## Facts

- The Bureau of Reclamation operated the Klamath Project, a federal irrigation system affecting Klamath River flows; Iron Gate Dam substantially controlled flows in habitat used by the threatened Southern Oregon/Northern California Coast coho salmon.
- The coho salmon was listed as threatened under the Endangered Species Act (ESA) in 1997 and is vulnerable to low flows and elevated water temperatures.
- A 1999 NMFS biological opinion recommended higher reservoir and mainstem river flows to protect coho; during the 2001 drought, implementing those recommendations limited irrigation deliveries and caused major agricultural losses.
- NMFS later identified a minimum summer flow target (about 1,000 cfs) to reduce temperature-related mortality risks to coho.
- In 2002, Reclamation submitted a long-range biological assessment for Project operations; NMFS concluded the proposed operations would likely jeopardize coho and therefore issued a new biological opinion containing a “reasonable and prudent alternative” (RPA).
- The 2002 RPA phased in protections over time; during the first eight years (Phases I and II), it required flows substantially below levels NMFS had indicated were needed (at most about 57% of identified needs).
- The 2002 biological opinion did not provide a contemporaneous scientific explanation analyzing how eight years of reduced flows would affect coho survival, reproduction, or habitat, or how jeopardy would be avoided during the interim period.
- Environmental and fishing organizations sued under the ESA and Administrative Procedure Act (APA); the district court invalidated substantial portions of the RPA but left the short-term Phases I and II intact.
- The plaintiffs appealed, challenging the lawfulness of leaving the short-term, reduced-flow phases in place.

## Issues

1. Whether NMFS’s 2002 biological opinion and RPA, including eight years of reduced flows, satisfied ESA § 7(a)(2)’s requirement to ensure Project operations were not likely to jeopardize the continued existence of the threatened coho salmon or adversely modify its habitat.
2. Whether NMFS’s approval of the phased reduced-flow regime was arbitrary and capricious under the APA because NMFS failed to provide a reasoned, science-based explanation linking the record to its no-jeopardy conclusion for the interim period.

## Decision

- The Ninth Circuit held that NMFS’s 2002 biological opinion and RPA were arbitrary and capricious and did not satisfy ESA § 7(a)(2) as to the phased interim flow regime.
- The court concluded NMFS failed to explain, using the best available science and a reasoned analysis, how allowing substantially reduced flows for eight years would avoid jeopardy.
- The court reversed in part and remanded with instructions to remand the biological opinion and RPA to NMFS for further proceedings consistent with the court’s opinion.

## Legal Principles

- ESA § 7(a)(2) requires federal agencies, through consultation, to ensure their actions are not likely to jeopardize listed species or adversely modify protected habitat.
- A biological opinion and RPA must be supported by the best scientific and commercial data available and must show a rational connection between the facts found and the agency’s conclusions.
- Under APA review, an ESA consultation product is unlawful if the agency offers conclusions without reasoned analysis addressing material gaps—especially where the agency knowingly authorizes sub-protective conditions for an extended period.
- Long-range plans cannot satisfy the ESA if they permit prolonged interim conditions that the agency has not shown will avoid jeopardy during the interim period.

## Conclusion

The Ninth Circuit required NMFS to provide a scientifically grounded, reasoned explanation demonstrating that any phased-in flow regime would avoid jeopardy throughout the interim period, not merely after later protective measures take effect.


Pac. Coast Fed’n of Fishermen’s Ass’ns v. U.S. Bureau of Reclamation, 426 F.3d 1082 (9th Cir. 2005)