Salmon and steelhead are anadromous fish, meaning they are born in freshwater, migrate to the ocean to mature, and return to their place of birth to spawn. Dams and their operations make the migrations treacherous both up and downstream. 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). (See Figure 1 .) Electric power from these projects is marketed by Bonneville Power Administration (BPA). 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 ESA-protected fish in the Colombia River Basin are Snake River sockeye salmon (endangered); Snake River spring/summer-run Chinook salmon (threatened); Snake River fall-run Chinook salmon (threatened); Snake River basin steelhead (threatened); Upper Columbia River spring-run Chinook salmon (endangered); Upper Columbia River steelhead (threatened); Middle Columbia River steelhead (threatened); Lower Columbia River Chinook salmon (threatened); Lower Columbia River coho salmon (threatened); Lower Columbia River steelhead (threatened); Columbia River Chum salmon; (threatened); Upper Willamette River Chinook salmon (threatened); and Upper Willamette River steelhead (threatened). 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." Additionally, timber management and grazing have decreased habitat from "approximately 21,000 miles (33,600 km), historically, to approximately 16,000 miles (25,600 km) in 1990, largely due to management practices on U.S. Forest Service (USFS) land." Today salmon and steelhead trout in the Columbia River Basin are a mixture of wild fish and those produced in fish hatcheries. Experiments with artificial propagation of salmon to bolster faltering wild stocks began in the late 1800s. Dozens of federal- and state-managed salmon and steelhead trout hatcheries in the Columbia River basin produce more fish annually than do wild stocks. 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. This process is called consultation . By statute, the Secretary of the Interior administers the consultation process, but it has delegated its authority to either NMFS or the U.S. Fish and Wildlife Service (FWS) (in the Department of the Interior ). With regard to protected anadromous salmon and steelhead in the Columbia Basin, NMFS has administrative authority over the consultation process. Thus, if the actions of a federal agency might adversely affect listed salmon or steelhead, they must engage in the consultation process with NMFS. The Corps, Reclamation, and BPA are the action agencies for purposes of operating the FCRPS and the consultation process under the ESA. Formal consultation is initiated when an action agency submits a biological assessment to NMFS describing the proposed action and its impact on listed species. ESA consultation may be triggered by new ESA listings or new or changed federal actions. In the case of salmon and steelhead, NMFS considers the biological assessment and the proposed federal action and then issues a biological opinion (BiOp) indicating whether the action would jeopardize protected species. In developing a BiOp, NMFS must determine whether the action agencies' conduct will likely jeopardize a listed species or destroy or adversely modify its critical habitat. 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. In those cases where NMFS concludes that the action agencies' conduct as originally proposed or as modified by RPAs is not likely to result in jeopardy or adverse modification or destruction of critical habitat, NMFS will issue an Incidental Take Statement to the action agencies. The Incidental Take Statement excuses any takes (killing or harming) of listed species for operations covered in the BiOp so long as the action agency complies with the terms and conditions of the statement. Without the BiOp and the Incidental Take Statement, the action agency risks violating (and being prosecuted under) the ESA. In addition to BiOps for FCRPS operations, NMFS issues salmonid BiOps for Upper Snake River activities and harvest operations (fishing). The configuration and operation of the FCRPS dams can be a polarizing issue for proponents of hydropower development, irrigation, and river navigation and those who support commercial, sport, and tribal fishing as well as environmental conservation. Commentators note that Columbia Basin salmon populations have declined due to a number of human actions besides FCRPS operations, including fishing, predation by native and invasive species, water pollution, reduced habitat, and water withdrawals for irrigation. Many also assert that these populations will be subject to increasing stress from factors related to climate change such as higher water temperatures, changes in ocean conditions, and lower river flows. Actions intended to aid the recovery of these stocks generally fall into one of four categories, known as "the 4-H's": habitat, harvest, hatchery, and hydrosystem. Habitat actions focus on access to, and improvement of, habitat suitable for rearing juvenile salmon and spawning by returning adults. Historically, many parts of the Columbia River watershed have been degraded by logging, mining, farming, and development. Although legitimate economic activities, they have often caused unintended negative consequences for salmon populations. Salmon habitat has been fragmented and degraded by water diversions, obstacles to habitat by structures such as culverts and dams, and loss of vegetation adjacent to rivers and in watersheds. The RPAs specify actions related to upriver habitat where salmon spawn and down-river estuary habitat where salmon transition to their ocean phase. Actions to improve habitat include increasing stream flows, reducing water temperature, removing barriers to habitat, and increasing pools, spawning gravels, and side channel habitats. Other habitat actions include efforts to remove the salmon's predators, including California sea lions. Sea lions generally prey on the salmon congregating at the fish passage facilities, although it is suspected that they also consume salmon in other parts of the Lower Columbia River. In 2015, the Corps' monitoring program estimated that sea lions at the Bonneville Dam consumed 10,859 salmonids between January 1 and May 31, 2015, which accounts for 4.3% of the adult salmonid passage. To reduce predation on upstream migrating adult salmon, NMFS authorized Washington, Idaho, and Oregon to lethally take (i.e., kill) California sea lions that gather seasonally below Bonneville Dam. Individuals and animal rights groups challenged the take authorization in multiple lawsuits, but NMFS's latest authorization from 2012 survived the most recent court challenge, which has led to ongoing efforts to capture and euthanize California sea lions. Other predators include the pikeminnow, which feed on juvenile salmon and steelhead. BPA sponsors a program that pays for each pikeminnow caught in the Columbia River. For 2016, there is a reward of $5 to $8 per pikeminnow of at least 9 inches and a $500 reward per tagged fish. According to BPA, since the program started, over 4.2 million pikeminnow have been caught, reducing their predation on juvenile salmonids by 40%. Historically, salmon harvest was one of the main factors that contributed to the decline of Columbia Basin salmonid populations. Commercial and recreational fisheries in the Columbia River are co-managed by the states of Washington, Oregon, and Idaho, four treaty tribes, and other tribes that traditionally fished these waters. All fisheries are subject to review by NMFS for compliance with the ESA. Generally, managers have attempted to minimize the harvest of wild fish, especially listed populations, through a variety of actions. Harvest actions focus on limiting harvest or harm to listed species by requiring selective fishing gear or timing harvest periods to focus fishing on hatchery stocks. In mark-selective fisheries, the adipose fins are clipped on hatchery juveniles so fishermen can differentiate returning hatchery fish from wild adults. Hatchery efforts are intended to increase the number of fish through artificial propagation. Some assert that hatchery production reduces predator and harvest pressures on wild fish, while others are concerned that hatchery fish compete with wild salmon and steelhead for food and habitat. Hatcheries also may alter the genetic diversity of specific stocks. According to the Hatchery Scientific Review Group, a congressionally funded scientific review panel, hatchery management alone will not lead to the recovery of the endangered salmon and steelhead in the Pacific Northwest, but must be done as part of a broader strategy that incorporates actions affecting habitat, harvest rates, water allocation, and other components of the human environment. According to the NMFS Hatchery Listing Policy, under certain circumstances hatchery fish may be considered when estimating the populations of fish for listing determinations (i.e., when deciding whether an ESU might be threatened or endangered). Finally, hydrosystem actions that promote species recovery have concentrated on improving the survival of juvenile and adult salmon and steelhead as they migrate past dams and through reservoirs. Hydrosystem actions include structural and operational changes at the dams, such as the addition of juvenile bypass systems and surface-oriented passage routes; the collection and transportation of juveniles in barges and trucks past the dams; the installation of structures to guide fish toward safer passage routes; and water releases either to speed travel down the river or provide safer passage past a dam. Although some federal salmon and steelhead protection measures have been in place for nearly 70 years--Bonneville Dam was constructed in 1938 with a fish ladder to allow upstream passage of returning adult salmon --the Pacific Northwest Electric Power Planning and Conservation Act (Northwest Power Act) codified a fish protection program to mitigate losses associated with the FCRPS. Four options are available to allow downstream migration of fish at a hydropower dam: spill over the dams; pass through the turbines; bypass the dams via a barge or truck; or bypass back into the river. 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. Such actions may significantly increase power rates in the region. Additionally, spill can increase juvenile fish mortality due to injury or disorientation caused by gas bubble disease, making fish susceptible to predation. Although gas bubble disease may occur when fish are exposed to gas supersaturation, especially during vulnerable or sensitive life stages, research suggests that harm to migratory juvenile or adult salmonids depends on characteristics of the site or reach adjacent to the dam. Often migration can be assisted by "fish ladders" that allow the fish to pass upstream around the dams or bypasses that allow juveniles to avoid passing through turbines. However, dams also may change the ecology of rivers including food webs and physical conditions, especially in cases where large reservoirs are created. Although fish may be successful in passing around dams, reservoirs decrease the river's flow and may delay fish movement, expose fish to more predation, and increase water temperature to potentially lethal levels. Reservoirs also may inundate spawning and shoreline areas that were formerly productive spawning and rearing habitat. As an alternative to altering dam operations to make them more favorable to salmon, some parties advocate partially or entirely removing four dams on the Lower Snake River in Washington. They believe this is the only way to ensure survival of the Snake River salmon and steelhead populations. Dam removal could also result in economic benefits to various fishing and recreation interests. Proponents of dam removal argue that the four Lower Snake River dams do not produce a significant amount of power and assert that these dams cause significant harm to listed species. They claim that removal of the Snake River dams would reduce federal expenditures and revitalize local economies. Opponents note that dam removal would only benefit four of the 13 listed salmon and steelhead populations in the Columbia Basin, and the federal agencies should focus on all of the basin's listed salmonids. According to BPA, the Lower Snake River dams are an important part of the Northwest's power supply. Additionally, dam removal would preclude downstream barge transport of wheat from Idaho. Dam removal, especially for older dams, may become an economic necessity if dam relicensing by the Federal Energy Regulatory Commission requires expensive modifications to provide for fish passage. The removal of Condit Dam on the White Salmon River, a Columbia River tributary above Bonneville Dam, began with initial breaching on October 26, 2011, and its complete removal the following year. Removal of Condit dam has reopened habitat above the former dam to steelhead and salmon for the first time in nearly 100 years. Reportedly, Chinook salmon and steelhead have spawned in areas above the removed structure. Many uncertainties remain, and long-term monitoring and adaptive management of the newly accessible habitat are recommended. More than 20 years of ESA litigation has tracked each BiOp covering the FCRPS, and legal challenges have frequently altered those operations. As referenced above, when agencies' planned operations may jeopardize listed species, NMFS may offer reasonable and prudent alternatives (RPAs) to the action agencies' proposal. In the FCRPS context, these alternatives can include habitat protection, flow alterations, and fish passage systems, such as ladders or trucks. Since the early 1990s, states, conservation organizations, fishing and sporting groups, users of FCRPS-generated energy, and others have challenged NMFS's jeopardy conclusions and RPAs in each BiOp for the FCRPS under the Administrative Procedure Act (APA). The APA authorizes reviewing courts to "hold unlawful and set aside agency actions, findings, and conclusions found to be arbitrary, capricious, [or] an abuse of discretion.... " To satisfy the arbitrary and capricious standard and survive an APA challenge, a federal agency must show that it "examine[d] the relevant data and articulate[d] a satisfactory explanation for its action, including a 'rational connection between the facts found and the choice made.'" A central question raised in the ESA litigation related to the FCRPS was whether NMFS and the action agencies could meet the APA's arbitrary and capricious standard. A summary of major ESA actions and litigation is presented in the Appendix and discussed below. On April 10, 1992, NMFS issued its first BiOp for FCRPS, finding the operations did not jeopardize the continued existence of ESA-protected fish or detrimentally alter its critical habitat. NMFS issued additional BiOps later that year (1992 BiOps) in which it found no jeopardy to protected salmonids in the Columbia Basin as a result of ocean fisheries and in-river fisheries. Several high volume users of FCRPS-generated energy filed suit challenging the 1992 BiOps. Among other legal theories, they asserted that the FCRPS consultation led to restricted hydroelectric operations which caused increased electricity rates. The U.S. District Court for the District of Oregon dismissed those claims on the grounds that the energy users lacked standing due to an inherent conflict between the their desire for lower power rates and the ESA's objective of protecting listed salmonids. It likened the plaintiffs to a fox guarding a chicken coop: "sure, [the fox] has an interest in seeing that the chickens are well fed, but its [sic] just not the same interest the farmer has, nor is it an interest shared by the chickens." On appeal, the Ninth Circuit disagreed with the chicken coop analogy and the ruling on standing, but it affirmed the district court's alternative basis for dismissal that the case was moot in light of the fact that NMFS issued a revised BiOp in 1993. On May 26, 1993, NMFS issued a second "no jeopardy" BiOp for FCRPS (1993 BiOp), which was challenged in the District of Oregon in Idaho Department of Fish & Game v. National Marine Fisheries Service . There, the district court found the 1993 BiOp was "arbitrary and capricious" because NMFS relied on improper data in calculating the baseline number of protected salmonids in the Columbia Basin. According to the court, NMFS used five drought years in which the number of fish were atypically low as a baseline to evaluate the future effect of FCRPS operations on protected species. In the 1992 BiOp, by comparison, NMFS used a 15-year range of data from 1975 to 1990 for its baseline. The district court also called the overall process used to create FCRPS BiOps "significantly flawed," and it remarked that "the situation literally cries out for a major overhaul. Instead of looking for what can be done to protect the species from jeopardy, NMFS and the action agencies have narrowly focused their attention on what the establishment is capable of handling with minimal disruption." The district court directed NMFS to consult with the action agencies and revise the 1993 BiOp, but it did not enjoin FCRPS operations. One year later, the Ninth Circuit vacated the district court's decision as moot after the 1993 BiOp expired by its own terms, and NMFS released subsequent BiOps governing FCRPS operations. In March 1994, NMFS issued a BiOp (1994 BiOp) covering FCRPS operations for 1994-1998. The 1994 BiOp concluded that FCRPS would not jeopardize protected species or adversely modify the designated critical habitat; however, NMFS relied on the same baseline methodology in reaching that conclusion that the district court criticized in the 1993 BiOp. NMFS informed the district court in Idaho Department of Fish & Game of the carry-over issue, and, because the 1993 BiOp was set to expire, the court directed NMFS and the action agencies to correct the 1994 BiOp rather than the 1993 BiOp. In a separate lawsuit, American Rivers v. National Marine Fisheries Services , a group of environmental and commercial fishing organizations challenged the 1994 BiOp, but the court stayed the case while NMFS revised the 1994 BiOp in an attempt to comply with the ruling in Idaho Depart ment of Fish and Game . In March 1995, NMFS issued a new biological opinion (1995 BiOp), which superseded the 1994 BiOp and concluded that operation of FCRPS jeopardized the continued existence of protected species and adversely modified their critical habitat. Given this finding, NMFS proposed RPAs, including a program in which juvenile salmonids would bypass the dam system while being transported in tanker trucks or barges. The American Rivers plaintiffs renewed their challenge and argued that the ESA did not permit such a long-term transportation program, but the Ninth Circuit dismissed the suit as non-justiciable. Although the Ninth Circuit affirmed earlier dismissals as moot in light of superseding BiOps, it found the American Rivers challenge to the 1995 BiOp to be premature given that the salmonid transportation program was not certain to be implemented. "Consideration of long-term salmon transportation as a possible future option is not a final agency action" subject to judicial review, the court concluded. In a second lawsuit related to the 1995 BiOp, a group of hydroelectric power users challenged BPA's decision to adopt the jeopardy opinion and to propose RPAs. The power users claimed the proposed RPAs were based on inappropriate data and failed to balance salmon protection with the production of hydroelectric power. The Ninth Circuit held that, although there was scientific uncertainty regarding the salmon decline, that uncertainty was not so great as to vacate the 1995 BiOp on the grounds that it was arbitrary and capricious. In a BiOp issued in December 2000 (2000 BiOp), NMFS again found that the action agencies' operation of the FCRPS would jeopardize protected salmonid species. NMFS proposed RPAs to alleviate the effect of FCRPS operations, but found that, even after implementing RPAs, jeopardy would not be avoided. Consequently, NMFS assessed whether the impact of offsite activities that were unrelated to FCRPS operations would avoid jeopardy when coupled with RPAs. The 2000 BiOp concluded the cumulative effect of RPAs and offsite activity was sufficient to avoid jeopardy. In the first iteration of a case that is still ongoing after 15 years-- National Wildlife Federation v. National Marine Fisheries Service --a group of plaintiffs challenged whether the 2000 BiOp complied with the ESA. The matter was assigned to Judge James Redden of the U.S. District Court for the District of Oregon, who would continue to oversee the matter for a decade. In his first decision (commonly called NMFS I ), Judge Redden found the 2000 BiOp to be inconsistent with the ESA, in large part due to his conclusion that the "offsite activities" which NMFS relied upon were dependent on the actions of states, tribes, and third parties that were not reasonably certain to occur. Judge Redden remanded the case to the agency level to revise the 2000 BiOp to conform to his decision. Rather than revise the 2000 BiOp to address the NMFS I court's concerns on remand, NMFS issued "an entirely new biological opinion" in 2004 (2004 BiOp). The 2004 BiOp employed what the Ninth Circuit called a "novel approach" in which NMFS excluded the effect of "each of the dams [that] already exists" from its evaluation because those dams' "existence is beyond the scope of the present discretion of the Corps and [Reclamation] to reverse." Rather than evaluate the aggregate impact of the FCRPS on the protected species, NMFS only evaluated the discretionary elements of the FCRPS operations. In revising its analyses in this way, the 2004 BiOp reached a no-jeopardy conclusion. Judge Redden found this approach to be incompatible with the ESA, and, after identifying four fundamental flaws in the 2004 BiOp, he issued a preliminary injunction requiring the action agencies to modify the FCRPS operations proposed in the 2004 BiOp. On an expedited appeal, the Ninth Circuit largely affirmed the district court's preliminary injunction award without addressing the merits of whether the 2004 BiOp complied with the ESA. Following remand by the Ninth Circuit, Judge Redden ordered NMFS to reengage in consultation and produce a new BiOp. Although NMFS argued that it was inappropriate for the court to supervise an interagency consultation, Judge Redden monitored the agencies' progress and provided detailed instructions on activities he required to take place during the consultation process. Two months later, the district court partially granted another motion for preliminary injunction, modifying a portion of the FCRPS' dam operations during the spring and summer of 2006. On April 7, 2007, two and a half years after NMFS issued the 2004 BiOp, the Ninth Circuit affirmed the district court's decision that the 2004 BiOp was structurally flawed. Among other issues, the Ninth Circuit criticized NMFS for limiting its evaluation to a study of whether the effects of the proposed FCRPS' operations were "appreciably" worse than baseline conditions. According to the Ninth Circuit, this approach failed to take into account the severely degraded baseline conditions, which, even if appreciably improved, could result in a "slow slide into oblivion" in which a "listed species could be gradually destroyed, so long as each step on the path to destruction is sufficiently modest." 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). This BiOp was also challenged in the District of Oregon in a case before Judge Redden. Although Judge Redden rejected the argument that the Snake River must be included in the FCRPS BiOp, he still found the 2005 Snake River BiOp to be arbitrary and capricious because it utilized the same methodology as in the 2004 BiOp for the FCRPS that the Court held to be flawed. Judge Redden remanded the 2005 Snake River BiOp to the agency level, and NMFS issued a revised BiOp on May 5, 2008. In 2008, BPA, the Corps, and Reclamation entered into 10-year agreements with the Columbia Basin tribes and states of Idaho, Montana, and Washington. In what has come to be known as the "Fish Accords," the parties agreed upon the terms of a BiOp for the FCRPS, and BPA committed to funding up to $933 million in mitigation projects in exchange for the state and tribal parties' commitment to support the BiOp in litigation. Environmental groups, fishing interests, and the state of Oregon, who have also acted as plaintiffs, were not parties to the Fish Accords. In May 2008, NMFS issued a new FCRPS BiOp (2008 BiOp) in which it used the Fish Accords as the foundation for its habitat restoration and mitigation plans. Relying on RPAs and the proposed actions in the Fish Accords, NMFS concluded that FCRPS operations would not jeopardize listed species through 2018. NMFS supplemented the 2008 BiOp in December 2010 (2010 Supplement) in order to address concerns expressed by Judge Redden and incorporate its latest agreements with Columbia Basin states and tribes. In a continuation of the case before Judge Redden that began with the 2000 BiOp, a group of environmental organizations, anglers, energy conservationists, and the state of Oregon challenged the 2008 BiOp and 2010 Supplement (collectively, the 2008/2010 BiOp). For the first time since 1995, the court ruled that a portion of NMFS's BiOp complied with the ESA. Specifically, Judge Redden found that the section of the 2008/2010 BiOp addressing FCRPS operations through the end of 2013 identified "specific and beneficial mitigation measures" which were lawful and could remain in place. For the portion of the BiOP addressing operations between 2014 and 2018, however, the court ruled that NMFS relied on "habitat mitigation measures that are neither reasonably specific nor reasonable certain to occur, and in some cases not even identified." Judge Redden remanded the 2008/2010 BiOp for further consultation on post-2013 operations, and he ordered NMFS to produce a supplement by January 1, 2014, that considers "whether more aggressive action, such as dam removal and/or additional flow augmentation and reservoir modifications are necessary to avoid jeopardy." In January 2014, NMFS issued a second supplement to the 2008 BiOp. In this most recent BiOp (2014 Supplement), NMFS did not reverse its finding from 2008 that jeopardy could be avoided through RPAs. 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. NEPA requires certain agencies to complete an environmental impact statement in connection with any "major Federal actions significantly affecting the quality of the human environment." The court found the Corps and Reclamation relied upon environmental impact statements that were either "too stale" or too "narrowly focused," and it asked for additional briefing from regarding a timeline in which the EIS should be completed. NMFS, the Corps, and Reclamation have requested five years to prepare the EIS. Other litigation has affected the way in which the ESA has been applied to Columbia River anadromous fish. When the U.S Court of Appeals for the Tenth Circuit ruled that the FWS's method of determining critical habitat under the ESA was flawed, NMFS agreed to settle a suit that challenged its critical habitat determination for the Columbia River. NMFS had used a methodology similar to FWS in determining how economic factors were used in its determination of critical habitat. Litigants have also challenged whether hatchery-raised salmon and steelhead should be listed as threatened under the ESA under NMFS's Hatchery Listing Policy (HLP). Issued as interim policy in 1993, the HLP provides guidance on how NMFS treats stocks of hatchery salmon and steelhead when deciding which species should be listed as protected under the ESA. In the interim policy, NMFS concluded that certain hatchery fish could be included in the same evolutionary significant unit (ESU) as wild fish, which were listed, but it nevertheless excluded stocks of hatchery fish in its listing. A federal court found this approach violated the ESA by listing distinctions below the species level. If hatchery and wild salmon were in the same ESU, the court reasoned, they should have the same listing status. NMFS revised the interim policy and issued a final HLP in 2005. When determining whether to list a species as threatened or endangered, the final HLP requires NMFS to consider the status of the ESU as a whole rather than the status of only the wild fish. It also states that an entire ESU would be listed, rather than just the wild fish. This revised approach resulted in a downlisting of certain fish, such as steelhead trout, from endangered to threatened. Two suits were filed in two federal district courts challenging the final HLP. A suit in the Western District of Washington addressed the HLP's application to steelhead (the "steelhead case"), and a suit in the District of Oregon challenged its effect on salmon (the "salmon case"). In the steelhead case, a diverse set of plaintiffs challenged both sides of the hatchery argument: one group argued that hatchery steelhead should be considered distinct from wild steelhead, while another argued that NMFS should make no distinction between places of origin. The district court concluded NMFS erred in downlisting steelhead based on the condition of the entire ESU--both hatchery and wild--rather than focusing on the "benchmark of naturally self-sustaining populations that is required under the ESA[.]" The U.S. Court of Appeals for the Ninth Circuit reversed that portion of the district court's ruling and concluded that the final HLP complied with the ESA. The Ninth Circuit gave discretion to NMFS's analysis and concluded that the downlisting was based on "substantial ... scientific data, and not mere speculation[.]" In the salmon case, NMFS distinguished between hatchery stocks of salmon and wild or "natural" salmon. The U.S. District Court for the District of Oregon rejected the plaintiffs' argument that the ESA required hatchery salmon and wild salmon to be treated equally for listing purposes when they are included in the same ESU, and the Ninth Circuit affirmed. To reduce predation on upstream migrating adult salmon, NMFS authorized Washington and Oregon in March 2008 to lethally take California sea lions that gather below the Bonneville Dam. The authorization was revoked in November 2010, following a Ninth Circuit decision that the permit for lethal removal was contrary to law. The court found that NMFS could not justify killing California sea lions when their take of the salmon was shown to be no larger than that of commercial fishing; NMFS had described the effect of commercial fishing as "minor" and "minimal" in past statements. In May 2011, NMFS authorized states to euthanize up to 85 California sea lions, but withdrew that authorization in July 2011, in response to a lawsuit. Following a second application process, NMFS reissued Letters of Authorization in March 2012 to Washington, Oregon, and Idaho allowing the states to remove up to 92 animals. A group of plaintiffs, including the Humane Society, challenged the 2012 authorization in the U.S. District Court for the District of Columbia arguing that it did not comply with the Ninth Circuit's decision. On review (and after the case was transferred to the District of Oregon), the Ninth Circuit sided with NMFS in this legal bout, finding that, although the plaintiffs raised "valid concerns," the 2011 authorization was sufficiently grounded in scientific data to explain the need to euthanize. With the legal challenge resolved, states have since lethally removed sea lions under the 2012 authorization. Between 2008 and 2015, the Departments of Fish and Wildlife for the states of Oregon and Washington have removed 102 California sea lions. Of those removed, 15 were placed in a zoo or aquarium, 87 were euthanized by lethal injection, and seven died in captivity. The 2012 letter of authorization expired on June 30, 2016, and, on January 27, 2016, Washington, Oregon, and Idaho submitted an application for a five-year extension. NMFS agreed that the states' applications showed "sufficient evidence of the [predation] problem[,]" and it issued a new letter of authorization on June 30, 2016.

Summary:
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.