Home » Case Summaries » 2015 » San Luis and Delta-Mendota Water Authority v. Locke, 776 F.3d 971 (9th Cir. 2014)


San Luis and Delta-Mendota Water Authority v. Locke, 776 F.3d 971 (9th Cir. 2014)


San Luis and Delta-Mendota Water Authority (San Luis)[1] filed suit against the Secretary of Commerce Gary Locke (Locke)[2] under the Endangered Species Act of 1973 (ESA)[3] and the Administrative Procedure Act (APA).[4] San Luis challenged the legality of a 2009 Biological Opinion (BiOp) prepared by the National Marine Fisheries Service (NMFS) under the directive of the Department of Commerce regarding water extractions from the San Joaquin River Delta. The United States District Court for the Eastern District of California held that some provisions of the BiOp violated the APA because they were arbitrary and capricious. On appeal, the Ninth Circuit reversed in part, affirmed in part, and remanded. The Ninth Circuit primarily held that the district court failed to grant NMFS the appropriate level of deference under the APA.

The San Joaquin River Delta (Delta), located in Central California, is formed by the convergence of the Sacramento and San Joaquin Rivers. Upstream of the Delta, the State Water Project and the Central Valley Project (the Water Projects) pump water for irrigation and drinking purposes. The Water Projects are two of the largest water projects in the nation, providing water to more than 25 million consumers. In addition to pumping, the Water Projects also control the volume of water flow in the rivers.

This case arises out of the fact that the Delta is home to various endangered species. The five species at issue here are: 1) the endangered Sacramento River winter-run Chinook salmon; 2) the threatened Central Valley spring-run Chinook salmon 3) the threatened Central Valley steelhead; 4) the threatened Southern Distinct Population Segment of North American green sturgeon; and 5) the endangered Southern Resident orca whale.[5] The Water Projects affect the ability of the anadromous species—the first four fish listed—to return to inland rivers and lakes for reproduction by increasing pollution, encouraging non-native species growth, causing water shortages in the river, and regulating flows in a way that makes the river less suitable for reproduction. These fish also struggle to pass through the Water Project impediments, such as dams and pumps, and are sometimes caught in the pumps and killed.

Under the ESA, a federal agency may not take any action that is “likely to jeopardize the continued existence” of an endangered species or cause the “destruction or adverse modification” of the species’s critical habitat.[6] If an agency pursues a project that could result in either of these effects, the agency must consult NMFS.[7] As part of this consultation process, NMFS must prepare a BiOp analyzing the risk to the endangered species.[8] If the proposed action will jeopardize species or critical habitats, NMFS must also propose “reasonable and prudent alternatives” (RPAs) that would allow the agency to proceed without negatively affecting endangered species.[9] In developing its BiOp, NMFS must use the “best scientific and commercial data available.”[10] If NMFS fails to adhere to the best science standard, it violates the APA.[11] Under the APA, a court should reverse an agency’s action only if the action is “arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law.”[12]

In this case, NMFS prepared the BiOp in 2009 in response to a 2006 request from the Bureau of Reclamation (BOR). In the BiOp, NMFS determined that endangered species would be jeopardized by the agency action and that the critical habitat of the fish would be destroyed or adversely modified. As a result, NMFS proposed over seventy RPAs by which the agency could avoid negatively affecting endangered species.

In the district court, both parties moved for summary judgment, and the court found that various provisions of the BiOp were arbitrary and capricious. The Ninth Circuit reviewed the grant of summary judgment and the district court’s evaluation of agency actions de novo. The Ninth Circuit reviewed the district court’s decision to admit extra-judicial evidence for abuse of discretion.

As a threshold matter, the Ninth Circuit addressed whether the district court erred by admitting extra-record scientific opinions to aid in its evaluation of the BiOp. The Ninth Circuit concluded that the district court erred because, under Lands Council v. Powell[13]and San Luis & Delta-Mendota Water Authority v. Jewell,[14] the court may only admit extra-judicial evidence to help the court to develop a framework for the issue—not to call the agency’s decision into question. Because the experts debated the merits of the BiOp at the district court and the district court used these declarations to question NMFS’s judgment, the Ninth Circuit held that the extra-record evidence was inappropriate.

The Ninth Circuit next explained the requisite deference to the agency under the APA and the ESA. Noting that the ESA does not have its own standard of judicial review, the Ninth Circuit stated that the district court should have applied the APA’s arbitrary or capricious standard. Furthermore, the court noted that it defers most to an agency when the agency action requires a high level of technical expertise. Under the ESA, the court must give deference to the agency’s scientific determinations in formulating the BiOp.

Turning to the merits, the Ninth Circuit began by addressing the district court’s objections to NMFS’s consideration of the raw number of fish salvaged during periods when the Water Project’s pumping resulted in negative flow. NMFS used this raw salvage data to develop several of the RPA proposals, which regulated negative flows to enhance the likelihood of salmonids avoiding entrainment. The district court held that NMFS should have used scaled salvage numbers—which would better adhere to accepted biostatistical principles—instead of the raw data.[15] The Ninth Circuit rejected this conclusion, relying on its controlling decision in San Luis & Delta-Mendota Water Authority. In that case, the Ninth Circuit determined that the use of raw salvage data was appropriate for three reasons, all of which were similarly present in this case.[16] First, NMFS adequately explained how the raw data assisted it in identifying the relationship between negative flow velocity and fish loss. Second, NMFS did not just use the raw data—it supplemented its findings with other studies to create the flow prescriptions. Third, the RPAs implemented data from incidental take statements, working in tandem with these findings to account for population-level impacts. Because all three bases existed in the present case, the Ninth Circuit held that NMFS properly exercised its discretion.

The Ninth Circuit next examined the NMFS jeopardy opinion and the specific components invalidated by the district court. The Ninth Circuit held that none were arbitrary and capricious. Regarding the winter-run Chinook finding, the Ninth Circuit held that NMFS properly relied on several studies in characterizing the species as not viable in its BiOp. This conclusion led to NMFS finding that Southern Resident orca are also jeopardized, as the Chinook is a critical food source. The district court remanded this finding and held that NMFS had failed to consider an apparently contrary 2009 Orca BiOp, which concluded that the commercial harvest of salmon would not jeopardize Southern Resident orca whales.[17] However, the Ninth Circuit held that NMFS sufficiently distinguished those findings in the BiOp at issue and that this effort was sufficient to show consideration of the 2009 Orca BiOp.

Another component of the jeopardy opinion was the adverse effect on steelhead spawnable area and spawning gravel—both elements of the steelhead’s critical habitat. The district court held that NMFS’s use of maximum habitat as a benchmark for spawnable area and its conclusion that Water Project operations led to gravel degradation were arbitrary and capricious. However, the Ninth Circuit held that NMFS’s reliance on a study with the goal of maximizing habitat was not abandonment of ESA’s prescription to avoid jeopardy. Additionally, the Ninth Circuit concluded that NMFS provided adequate support for its finding that Water Project operations negatively affected spawning gravel quality and quantity.

Finally, the Ninth Circuit addressed the NMFS findings of indirect mortality factors, such as the creation of favorable conditions for invasive species and increased exposure to pollution. The district court held that NMFS’s conclusions were arbitrary or capricious because they inadequately explained the connection between Water Project operations, invasive species, and harm to salmonid species. Although the Ninth Circuit acknowledged that NMFS’s analysis was not perfect, the court found that NMFS adequately connected these factors to the Water Projects by citing to sufficient scientific evidence. As such, the agency’s analysis was reasonably discernable and not arbitrary or capricious.[18]

Next, the Ninth Circuit addressed the RPA proposals invalidated by the district court. In recognizing that the district court applied the incorrect legal standards, the Ninth Circuit again relied on San Luis & Delta-Mendota Water Authority for guidance. Contrary to the district court’s opinion, neither ESA section 7 nor 50 C.F.R. § 402.02 requires the agency to explain how each RPA is essential to avoiding jeopardy or to articulate compliance with non-jeopardy factors. Instead, the agency’s choice will be upheld if it is reasonably supported by the record that the RPAs do not further jeopardize the listed species or adversely affect critical habitat. Having established this more deferential standard, the court reviewed each particular action in turn and held that they were sufficiently supported by the corresponding evidence procured by the agency.[19] As such, the Ninth Circuit held that the district court erred in invalidating the RPA proposals.

Lastly, the Ninth Circuit addressed San Luis’s cross-appeal on three issues and reviewed the district court’s opinion in which it upheld the BiOp. First, the court rejected San Luis’s argument that NMFS was required to separate discretionary from nondiscretionary aspects of the Water Projects when defining the BiOp’s environmental baseline.[20] Second, the court rejected the argument that NMFS was required to make effect findings for the Water Projects’ indirect mortality factors.[21] The Ninth Circuit agreed with the district court that indirect mortality factors constituted direct effects—they are directly and concurrently caused by the Water Projects instead of merely being more likely or probable due to the agency action. Third, San Luis also argued that Reclamation was independently liable under the ESA for a legally unsound BiOp. However, as the Ninth Circuit held that the BiOp was legally sound, it dismissed this issue of independent liability.

Overall, the Ninth Circuit reversed the district court’s invalidation of NMFS’s BiOp and affirmed its judgment upholding the BiOp. Therefore, the Ninth Circuit remanded for entry of summary judgment in favor of Locke.


Footnotes    (↵ returns to text)

  1. In addition to San Luis and Delta-Mendota Water Authority, plaintiffs include Westlands Water District, Stockton East Water District, Metropolitan Water District of Southern California, Oakdale Irrigation District, South San Joaquin Irrigation District, Kern County Water Agency, Coalition for a Sustainable Delta, and State Water Contractors. California Department of Water Resources also joined the action as an intervening plaintiff.
  2. In addition to Locke, defendants include the United States Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, James W. Balsiger, Rodney R. McInnis, U.S. Department of the Interior, United States Bureau of Reclamation, Michael L. Connor, Donald R. Glaser, Jane Lubchenco, and Sally Jewell. In addition, intervenor-defendants 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; Pacific Coast Federation of Fishermen’s Associations, Inc.; and Institute for Fisheries Research.
  3. 16 U.S.C. §§ 1531–1544 (2012).
  4. 5 U.S.C. §§ 551–559, 701–706, 1305, 3105, 3344, 4301, 5335, 5372, 7521 (2012).
  5. A “critical prey base for the Southern Resident orca” whales is Chinook salmon. Thus any reduction in population of the prey-base also jeopardizes whale populations. San Luis & Delta-Mendota Water Auth. v. Locke, 776 F.3d 971, 998 (9th Cir. 2014).
  6. 16 U.S.C. § 1536(a)(2) (2012).
  7. Id.; see U.S. FWS Serv., ESA Basics: 40 Years of Conserving Endangered Species 1–2 (2013) (noting that agencies must “consult with the FWS and NMFS, as appropriate”).
  8. 16 U.S.C. § 1536(b)(3) (2012).
  9. Id. § 1536(b)(3)(A).
  10. Id. § 1536(a)(2).
  11. See 5 U.S.C. § 706(2)(A) (2012).
  12. Id.
  13. 395 F.3d 1019 (9th Cir. 2005).
  14. 747 F.3d 581 (9th Cir. 2014).
  15. See In re Consolidated Salmonid Cases, 791 F. Supp. 2d 802, 827 (E.D. Cal. 2011) (“The agency is required to apply generally recognized and accepted biostatistical principles, which constitute best available science, in reaching its decisions.”).
  16. San Luis & Delta-Mendota Water Auth., 747 F.3d at 608–16.
  17. See In re Consolidated Salmonid Cases, 791 F. Supp. 2d at 864–65.
  18. See Bowman Transp. v. Ark.-Best Freight Sys., Inc., 419 U.S. 281, 286 (1974) (noting that the Court “will uphold a decision of less than ideal clarity if the agency’s path may reasonably be discerned”).
  19. The challenged RPA proposals were the following: Action IV.2.1, Action IV.2.3, Action IV.3, Action IV.4.2, Action III.1.2, Action III.1.3, and Action III.2.2.
  20. Under ESA § 7, a consulting agency must analyze an agency action in relation to an environmental baseline when preparing a BiOp. 50 C.F.R. § 402.02 (2014). This environmental baseline is the status of the species at a particular moment in time before the agency action. See Lawrence R. Liebesman & Rafe Petersen, Endangered Species Deskbook 46 (2d ed. 2010).
  21. The effect of a proposed action includes both direct and indirect effects. 50 C.F.R. § 402.02 (2014). Regarding indirect effect findings, an agency is required to show that the effect is caused by the action, that it is later in time than the action, and that it is reasonably likely to occur. Id.
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