Opinion ID: 2763492
Heading Depth: 4
Heading Rank: 2

Heading: Legal Background—The Endangered Species Act

Text: We must review NMFS’s formal opinion as to how Reclamation and DWR should operate the Projects to avoid jeopardizing endangered Salmonid species. Before further discussing the relationship between the Projects and the species, we briefly review the legal framework for that opinion. The federal government protects listed and threatened species, such as the five at issue here, primarily through the ESA. See Endangered Species Act, 16 U.S.C. §§ 1531–1544 (2012). When Congress passed the ESA in 1973, it sought to bring about the “better safeguarding, for the benefit of all citizens, [of] the Nation’s heritage in fish, wildlife, and plants.” Id. § 1531(a)(5). Section 7 of the ESA “addresses the obligations of federal agencies with respect to conservation and protection of species listed as either endangered or threatened under the ESA.” Lawrence R. Liebesman & Rafe Petersen, Endangered Species Deskbook 39 (2d ed. 2010). ESA section 7 prohibits a federal agency from taking any action that is “likely to jeopardize the continued existence” of any listed or threatened species or “result in the destruction or adverse modification” of those species’ critical habitat. 16 U.S.C. § 1536(a)(2). Section 7 requires an agency proposing a project that might harm listed or threatened species to consult with either NMFS or the Interior Department’s Fish and Wildlife Service SAN LUIS V. LOCKE 31 (“FWS”)7 about the proposed action. 16 U.S.C. § 1536(a)(2). As part of this consultation, the action agency prepares an initial assessment of the project in which it evaluates the project’s impact on any listed or endangered species. This is called a Biological Assessment (“BA”). 50 C.F.R. § 402.02 (2009). The appropriate consultation agency reviews the action agency’s BA and uses it to prepare a Biological Opinion (“BiOp”) in which it ultimately determines whether the proposed agency action is likely to adversely impact endangered or listed species, or negatively modify their critical habitats. See 16 U.S.C. § 1536(a)(2).8 If the agency concludes that the proposed action will jeopardize species or critical habitats, “the Biological Opinion must outline any ‘reasonable and prudent alternatives’ that the [agency] . . . believes will avoid that consequence.” Bennett v. Spear, 520 U.S. 154, 158, 117 S. Ct. 1154, 1159 (1997) (quoting 16 U.S.C. § 1536(b)(3)(A)). Reasonable and prudent alternatives (“RPAs”) are alternative actions identified during formal consultation that can be implemented in a manner consistent with the intended purpose of the action, that can be implemented consistent with the scope of the Federal 7 Whether an agency consults with NMFS or FWS depends on the species for which it is seeking consultation. NMFS consults on marine and anadromous species. See Liebesman & Petersen, supra, at 40. 8 The consultation agency’s determination with regard to whether the proposed project is likely to jeopardize listed species is called the “jeopardy opinion” component of the BiOp. See U.S. Fish & Wildlife Serv. & Nat’ l Marine Fisheries Serv., ESA Section 7 Consultation Handbook 4-37 (Mar. 1998) [hereinafter “Handbook”]. 32 SAN LUIS V. LOCKE agency’s legal authority and jurisdiction, that is [sic] economically and technologically feasible, and that the Director believes would avoid the likelihood of jeopardizing the continued existence of listed species or resulting in the destruction or adverse modification of critical habitat. 50 C.F.R. § 402.02. The consulting agency may also issue—with the BiOp—an incidental take statement (“ITS”) that permits the action agency to harm listed species when implementing the RPAs without violating the ESA. See id. B. Proceedings Leading to the Current Controversy 1. The 2009 Salmonid Biological Opinion
In 2006, Reclamation asked NMFS to prepare a BiOp assessing the impact of continued and future CVP/SWP operations on Delta Salmonid species.9 This request was motivated by the listing of new endangered species and the designation of new critical habitats. 2009 Salmonid BiOp at 31. In it, Reclamation asked NMFS to evaluate the effect of Reclamation and DWR’s proposal to continue to operate the Projects “to divert, store, and convey Project water . . . ,” OCAP BA at 2-1, on winter-run Chinook, spring-run Chinook, CV steelhead, CCC steelhead (a fish not at issue 9 Although the SWP is a state project, it is subject to federal consultation along with the CVP because of a 1986 agreement between the federal government and DWR. 2009 Salmonid BiOp at 31. SAN LUIS V. LOCKE 33 here), green sturgeon, and Southern Resident orca, see 2009 Salmonid BiOp at 30. Reclamation developed a BA that could provide the basis for such a consultation in the fall of 2008. Id. at 32. Using the data Reclamation provided in the BA, supplementing it with its own research, NMFS developed a draft Salmonid BiOp that it released to Reclamation and DWR for comment in the winter of 2008. Id. at 33. Reclamation and DWR reviewed and commented on the document. NMFS also requested and received peer review from the CALFED BayDelta Program and the Center for Independent Experts. See id. Based on the comments received, NMFS published a final 560-page BiOp on June 4, 2009. Reclamation provisionally accepted the BiOp that same day. Plaintiffs contest the legality of the 2009 BiOp here, arguing—for various reasons—that parts of it are arbitrary or capricious in violation of the APA. Before discussing Plaintiffs’ specific challenges and the issues on appeal, we briefly review the portions of the BiOp that are relevant.
In the first part of the BiOp, NMFS concludes that “the long-term operations of the CVP and SWP are likely to jeopardize the continued existence of the” winter-run Chinook, the spring-run Chinook, the CV steelhead, the green sturgeon, and the Southern Resident orca. Id. at 575. Similarly, “[t]he long-term operations of the CVP and SWP are likely to destroy or adversely modify critical habitat for” winter-run Chinook, spring-run Chinook, CV steelhead, and green sturgeon. Id. 34 SAN LUIS V. LOCKE
Because NMFS concludes that ongoing CVP/SWP operations would threaten listed species, it issued over seventy RPAs that Reclamation is supposed to implement to avoid jeopardy. See generally id. at 574–724. The proposed RPAs fall into five operational categories—(I) Sacramento River Division, (II) American River Division, (III) East Side Division, (IV) Delta Division, and (V) Fish Passage Program. See id. at 19. On appeal, the parties challenge provisions of the RPAs falling into categories III and IV. Actions in category III relate to CVP/SWP operations on the Stanislaus River, which provides critical spawning and smolting grounds for the CV steelhead. See id. at 619–20. Prior to the construction of the New Melones Dam on the Stanislaus River, CV steelhead spawned in the cold tributaries upstream of where the New Melones Reservoir is now located. See id. at 107–08, 619. Now, “[t]he steelhead population on the Stanislaus River is precariously small and limited to habitat areas below the [Goodwin and New Melones] Dams that historically were unsuitable owing to high summer temperatures.” Id. at 619. In RPA category III, NMFS prescribes certain volumes of releases from the Goodwin and New Melones Dams that, according to NMFS, will cool the rivers enough to facilitate steelhead spawning. See id. at 620. The flows will also rejuvenate the gravel that is essential to steelhead spawning habitat and provide migratory cues to adult and juvenile fish. Actions in category IV relate to operations in the Delta. See id. at 628–30 (describing Delta division action). NMFS concludes that the proposed actions for the Projects, which “include continued diversion of water from the Delta at the SAN LUIS V. LOCKE 35 project’s export facilities, with increased export levels,” “will increase the level of stressors in the Delta,” further degrading it as a habitat. Id. at 629. The category IV RPA Actions address this jeopardy finding by imposing flow-to-export ratios for the Old and Middle Rivers, see id. at 643–44, prescribing maximum negative flow rates for the Old and Middle Rivers, id. at 648, and requiring a certain salvage efficiency at major fish salvage stations, id. at 655. 2. The Present Case On June 15, 2009, Plaintiffs San Luis & Delta-Mendota Water Authority and Westlands Water District challenged the legality of the 2009 BiOp by filing suit against the Department of Commerce, the National Oceanic and Atmospheric Administration, and NMFS (collectively “Federal Defendants”)10 in the Eastern District of California. See Compl. at 1, ECF No. 1. The district court consolidated that case with several other cases in which state water districts challenged the 2009 BiOp.11 DWR intervened as a plaintiff. See Joinder by Calif. Dep’t of Water Res., ECF No. 137. And several environmental and fishing groups 10 Reclamation and the United States Department of the Interior were later joined. They are included under the umbrella of “Federal Defendants.” See In re Consolidated Salmonid Cases, 791 F. Supp. 2d at 813. 11 The plaintiffs fall into three separate groups. The Export Plaintiffs are San Luis & Delta Mendota Water Authority and Westlands Water District; State Water Contractors; Kern County Water Agency and Coalition for a Sustainable Delta; and Metropolitan Water District of Southern California. The Stanislaus River Plaintiffs (or “SR Plaintiffs”) are Stockton East Water District, Oakdale Irrigation District, and South San Joaquin Irrigation District. The DWR Plaintiff in Intervention is the California Department of Water Resources. 36 SAN LUIS V. LOCKE intervened as defendants.12 See In re Consolidated Salmonid Cases, 791 F. Supp. 2d at 813. On August 6, 2010, several Plaintiffs moved for summary judgment on their claim that the 2009 BiOp violates the ESA and the APA. Id. The Stanislaus River Plaintiffs and DWR filed separate motions for summary judgment. Id. The Federal Defendants and Defendant-Intervenors responded with cross-motions for summary judgment. Id. “These crossmotions, 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.” Id. On September 20, 2011, the district court filed a 157-page opinion granting in part and denying in part Plaintiffs’ claims, and granting in part and denying in part Defendants’ claims. Id. at 955–59. The district court made dozens of conclusions relating to almost every component of the BiOp when rendering this complex and lengthy opinion. We briefly review the conclusions at issue in this appeal. The Defendants ask us to overturn the following of the district court’s holdings in which it struck down components of the BiOp: • NMFS acted unlawfully by relying on raw salvage data to set negative flow thresholds for the Old and Middle 12 Those Defendant-Intervenors are The Bay Institute; California Trout; Friends of the River; Natural Resources Defense Council; Northern California Council of the Federation of Fly Fishers; San Francisco Baykeeper; Sacramento River Preservation Trust; Winnemem Wintu Tribe; and Pacific Coast Federation of Fishermen’s Associations, Inc. SAN LUIS V. LOCKE 37 Rivers. Basic scientific principles require the agency to use data scaled to population to determine the impact of exports on fish survival. Id. at 827. • NMFS erred by failing to provide sufficient support for its classification of the winter-run Chinook as “high risk” rather than the less serious classification of “not viable.” Id. at 864. • NMFS erred by failing to reconcile the 2009 Salmonid BiOp’s jeopardy determination relating to the Southern Resident orca with an apparently contradictory conclusion in a different 2009 BiOp (“2009 Orca BiOp”). Id. at 866. • NMFS failed to adequately explain how continued operation of the Projects will adversely modify the CV steelhead’s critical habitat by reducing spawnable area and degrading gravel quality and quantity. Id. at 936. • Although NMFS sufficiently established that delta hydrologic conditions—as altered in part by the Projects—are favorable to invasive species, the BiOp does not support the conclusion that continued CVP/SWP operations promote invasive species, which in turn threaten listed species. Id. at 870. Nor does the BiOp sufficiently explain “how the projects influence contaminants or cause food limitations.” Id. • NMFS provided no support for its decision to use “maximum steelhead habitat” as a benchmark for evaluating the effect of East Side Division operations on listed species in the Stanislaus River. Because the modeling related to the New Melones Dam flows are 38 SAN LUIS V. LOCKE based on the “maximum habitat” benchmark, the New Melones Dam flow limits violate the APA. Id. at 938. • NMFS’s modeling assumptions relating to the Stanislaus River are flawed because NMFS set its goal as “doubling” CV steelhead habitat. Id. at 950. • NMFS failed to establish how each RPA Action complies with 50 C.F.R. § 402.02’s non-jeopardy factors. Specifically, NMFS did not establish how each RPA Action complies with the many purposes of the CVPIA, id. at 918, nor did it consider how each Action is feasible, id. at 919. NMFS erred particularly by failing to show how Delta Action IV.4.2 is feasible. • NMFS erred by failing to explain how certain RPA Actions are “essential” to avoid jeopardy of the listed species or adverse modification of their habitats. Id. at 897 & n.26. Those actions are Delta Division RPAs IV.2.1, IV.2.3, and IV.3 and East Side Division RPAs