Federal dams have had an effect on salmon and steelhead populations in the Columbia Basin since the 1938 construction of Bonneville Dam, the first dam in the Federal Columbia River Power System (FCRPS). FCRPS now includes federal hydropower dams in the Columbia Basin that are operated by either the Army Corps of Engineers (Corps) or Bureau of Reclamation (Reclamation). Currently, eight evolutionarily significant units (ESUs) of salmon and five distinct populations segments (DPSs) of steelhead in the Columbia Basin are listed as threatened or endangered under the Endangered Species Act (ESA). The National Marine Fisheries Service (NMFS) of the Department of Commerce has found that the estimated "current annual salmon and steelhead production in the Columbia River Basin is more than 10 million fish below historical levels, with 8 million of this annual loss attributable to hydropower development and operation." Consultation and Biological Opinions

The ESA requires federal actions, such as FCRPS operations, to be reviewed to determine whether they are likely to jeopardize the continued existence of threatened and endangered species or damage the species' critical habitat. The Corps, Reclamation, and BPA are the action agencies for purposes of operating the FCRPS and the consultation process under the ESA. If jeopardy is found, NMFS is required to include reasonable and prudent alternatives (RPAs) to the proposed action in order to avoid jeopardy, provided such alternatives are possible. Some actions intended to benefit salmon, such as spilling water to help juveniles pass safely downstream, come at a cost in terms of energy production. Rather than evaluate the aggregate impact of the FCRPS on the protected species, NMFS only evaluated the discretionary elements of the FCRPS operations. 2005 Snake River BiOp

In 2005, NMFS issued a BiOp separately addressing the effects of Reclamation's proposed operations on a portion of the Snake River (2005 Snake River BiOp). For the first time since 1995, the court ruled that a portion of NMFS's BiOp complied with the ESA. 2014 Supplement—Avoiding Jeopardy Through RPAs

In January 2014, NMFS issued a second supplement to the 2008 BiOp. The plaintiffs challenged the 2014 Supplement, and, on May 6, 2016, the U.S. District Court for the District of Oregon again concluded that NMFS did not satisfy the ESA. Through a newly assigned judge, Judge Michael H. Simon, the court cited flaws in NMFS's conclusion that protected species could be "trending toward recovery" even if the overall population levels remained critically low, called NMFS's habitat improvement data "too uncertain," and found that NMFS did not properly analyze the effects of climate change. Although the court found the 2014 Supplement to be arbitrary and capricious, it did not vacate the BiOp. Instead, it remanded for further consultation to be completed by March 1, 2018, and ordered NMFS to keep the 2014 Supplement in place in the interim. The challengers to the 2014 Supplement also successfully asserted a new claim that the action agencies (the Corps and Reclamation) violated the National Environmental Policy Act of 1969 ("NEPA") because they did not prepare an environmental impact statement (EIS) in connection with the RPAs in the 2014 Supplement.
The decline of salmon and steelhead populations in the Columbia Basin began in the second half of the 19th Century. Activities such as logging, farming, mining, irrigation, and commercial fishing all contributed to the decline, and populations further declined since the construction and operation of the Federal Columbia River Power System (FCRPS) in the mid-1900s. In 1991, the Snake River sockeye became the first Pacific salmon stock identified as endangered under the Endangered Species Act (ESA). There are now 13 salmon and steelhead stocks that are listed as either threatened or endangered.
FCRPS operations have been analyzed through an ESA process intended to address the impact of operations on protected species. The ESA requires the federal operators of the FCRPS—the Bureau of Reclamation (Reclamation), the Bonneville Power Administration (BPA), and the Army Corps of Engineers (Corps)—to consult with the National Marine Fisheries Service (NMFS) of the Department of Commerce on how the FCRPS may impact listed species. At the end of the consultation, NMFS issues a biological opinion (BiOp) addressing whether the FCRPS action would jeopardize the continued existence of a listed species or damage its critical habitat. If jeopardy is found, NMFS is required to develop reasonable and prudent alternatives (RPAs) to the proposed action in order to avoid jeopardy.
NMFS can recommend mitigation measures to avoid jeopardy, but protective measures for fish often come at a cost in terms of energy generation or irrigation supply from FCRPS. This tension between natural resources and energy production and irrigation is at the heart of conflict in the Columbia Basin.
Beginning in 1992, NMFS issued a series of BiOps, nearly every one of which courts have found inconsistent with the ESA. Since 2000, federal courts have rejected all or part of NMFS's four prior BiOps and their supplements. While courts have consistently demanded changes to the BiOps, they also allowed portions of each BiOp to stay in place so that FCRPS operations could continue while the federal agencies attempted to remedy the BiOps.
Most recently, in May 2016, the U.S. District Court for the District of Oregon held that NMFS's 2014 supplemental BiOp (2014 Supplement) did not comply with the ESA. The court cited flaws in NMFS's conclusion that protected species could be "trending toward recovery" even if the overall population levels remained critically low. The court also called NMFS's habitat improvement data "too uncertain" and found that NMFS did not properly analyze the effects of climate change.
The district court also held that the FCRPS action agencies (the Corps, BPA, and Reclamation) violated the National Environmental Policy Act of 1969 (NEPA) by failing to prepare an environmental impact statement in connection with their proposals for operation of the FCRPS. Although it found the 2014 Supplement to be arbitrary and capricious, the court did not vacate the BiOp. Instead, it remanded for further consultation to be completed by March 1, 2018, and ordered NMFS to keep the 2014 Supplement in place in the interim.