered Species Act (“ESA”), namely the endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) (“winter-run”), threatened Central Valley spring-run Chinook salmon (O. tshawytscha) (“spring-run”), threatened Central Valley steelhead (O. mykiss) (“CV steelhead”), threatened Southern Distinct Population Segment (“DPS”) of North American green sturgeon (Acipenser medirostris), and endangered Southern Resident killer whales (Orcinus orea) (collectively, “Listed Species”); and associated impacts to the water supply for more than half the State of California. Plaintiffs, San Luis & Delta Mendota Water Authority and Westlands Water District; State Water Contractors (“SWC”); Kern County Water Agency and Coalition for a Sustainable Delta; and Metropolitan Water District of Southern California (“MWD” or “Metropolitan”) (collectively “Export Plaintiffs”) move for summary judgment on their claims that the United States National Marine Fisheries Service’s (“NMFS”) June 4, 2009 Biological Opinion, addressing the impacts of the coordinated operations of the federal Central Valley Project (“CVP”) and State Water Project (“SWP”) (collectively the “Project”) on the Listed Species (“2009 Salmonid BiOp” or “BiOp”) and its Reasonable and Prudent Alternative (“RPA”), violates the ESA and the Administrative Procedure Act (“APA”). Doc. 430. Plaintiffs Stockton East Water District, Oak-dale Irrigation District, and South San Joaquin Irrigation District (“Stanislaus River Plaintiffs” or “SR Plaintiffs”) filed a separate motion for summary judgment, raising unique challenges to the BiOp. Doc. 435. Plaintiff-in-Intervention, the California Department of Water Resources (“DWR”) filed a separate motion for summary judgment on narrower grounds. Doc. 446. Federal Defendants, the United States Department of Commerce (“DOC”), the National Oceanic and Atmospheric Administration (“NOAA”), the agency within DOC of which NMFS is a part, NMFS, the United States Department of the Interior (“DOI”), and its sub-agency the United States Bureau of Reclamation (“Reclamation”), oppose and cross move for summary judgment on all remaining claims, Doc. 477, as do Defendanb-Intervenors California Trout, Friends Of The River, Natural Resources Defense Council, Northern California Council of the Federation of Fly Fishers, Pacific Coast Federation of Fishermen’s Associations/Institute for Fisheries Resources, Sacramento River Preservation Trust, San Francisco Baykeeper, The Bay Institute, and the Winnemem Wintu Tribe, Doc. 474. All parties filed replies. Docs. 487, 492, 513, 515. These cross motions, which included over 700 pages of briefing and thousands of pages of supporting declarations and exhibits, came on for hearing on December 16 and 17, 2010. II. BACKGROUND A. The Listed Species. 1. Sacramento River Winter-Run Chinook Salmon. Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) (“winter-run”) is listed as “endangered” under the ESA. 70 Fed.Reg. 37,160 (June 28, 2005). Historical winter-run population estimates were as high as approximately 230,000 fish in the 1960s, BiOp at 82, but declined to under 200 fish in the 1990s. Id. at 81. In recent years, population surveys of winter-run estimated a high of 17,344 fish in 2006, followed by a decline in 2007 (2,542 fish) that persisted into 2008 (2,830 fish). Id. Adult winter-run Chinook salmon migrate upstream from the Pacific Ocean through the Bay-Delta estuary during November through July, moving upstream past Red Bluff Diversion Dam (“RBDD”) from mid-December through early August, with peak passage occurring in mid-March. BiOp at 80. Spawning typically occurs in the mainstream Sacramento River downstream of Keswick Dam during April through August, with the greatest spawning activity typically taking place during May and June. Id. Winter-run fry begin to emerge from the gravel beds where eggs are laid in late June and early July, continuing through October. Id. Juvenile rearing and emigration typically occurs between July and February in the upper Sacramento River, with juvenile migration downstream past RBDD beginning as early as mid-July, peaking in September, and continuing through March in some years. Id. at 80-81. Juvenile winter-run occur in the Delta from November through May. Id.; Pac. Coast Fed’n of Fisherman’s Ass’ns. v. Gutierrez (“Gutierrez II’), 606 F.Supp.2d 1195, 1216-17 (E.D.Cal.2008). Winter-run juveniles typically remain in the Delta until they reach a fork length of approximately 118 millimeters and are from 5 to 10 months of age. BiOp. at 81. Juveniles begin exiting to the ocean as early as November and continue to do so through May. Id. Designated critical habitat for winter-run includes the Sacramento River, the Delta, and downstream bays to the Golden Gate Bridge. 58 Fed.Reg. 33,212 (June 16, 1993). Gutierrez II, 606 F.Supp.2d at 1217. The following physical and biological features are identified as essential for the conservation of winter-run: (1) access from the Pacific Ocean to appropriate spawning areas in the upper Sacramento River, (2) the availability of clean gravel for spawning substrate, (3) adequate river flows for successful spawning, incubation of eggs, fry development and emergence, and downstream transport of juveniles, (4) water temperatures between 42.5 and 57.5°F for successful spawning, egg incubation, and fry development, (5) habitat areas and adequate prey that are not contaminated, (6) riparian habitat that provides for successful juvenile development and survival, and (7) access downstream so that juveniles can migrate from spawning grounds to San Francisco Bay and the Pacific Ocean. BiOp at 90. Currently, the value of winter-run critical habitat is “degraded,” by, among other things, the presence of dams, temperature control issues on the upper Sacramento River, unscreened diversions, and degraded spawning and riparian habitat. Id. at 93. 2. Spring Run Chinook. Central Valley spring-run Chinook salmon (O. tshawytscha) (“spring-run”) is listed as “threatened” under the ESA. 71 Fed. Reg. 834 (June 5, 2005); 70 Fed.Reg. 37160 (June 28, 2005) (critical habitat designated). There are three “independent” populations of spring-run, located on Butte, Deer and Mill Creeks, several “dependent” populations (which rely on the three independent populations for continued existence), and a population of hatchery fish from the Feather River Hatchery (FRH). BiOp at 93-94. Spring-run Chinook have been declining over recent years. The Central Valley as a whole is estimated to have supported spring runs as large as 600,000 fish between the late 1880s and 1940s. Id. at 94. The 2007 escapement was 7,819 for all tributary populations (all independent and dependent populations, excluding those fish returning to FRH). Id. at 97. Adult spring-run enter freshwater in the spring, beginning in late January, entering the Sacramento River between March and September, primarily in May and June, and entering spawning grounds between mid-April and mid-June. Id. at 93. Adults hold over the summer in cool, high elevation streams while they sexually mature, and then spawn in the fall, between September and October, depending on water temperatures. Id. at 93. Juveniles typically spend a year or more in freshwater before emigrating to the ocean. Id. at 93. The emigration period for spring-run extends from November to June and is highly variable. Id. at 94. Designated critical habitat for spring-run includes the Sacramento River, tributaries supporting spring-run, the Delta, and downstream bays to the Golden Gate Bridge. Gutierrez II, 606 F.Supp.2d at 1217. The value of spring-run critical habitat currently is “degraded.” BiOp at 101, 104. 3. Central Valley Steelhead. Central Valley steelhead (O. mykiss) (“CV steelhead”) is listed as “threatened” under the ESA. 71 Fed.Reg. 834 (Jan. 5, 2006). Wild CV steelhead are confined mostly to the upper Sacramento River and its tributaries. BiOp at 107. Recent surveys also have detected small, self-sustaining populations on the Stanislaus, Mokelumne, and Calaveras Rivers, as well as observations of juvenile steelhead on the Tuolumne and Merced Rivers. Id. These small populations make up the remaining representatives of the Southern Sierra Nevada Diversity Group (“SSNDG”) of CV Steelhead. Id. at 198. While there is limited information on population size, NMFS estimates that the current population for the entire distinct population segment (“DPS”) (including the SSNDG as well as all other populations) in the Central Valley is less than 3,628 spawning females, compared with 40,000 spawners in the 1960s. BiOp at 106. The CV Steelhead population has shown a pattern of negative growth since the late 1960s, and there is no indication that the trend has changed. BiOp at 108-09 & Figures 4-4 & 4-5. CV steelhead generally leave the ocean from August through April and spawn from December through April in small streams and tributaries where cool, well-oxygenated water is available year-round. Id. at 104. Unlike Pacific salmon, steel-head are capable of spawning more than once before death. Although one-time spawners are the great majority, approximately 17.2 percent in California streams are repeat spawners. Id. at 103-104. Steelhead eggs hatch approximately 30 days after spawning, and fry emerge from the gravel four to six weeks later into shallow areas where they feed. Id. at 105. Steelhead rear during the summer and emigrate “episodically” from their natal streams during fall, winter, and spring high flows. Id. at 106. Emigrating CV Steelhead use the lower reaches of the Sacramento River and Delta for rearing and as a migration corridor to the ocean. Id. Juvenile CV steelhead typically emigrate through the Delta from late September through June. Id. at 105 (Table 4-6). Approximately 80% of historical CV Steelhead range is blocked by dams. Id. at 109. CV steelhead critical habitat is degraded. Id. at 113. 4. Green Sturgeon. The southern distinct population segment of the North American green sturgeon (“green sturgeon”) (Acipenser medirostris) is listed as “threatened” under the ESA. 71 Fed.Reg. 17757 (Apr. 7, 2006); 73 Fed.Reg. 52,084 (critical habitat designated). Green sturgeon are anadromous fish that spawn and rear in freshwater rivers and estuaries but spend most of their lives in the ocean. See BiOp at 114-15. They are a long-lived, slow-growing species. 68 Fed.Reg. 4,433, 4,436 (Jan. 29, 2003). Juvenile green sturgeon are present in the Delta year round. BiOp at 119. There are no definitive population counts or figures for the Southern DPS green sturgeon. Evidence available at the time the BiOp was written suggests that the population in the Delta watershed is “relatively small,” ranging from several hundred to a few thousand adults. Id. at 124. Critical habitat for the Southern DPS of green sturgeon was proposed on September 8, 2008, 73 Fed.Reg. 52,084, but had not been adopted as of the issuance of the BiOp. Proposed critical habitat included “approximately 325 miles of riverine habitat and 1,058 square miles of estuarine habitat in California, Oregon, and Washington, and 11,927 square miles of coastal marine habitat off California, Oregon, and Washington within the geographical area presently occupied by the Southern DPS of green sturgeon.” BiOp at 126. In addition, approximately 136 square miles of habitat within the Yolo and Sutter bypasses, adjacent to the Sacramento River, are proposed for designation. Id. The BiOp concluded that the current condition of proposed critical habitat for the Southern DPS of green sturgeon is “degraded over historical conditions.” Id. at 134. 5. Southern Resident Killer Whale. The Southern Resident DPS of killer whale (Orcinus orea) (“Southern Residents”) was listed as “endangered” under the ESA on November 18, 2005, 70 Fed. Reg. 69,903 (Nov. 18, 2005), and the DPS is designated as “depleted” under the Marine Mammal Protection Act. BiOp at 158— 59. Southern Residents are found throughout the coastal waters off Washington, Oregon, and Vancouver Islands and are known to travel as far south as central California. Id. at 159. The BiOp addresses the impact of Project operations on Southern Residents and concludes that extinction of winter-run and spring-run Chinook salmon, as well as reductions in fall-run Chinook salmon populations, “would reduce prey availability and increase the likelihood for local depletions of prey in particular locations and times,” which would, in turn, increase the risk of extinction of the Southern Residents. BiOp at 573-74. B. The 2009 Salmonid BiOp and RPA. The 2009 Salmonid BiOp, prepared pursuant ESA § 7, 16 U.S.C. § 1536(a)(2), concluded that “the long-term operations of the CVP and SWP are likely to jeopardize the continued existence” of the Listed Species and “destroy or adversely modify” critical habitat for winter-run, spring-run, and CV steelhead. BiOp at 575. As required by law, the BiOp includes an RPA designed to allow the projects to continue operating without causing jeopardy to the species or adverse modification to its critical habitat. Id. at 575-671. The RPA “is composed of numerous elements for each of the various project divisions and associated stressors,” which, according to the BiOp, “must be implemented in its entirety to avoid jeopardy and adverse modification.” Id. at 578. The BiOp provides a succinct overview of the RPA: There are several ways in which water operations adversely affect listed species that are addressed in this RPA. We summarize the most significant here: 1) Water operations result in elevated water temperatures that have lethal and sub-lethal effects on egg incubation and juvenile rearing in the upper Sacramento River. The immediate operational cause is lack of sufficient cold water in storage to allow for cold water releases to reduce downstream temperatures at critical times and meet other project demands. This elevated temperature effect is particularly pronounced in the Upper Sacramento for winter-run and mainstem spring-run, and in the American River for steelhead. The RPA includes a new year-round storage and temperature management program for Shasta Reservoir and the Upper Sacramento River, as well as long-term passage prescriptions at Shasta Dam and re-introduction of winter-run into its native habitat in the McCloud and/or Upper Sacramento rivers. 2) In Clear Creek, recent project operations have led to increased abundance of Clear Creek spring-run, which is an essential population for the short-term and long-term survival of the species. Nonetheless, in the proposed action, continuation of these operations is uncertain. The RPA ensures that essential flows and temperatures for holding, egg incubation and juvenile survival will be maintained. 3) Red Bluff Diversion Dam (RBDD) on the Sacramento River impedes both upstream migration of adult fish to spawning habitat and downstream migration of juveniles. Effects are significant for winter-run and spring-run, but are particularly pronounced for green sturgeon and its proposed critical habitat in that a significant portion of the population is blocked from its spawning and holding habitat. The RPA mandates gate openings at critical times in the short term while an alternative pumping plant is built, and, by 2012, opening of the gates all year. 4) Both project and non-project effects have led to a significant reduction in necessary juvenile rearing habitat in the Sacramento River Basin and Delta. The project’s flood control operations result in adverse effects through reduced frequency and magnitude of inundation of rearing habitat. To minimize these effects, the RPA contains both short-term and long-term actions for improving juvenile rearing habitat in the Lower Sacramento River and northern Delta. 5) Another major effect of water operations is diversion of out-migrating juveniles from the north Delta tributaries into the interior Delta through the open DCC gates. Instead of migrating directly to the outer estuary and then to sea, these juveniles are caught in the interior Delta and subjected to pollution, predators, and altered food webs- that cause either direct mortality or impaired growth. The RPA mandates additional gate closures to minimize these adverse effects to winter-run, spring-run, and steelhead. 6) Similarly, water pumping causes reverse flows, leading to loss of juveniles migrating out from the Sacramento River system in the interior Delta and more juveniles being exposed to the State and Federal pumps, where they are salvaged at the facilities. The RPA prescribes Old and Middle River flow levels to reduce the number of juveniles exposed to the export facilities and prescribes additional measures at the facilities themselves to increase survival of fish. 7) The effects analysis shows that juvenile steelhead migrating out from the San Joaquin River Basin have a particularly high rate of loss due to both project and non-project related stressors. The RPA mandates additional measures to improve survival of San Joaquin steel-head smolts, including both increased San Joaquin River flows and export curtailments. Given the uncertainty of the relationship between flow and exports, the RPA also prescribes a significant new study of acoustic tagged fish in the San Joaquin Basin to evaluate the effectiveness of the RPA and refine it over the lifetime of the project. 8) On the American River, project-related effects on steelhead are pronounced due to the inability to consistently provide suitable temperatures for various life stages and flow-related effects caused by operations. The RPA prescribes a flow management standard, a temperature management plan, additional technological fixes to temperature control structures, and, in the long term, a passage at Nimbus and Folsom Dams to restore steelhead to native habitat. 9) On the Stanislaus River, project operations have led to significant degradation of floodplain and rearing habitat for steelhead. Low flows also distort cues associated with out-migration. The RPA proposes a year-round flow regime necessary to minimize project effects to each life-stage of steelhead, including new spring flows that will support rearing habitat formation and inundation, and will create pulses that cue out-migration. 10)Nimbus Fish Hatchery steelhead program contribute to both loss of genetic diversity and mixing of wild and hatchery stocks of steelhead, which reduces the viability of wild stocks. The Nimbus and Trinity River Hatchery programs for non-listed fall-run also contribute to a loss of genetic diversity, and therefore, viability, for fall-run. The RPA requires development of Hatchery Genetics Management Plans to improve genetic diversity of both steelhead and fall-run, an essential prey base of Southern Resident. Id. at 576-78. III. 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 the movant is entitled to judgment as a matter of law.” Fed.R.Civ.P. 56(c). The claims in this case involve NMFS’s issuance of a biological opinion, 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 APA judicial review 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 adminis trative record and otherwise consistent with the APA standard of review.” Id. at 90. IV. BASIC LEGAL FRAMEWORK A. Review under the APA. APA invalidation of a biological opinion requires Plaintiffs to prove that NMFS’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. U.S. Fish and Wildlife, 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 Hearing Transcript (“Tr.”)), 406, 407, 462, 740 (7/8/10 Tr.), 750, expert testimony has been considered solely 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 citation and quotation 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). [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. B. 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 NMFS 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, NMFS must give the action agency a written biological opinion “setting forth [NMFS’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 NMFS determines that jeopardy or destruction or adverse modification of critical habitat is likely, NMFS “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). 1. 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 Gutierrez II, 606 F.Supp.2d at 1244. “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 scientific and commercial data available standard “recognizes that better scientific evidence will most likely always be available in the future”). 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) (internal quotation 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 & Elec. 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 v. McNair, 537 F.3d 981, 993 (9th Cir.2008), 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); Nat’l 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 [NMFS] to take action based on imperfect data, so long as the data is the best available”). NMFS “must utilize the best sci entific ... 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. There, in the context of an ESA § 4 listing determination, NMFS “affirmatively relief] on ambiguous studies as evidence of persistence (i.e., stable and viable populations), and in turn argue[d] that this ‘evidence’ of persistence ... proves that the lizard’s lost range is insignificant for purposes of the ESA.” Id. The Ninth Circuit found this conclusion to be unreasonable because “[t]he studies do not lead to the conclusion that the [species] persists in a substantial portion of its range, and therefore cannot support [NMFS’s] conclusion.” Id. ; see also Rock Creek Alliance v. U.S. Fish & Wildlife Service, 390 F.Supp.2d 993, 1008 (D.Mont.2005) (rejecting section 7 biological opinion’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 [the conclusions of an environmental impact statement prepared under the National Environmental Policy Act] have a substantial basis in fact if the responsible agency has apparently ignored the conflicting views of other agencies having pertinent experience! ]”). A court should “reject conclusory 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. 2. Best Available Science Standards and the Application of Analytical/Statistical Methodologies. These 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. (internal quotations omitted). 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). V. EXPORT PLAINTIFFS’ & DWR’S CLAIMS. A. Alleged Clear Scientific Errors Pertaining to Delta Operations. A major premise of the BiOp is that pumping “causes reverse flows, leading to loss of juveniles migrating out from the Sacramento River system in the interior Delta and more juveniles being exposed to the State and Federal pumps, where they are salvaged at the facilities.” BiOp at 577. The effects analysis also concluded “that juvenile steelhead migrating out from the San Joaquin River Basin have a particularly high rate of loss due to both project and non-project related stressors.” Id. at 577-78. To mitigate for these impacts, the RPA “prescribes Old and Middle River flow levels to reduce the number of juveniles exposed to the export facilities and prescribes additional measures at the facilities themselves to increase survival of fish.” Id. at 577. In addition, “to improve survival of San Joaquin steelhead smolts,” the RPA prescribes “both increased San Joaquin River flows and export curtailments.” Id. at 578. Plaintiffs strenuously argue that NMFS made certain “clear” scientific errors in reaching the conclusion that exports adversely affect juvenile salmonid survival. 1. Challenged Statistical Methodologies. a. Use of Raw Salvage in Figures 6-65 and 6-66. NMFS relied on salvage data provided by Plaintiff-Intervenor, DWR, presented in Figures 6-65 and 6-66 of the BiOp: Id. at 361-62. These figures were cited to demonstrate that “[l]oss of older juveniles at the CVP and SWP fish collection facilities increase sharply at [OMR] flows of approximately -5,000 cfs and depart from the initial slope at flows below this.” Id. at 361. Federal Defendants’ cross motion explains that NMFS used this data to “help evaluate where along the spectrum of OMR flows any significant change in salvage could be observed.” Doc. 477-1 at 53. These figures, which are based upon average salvage figures over many years, use “raw” salvage numbers that are not scaled to reflect the size of the population from which the fish were salvaged at the time the particular sample was taken. Previous rulings in this and the related Consolidated Delta Smelt Cases have discussed at length why the use of such data is not consistent with standard practice in the fields of fish biology and population dynamics. See San Luis & Delta-Mendota Water Authority v. Salazar, 760 F.Supp.2d 855, 885-90 (E.D.Cal.2010). The May 18, 2010 Findings of Fact and Conclusions of Law Re Plaintiffs’ Request for Preliminary Injunction (“PI Decision”) in this case found: 125. ... The comparisons of salvage to negative OMR flows relied upon in the BiOp utilize raw salvage numbers, rather than scaling salvage to population size. See Doc. 179, Declaration of Richard B. Deriso at ¶¶ 3-5. Scaling salvage to population size is standard fisheries science practice and could have been accomplished for several of the Listed Species based on existing population data. See id. at ¶¶ 5-6. This failure is a fundamental and inexplicable error. Salvage may have been higher in some years simply because the population was higher, not because of any differences in negative OMR flows. Salvage may have been lower in other years because the population was lower. Dr. Deriso demonstrated the potential significance of this failure by plotting the population adjusted Juvenile Chinook Incidental take rate against OMR flow. Based upon this revised analysis for spring-run and winter-run, Dr. Deriso concluded that there is no statistically significant relationship between the take index and OMR flows. Id. at ¶ 6. 126. The BiOp’s conclusions reached about the spring-run and winter-run Chinook failed to utilize the best available scientific methodology, because population data was available at the time the BiOp was issued that would have permitted NMFS to perform the straightforward population adjustment required to conform to standard, generally accepted practices for fisheries population measurements utilized in their field of expertise. If, in those years when salvage was greatest, population sizes overall were 10 or 100 times larger than other years, the effects might not be jeopardizing. Without adjustment for population size, NMFS’s reliance on that figure was arbitrary and capricious. 127. As to the CV steelhead, for which no population numbers are available, it is less clear whether the use of raw salvage numbers is always inappropriate. Figures 6-65 and 6-66 ambiguously reference monthly CVP and SWP “Older Juvenile Loss” on the y axis. Were most of the salvaged fish represented on these charts Chinook salmon? No reason is offered why NMFS did not segregate the steelhead figures from those of Chinook salmon. If the species had been evaluated separately, would it have been reasonable for NMFS to fail to adjust the steelhead figures for population size? Separate analysis was not done. Consol. Salmonid Cases, 713 F.Supp.2d 1116, 1142-43 (E.D.Cal.2010) (emphasis added). Federal Defendants attempt to explain their use of these figures in two ways. First, Jeffrey Stuart, NMFS Fisheries Biologist and the primary author of the Delta section of the BiOp, opines that “the general trend in fish loss should still be apparent regardless of scaling.” Fourth Stuart Deck, Doc. 485 at ¶ 72. He insists that this data “indicates that additional loss of fish occurs with increasing export levels as measured by the OMR flow values.” Id. This explanation simply defies common sense. When trying to discern trends from data points that range across many years, an obvious “confounding variable” is population size. A trend observed in data that is unsealed for population size may change or completely disappear when scaled for population size. See Deriso Deck, Doc. 440 at ¶¶ 13 — 31. Federal Defendants had the information needed to perform such a simple analysis of the available data, but did not do so, and unjustifiably relied on the unsealed data to form a quantitative conclusion that salvage rates increased sharply above — 5,000 cfs OMR. This was a clear scientific error. DefendanWlntervenors argue that the agency cannot violate the ESA by failing to take an additional step to scale the salvage data to salmonid population abundance. They maintain that all the ESA requires is that NMFS consider the “available” evidence not that it create new data or “follow scientific practices defined by Export Plaintiffs experts.” Doc. 484 at 51. It is true that the best available science standard does not require NMFS to create new data or apply new models to existing data, Building Indus. Ass’n, 247 F.3d at 1246. However, here, NMFS put data to a use for which it is not appropriate, as it produces unreliable results. Cf. NWF v. EPA, 286 F.3d at 565 (a court may reject agency’s choice of model when it “bears no rational relationship to the characteristics of the data to which it was applied”). Every biostatistics expert who presented evidence in this and related fish cases has agreed that it is wholly inappropriate and scientifically unreasonable to draw management conclusions from a plot comparing unsealed salvage data to OMR flows collected over a period of years when population varied. The agency is required to apply generally recognized and accepted biostatistical principles, which constitute best available science, in reaching its decisions. b. Was the BiOp’s Reliance on Figures 6-65 and 6-66 Hamiless? Alternatively, Federal Defendants argue that any such error was harmless given the other record evidence that supports the BiOp’s conclusions. No party has provided authority that a harmless error rule applies when the agency commits a substantive error under the ESA. Arguendo, Defendants’ alternative evidence is considered. (1) Record Citations Provided by Mr. Stuart. Mr. Stuart states: “[additional assessment of the effects of the OMR flow levels on salmon loss was derived from data provided by NMFS staff for the BDCP. NMFS 79238-239; 79240-83808; 90852-98.” Fourth Stuart Decl., Doc. 485 at ¶ 73. These are several thousand pages of documents. Mr. Stuart does not explain how the voluminous referenced information was used or analyzed. It is impossible to determine whether these referenced pages provide a sufficient alternative basis for the BiOp’s conclusions. NMFS has provided no explanation for an alternative to its scientifically unreliable conclusions. Humane Soc. v. Locke, 626 F.3d at 1048 (holding NMFS did not offer a satisfactory explanation for its findings); Am. Tunaboat Ass’n, 738 F.2d at 1016 (finding that despite broad discretion afforded NOAA, where record evidence detracts from that relied upon by the agency, a court may find the agency’s decision arbitrary and capricious). Citing this information and then failing to explain it is arbitrary and capricious. (2) Particle Tracking Model Results. The BiOp also relied on outputs from computer model runs utilizing the so-called Particle Tracking Model (“PTM”). Export Plaintiffs’ and DWR’s 2010 PI Motion challenged the use of PTM, arguing that while PTM is useful to track the fate of neutrally buoyant particles, it does not accurately reflect the behavior of salmonids, which are strong, volitional swimmers. These challenges were rejected in the May 18, 2010 PI Decision on the grounds that the BiOp acknowledged the limitations of PTM and reasonably relied on PTM studies to support certain conclusions: 120. This is a dispute among scientists. While DWR criticizes PTM modeling, Stuart and NMFS recognized its limitations and found PTM studies helpful to support its conclusions that: (a) as exports increase, negative OMR flows also increase; and (b) that at Station 815 (the confluence of the Mokelumne River and the San Joaquin River), particle entrainment increases from 10% at -2,500 cfs, to 20% at -3,500 cfs, to 40% at -5,000 cfs, and 90% at -7,000 cfs. NMFS, through Mr. Stuart, took into account inherent differences in the movement of neutrally buoyant particles and then-speed and direction of travel. Administrative law requires deference to the Agency. Additional record analysis is necessary to determine the extent of support for NMFS’s additional opinion that exports affect salmonid survival. Consol. Salmonid Cases, 713 F.Supp.2d at 1141. These challenges are discussed in other sections of this decision. Here, it is sufficient to note that the PTM results are not a complete replacement for Figures 6-65 and 6-66, as they only explain how particles, not actual fish, would respond to increased OMR flow. Nor do Federal Defendants point to any other information in the record that delineates “where along the spectrum of OMR flows any significant change in salvage could be observed,” the purposes for which Federal Defendants use 6-65 and 6-66. The same reasoning applies to acoustic tag studies and other data the BiOp relies upon. This other data was treated in the May 18, 2010 decision and below in greater detail. It is undisputed that none of these studies or additional data pinpoint for management purposes at what point negative OMR flows must be controlled. Doc. 347 ¶¶ 128-138. It is not appropriate to speculate how NMFS’s analysis and/or conclusions would have changed had the data used in figures 6-65 and 6-66 been scaled to population size. This must be done on remand. Whether there is sufficient data to scale CV steelhead salvage information to population size is unclear. Compare BiOp at 107 (discussing existing population data and difficulties posed by “lack of monitoring program”) with Doc. 431 at 11 (citing Burnham Deck, Doc. 439 at ¶ 42 (“NMFS has access to the number of hatchery-produced salmon each year”), for the proposition that NMFS had “readily available” data regarding how many CV Steelhead were released from hatcheries each year)). That scaling for population size may not be possible for all species may limit NMFS’s efforts. If population data is unavailable for certain species, the agency must nevertheless explain how it can make management conclusions without such information. The extent to which any such limitations mitigate NMFS’s failure to scale raw salvage data cannot be discerned from the present record. (3) Figures 6-71, 6-72, and 6-73. The BiOp also relies on a series of plots, taken directly from Reclamation’s Biological Assessment (“BA” or “OCAP BA”), of monthly juvenile salmonid “loss” against average exports. The first set of plots, Figure 6-71, depicts loss of juvenile Chinook salmon versus average monthly CVP and SWP exports for a period from 1995 through 2007. BiOp at 370. This plot was specifically cited as quantitative evidence of a relationship between exports and loss at the pumps: The CVP/SWP operations BA presented data that regressed the loss of older juvenile Chinook salmon against exports (figure 6-71) and found that a significant relationship existed. The relationship was stronger for exports at the SWP (p = 0.000918) than for exports at the CVP (p = 0.0187). The months of December through April resulted in the most informative relationship based on the historical number of older juvenile Chinook salmon salvaged each month and the relationship of each month to salvage and exports. Conversely, regressions performed for monthly salvage of YOY Chinook salmon against exports did not result in a significant relationship at either the SWP or CVP facilities.... Id. at 368-69. In this way, the BiOp used Figure 6-71 as quantitative evidence of a statistically significant connection between loss of older juvenile Chinook salmon and export levels. These plots suffer from the same flaw of misusing raw salvage data. They must be re-analyzed and explained on remand if they are to be used as scientific justification for the BiOp’s conclusions. Figures 6-72 and 6-73 present a more difficult issue, as they concern CV steel-head salvage, for which much less data is available. Figure