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Environmental Groups Sue Federal Agencies Over Recent Delta Biological Opinions

Environmental Groups Sue Federal Agencies Over Recent Delta Biological Opinions
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On December 2, 2019, several environmental organizations filed a lawsuit in the U.S. District Court for the Northern District of California challenging the Biological Opinions of the U.S. Fish and Wildlife Service (FWS) and National Marine Fisheries Service (NMFS), each of which conclude that a proposed operations plan by the U.S. Bureau of Reclamation (Bureau) would not jeopardize threatened and endangered species in and around the Sacramento-San Joaquin Delta. Claims for relief are premised on violations of the Administrative Procedure Act and the federal Endangered Species Act. [Pacific Coast Federation of Fishermen’s Associations, et al. v. Ross, et al., Case No. 19-7897 (N.D. Cal.).]


The Bureau and the California Department of Water Resources (DWR) operate two of the nation’s largest water projects—the federal Central Valley Project and the California State Water Project, respectively. Together, these projects deliver millions of acre-feet of water to agricultural, municipal, and industrial water users throughout California. Both the CVP and SWP take water from the Sacramento and San Joaquin River systems, and the Sacramento-San Joaquin Delta (Delta) that empties into San Francisco Bay. The river systems and Delta are spawning, migration, and critical habitat for several endangered and threatened fish species, including species of Chinook salmon, steelhead, and Delta smelt.

The federal Endangered Species Act (ESA) imposes requirements for the protection of endangered and threatened species and their ecosystems. In 2008 and 2009, the FWS and NMFS determined, in documents called Biological Opinions (BiOps) issued under the federal Endangered Species Act (ESA), that the continued long-term operation of the CVP and SWP would jeopardize certain endangered or threatened species. The FWS and NMFS BiOps included alternative project operations (“reasonable and prudent alternatives”) that effectively compelled the Bureau and DWR to operate many aspects of the CVP and SWP according to the direction of the federal wildlife agencies, rather than in compliance with the proposed operating plans offered by the Bureau and DWR.

In 2017, the Bureau proposed a new operations plan following its 2016 request to reinitiate consultation with FWS and NMFS regarding those agencies’ 2008 and 2009 BiOps. On October 22, 2019, FWS and NMFS each issued BiOps concluding that newly proposed operation plans for the CVP and SWP would not jeopardize endangered and threatened species. The proposed operations plan contemplates significant investments in research and restoration actions for smelt and salmonid species, revised management plans for operations of river systems tributary to the Delta, and changes to cold water pool management at Lake Shasta (part of the CVP) for the benefit of salmon.

On December 2, 2019, the Pacific Federation of Fishermen’s Associations, Institute for Fisheries Resources, Golden State Salmon Association, Natural Resources Defense Council, Defenders of Wildlife, and the Bay Institute (collectively: plaintiffs) filed suit in the U.S. District Court for the Northern District of California alleging violations of the Administrative Procedure Act and ESA. Plaintiffs challenge FWS and NMFS’ adoption of their respective BiOps as allegedly arbitrary, capricious, and not in accordance with law. According to plaintiffs, the BiOps were improperly influenced by political motivations and authorize CVP and SWP operations that will further injure endangered and threatened species and their habitats.

The Complaint

The BiOps are the result of the Bureau’s request in 2016 to reinitiate consultation with FWS and NMFS regarding those agencies’ BiOps for Delta operations from 2008 and 2009, respectively. Both of those opinions were “jeopardy” opinions and included reasonable and prudent alternatives. In their complaint (Complaint), plaintiffs allege that the Bureau’s request to reinitiate consultation resulted from new information related to multiple years of drought and data demonstrating low Delta smelt populations and “extremely low” populations for certain salmonid species. FWS and NMFS both agreed to reinitiate consultation, and in 2017, NMFS issued a draft amendment to its BiOp that plaintiffs allege would have immediately strengthened protections for endangered winter-run Chinook salmon, but which The Bureau refused to accept or implement under the 2009 BiOp.

Instead, plaintiffs allege that, in 2017, the Bureau prepared a Biological Assessment for a newly proposed CVP and SWP operation plan that sought to maximize water deliveries and river system diversions that would correspondingly harm protected fish species.

Specifically, plaintiffs allege that the Bureau’s proposed operations plan would entrain Delta smelt and salmonids, reduce Delta outflows on which those species rely for habitat and reproduction, fail to provide adequate water temperatures required by those species, reduce Delta inflows from the Sacramento and San Joaquin River systems, and increase salinity. As a result of the Bureau’s Biological Assessment, plaintiffs allege that the FWS and NMFS began drafting BiOps, the final versions of which conclude that the proposed operations plan would not be likely to jeopardize the continued existence of listed threatened or endangered fish species, nor adversely modify their designated critical habitat.

Allegation of ‘No Reasoned Explanation’

Plaintiffs primarily challenge the BiOps on the ground that there is no “reasoned explanation” between, on the one hand, the agencies’ findings related to the status of the fish species, the propriety of increased protections, and the impacts of the Bureau’s proposed operations plan, and, on the other hand, the BiOps’ no jeopardy/adverse habitat modification conclusions. In particular, the Complaint alleges that the BiOps eliminate existing protections for listed species, fail to increase protections for the species, and fail to provide a reasoned explanation why increased protection is not necessary. The Complaint references earlier wildlife agency findings to the contrary and language in the new BiOps regarding the imperiled status of protected species and the additional adverse effects that the proposed plan will allegedly have on those species and their habitat.

Additional Claims

Plaintiffs allege four additional categories of ESA violations: 1) future mitigation measures in the BiOps are not reasonably certain to occur, 2) the BiOps do not consider the full extent of proposed operations or long-term impacts, 3) the BiOps are not based on the best available science, and 4) the incidental take statements contained in the BiOps threaten the survival of the protected species the BiOps are designed to cover.

In particular, plaintiffs allege that the BiOps improperly rely on future mitigation measures without supporting evidence indicating that the measures are reasonably certain to occur and will be effective in mitigating negative impacts to certain species and their habitats. For instance, plaintiffs point to the BiOps allowance for increased pumping during storm events despite protective restrictions on Delta pumping, and that BiOp provisions providing for real-time adaptive management will be less protective of listed fish species. Similarly, plaintiffs contend that the BiOps do not account for the possibility of future waiver of pumping restrictions during periods of drought, under adaptive management protocols.

Plaintiffs also fault the BiOps for allegedly failing to consider the full extent of the proposed project operations and their long-term impacts. For instance, plaintiffs allege that some water supply contracts for CVP/SWP water extend beyond 2040, yet the BiOps only analyze impacts through the year 2030. Additionally, plaintiffs allege that the BiOps do not consider full water deliveries under water supply contracts, instead relying on historical modeling and analysis that only accounts for partial water deliveries. According to plaintiffs, greater water deliveries would increase impacts on protected species, but such outcome is not analyzed in the BiOps. With respect to long-term impacts, plaintiffs allege, among other things, that the BiOps fail to consider the effects of climate change on the proposed operations and corresponding effects on protected species. Allegedly outdated climate change data also forms the basis of plaintiffs’ contention that the BiOps are not based on the best available science—a contention further colored by allegations that the BiOps do not consider the impacts of reduced Delta inflows and outflow on Delta smelt and other protected species.

Finally, plaintiffs challenge the BiOps’ incidental take statements, and allege that the incidental take limits set by the BiOps would jeopardize protected species. For instance, plaintiffs contend that the NMFS BiOp allows for three consecutive years of complete mortality—“zero percent egg to fry survival of winter-run Chinook salmon below Shasta Dam”—before reinitiation of consultation is required. In plaintiffs’ view, this means that high water temperatures could result in the extinction of winter-run Chinook salmon in the wild before reinitiation of consultation would be required, which plaintiffs allege sets a “meaningless reinitiation trigger” and would jeopardize the continued existence and recovery of the species.

Conclusion and Implications

Given the continuing controversy over Delta and Sacramento and San Joaquin River system water use, the initiation of a lawsuit challenging the recently released federal BiOp is not surprising. This litigation, like its predecessor over the 2008 and 2009 BiOps, will likely be long, highly technical, and heavily dependent on expert reports and testimony. This case differs from its predecessor in part because of political influence allegations, although what role those alleged actions may have on the outcome of the litigation is unclear. The Complaint is available online at: