Opinion ID: 3034358
Heading Depth: 3
Heading Rank: 3

Heading: The SONCC Coho Salmon

Text: The SONCC coho ranges throughout the North Pacific Ocean. During the twentieth century, populations of coho declined substantially in California and Oregon. The BiOp states that the number of wild coho in the Klamath River is “extremely low, and has been declining for most of the past two decades.” The population of the SONCC coho is estimated to have declined from an estimated range of 50,000 to 125,000 wild coho in the 1940s to fewer than 6,000 wild coho in 1996. The SONCC coho salmon was listed as a threatened species under the ESA in 1997.3 The major factors threatening the SONCC coho include logging, grazing, dams, and water withdrawal for irrigation. The facts below are drawn from the NMFS’s description of the SONCC coho’s life cycle and assessment of its habitat needs in the BiOp. The SONCC coho has a three-year life cycle, spending half its life in fresh water and half in salt water. Coho eggs typically hatch in March. Coho fry emerge two weeks after hatchAss’n v. Patterson, 204 F.3d 1206 (9th Cir. 1999) (addressing contract issues relating to water allocation; holding that the BOR’s obligations under the ESA allow it to override rights of water users); Moden v. U. S. Fish & Wildlife Serv., 281 F.Supp. 2d 1193 (D. Or. 2003) (holding that delisting of the fish residing in reservoir is not supported); Kandra, 145 F.Supp. 2d at 1192 (upholding the BOR’s implementation of conservation measures against challenge by irrigators); PCFFA I, 138 F.Supp. 2d at 1228 (overturning the BOR’s operation plan for failure to consult with the NMFS as required by the ESA). 3 The NMFS recently reconfirmed the SONCC coho’s status as a threatened species in response to a lawsuit challenging the listing of a different subgroup of coho salmon. See Alsea Valley Alliance v. Evans, 161 F.Supp. 2d 1154 (D.Or. 2001), appeal dismissed for lack of jurisdiction sub nom. Alsea Valley Alliance v. Dep’t of Commerce, 358 F.3d 1181 (9th Cir. 2004). See Endangered and Threatened Species: Final Listing Determination for 16 ESUs of West Coast Salmon, and Final 4(d) Protective Regulations for Threatened Salmonid ESUs, 70 Fed. Reg. 37,160, 37,193 (June 28, 2005) (to be codified at 50 C.F.R. pts 223 and 224). 14302 PACIFIC COAST v. BUREAU OF RECLAMATION ing, and spend up to 15 months in fresh water. The fry’s preferred habitat is shallow areas near stream banks. Fry become smolt after 15 months and migrate to the sea between March and June. After about three years, coho return to the same streams in which they were born to spawn, migrating upstream between September and February, and spawning between November and January. Sufficient water flows must be available in the main stem of the Klamath River to enable the fish to migrate upstream during September through February and to migrate downstream at maturity from March through June. Habitat conditions in the main stem are also important because degraded habitat or low flow in tributaries causes coho fry to seek additional habitat in the main stem. During the spring months, March through June, newly hatched fry need shaded habitat near stream banks and migrating smolt need sufficient water in the river to leave tributaries and migrate to the sea. The BiOp makes clear that NMFS considers these the most critical months in which to provide an adequate amount of water in the main stem because of the needs of the fry and smolt. The NMFS reports that studies in other basins show that increased flow during these months resulted in “lower mortality due to migratory delay, predation, and exposure to potentially poor main stem habitat conditions.” During the summer months, the primary concerns are to ensure that there is sufficient habitat in the main stem for juveniles displaced from tributaries by poor water quality or competition, and that the water temperatures are sufficiently cool. From October through February, the primary concern is maintaining sufficient water in the main stem for upstream migration and access to tributaries. The NMFS notes that in fall and winter water often flows freely past the Iron Gate Dam, resulting in “uncontrolled releases” of water. D. Prior Scientific Assessments of the Klamath River Basin The BiOp at issue here is the product of several iterations of scientific study and review, including two previous BiOps PACIFIC COAST v. BUREAU OF RECLAMATION 14303 and two government studies of the basin that reached conflicting conclusions. The NMFS issued the first BiOp for the Klamath Project in 1999. At this time, a governmentcommissioned scientific assessment of the flow needs of anadromous species in the Klamath River basin was released. Known as Phase I of the “Hardy Report,” that assessment provided interim recommendations on flow levels needed to support aquatic life. In 2001, a severe drought limited water availability in the basin. Kandra, 145 F.Supp. 2d at 1198. Two BiOps, one for the SONCC coho and one for the other endangered fish that inhabit the reservoir, called for maintenance of high levels of water in both the reservoir and the main stem of the river. The BOR complied with the BiOps and, as a result, did not deliver water to irrigators. Significant agricultural losses followed. Following the dry 2001 irrigation season, the National Research Council (NRC) was asked by the Department of Interior to “independently review the scientific and technical validity of the government’s biological opinions.” The NRC Report, released in February 2002, found that there was not scientific support for the flow recommendations in the NMFS’s coho salmon BiOp. The report reviewed existing scientific literature and data on coho in the Klamath River basin. It concluded that “incremental depletions beyond those that are reflected in the recent historical record could be accomplished only with increased risk to coho salmon. At the same time, the available information provides little support for benefits presumed to occur through the increase of flows beyond those of the last decade.” The conclusion questioned the validity of the 2001 BiOp. The NMFS requested clarification from the NRC, which responded that “the NRC committee did not conclude that NMFS must be wrong in its recommendations on main-stem flows.” In its BiOp, the NMFS attributed the conclusions of the NRC report to “lack of information on distribution and abundance of coho . . . and the lack of studies focused on coho and factors limiting its population in the 14304 PACIFIC COAST v. BUREAU OF RECLAMATION Klamath River Basin.” The NMFS did not dismiss the NRC Report, but it did not adopt its conclusions in full. Phase II of the “Hardy Report” was released in draft form in November 2001. Its conclusions about flow requirements conflict with those of the NRC.4 The Phase II report, calling itself the “best available science,” used site-specific habitat modeling and estimates of the unimpaired flows in the main stem to arrive at a recommendation for flows for each river reach. The report determined that flows lower than approximately 1000 cubic feet per second (cfs) during the late summer would likely expose the SONCC coho to dangerously high water temperatures, thereby increasing the risk of harm to the species. E. The Current Biological Opinion The process through which the current BiOp was created began when the BOR prepared its most recent long-range biological assessment in February 2002. The BOR proposed maintaining a flow regime that varied river flows by “water year type,” meaning that less water need be provided in years in which less precipitation has fallen in the region, reflecting natural variations in river flows. For each type of “water year” (for instance, dry or wet), the BOR used the historic average water flow for that type over the previous ten-year period to set its goals by type of year for the next ten years of operation. Any available water beyond that needed to meet the goal would be allotted for irrigation. In addition, the BOR would establish a water bank to store 100,000 total acre feet of water to meet the flow requirements. When the NMFS reviewed the proposed operations plan in the BOR’s biological assessment to prepare the current BiOp, it determined that if the Klamath Project were operated as the 4 The NRC report did not consider the Hardy Phase II report in making its findings because it was in draft form. PACIFIC COAST v. BUREAU OF RECLAMATION 14305 BOR intended, it would cause jeopardy to the SONCC coho and adversely modify its critical habitat. The NMFS was concerned that the BOR’s use of the minimum flow over the past ten years as the planning target for establishing monthly flows would drive down the average flow in the Klamath River from below its ten-year average, which would lead to adverse effects to habitat and individual coho in the main stem. Among the NMFS’s concerns were that decreased flows would reduce the amount of suitable coho fry habitat, make it more difficult for smolt to migrate downstream, and prevent adult coho from accessing tributaries during their upstream migration. In the BiOp, therefore, the NMFS developed an RPA to replace the BOR’s proposed plan of operations. The RPA is the subject of the instant appeal. The RPA covers operations for the Klamath Project from 2002 until 2012. An organizing principle of the RPA is that the BOR should bear responsibility only for the share of water losses caused by the Klamath Project. Because the project irrigates 57 percent of land in the basin, the RPA provided that the BOR would provide 57 percent of the water needed for the coho, and establish an intergovernmental workgroup to “develop the other 43 [percent] of the flows.” The RPA permitted the BOR to use a “water bank” to provide its share of the water. The RPA is divided into three phases. Phase I, lasting from 2002 through 2005, calls upon the BOR to gradually develop resources in the water bank, begin development of the intergovernmental task force, and conduct scientific studies. During Phase I, the BOR must provide, at a minimum, the flows that were established in its biological assessment, supplementing those flows in the spring and/or summer by use of the water bank. Phase II, which is to last from 2006 to 2010, requires the BOR increase the water bank to 100,000 acre feet and provide 14306 PACIFIC COAST v. BUREAU OF RECLAMATION the greater of the 57 percent share or the flows proposed in the biological assessment. During Phase III, which encompasses water years 2010 and 2011, NMFS anticipates that 100 percent of the salmon’s flow needs will be met through the BOR’s 57 percent share and the 43 percent contribution from unspecified sources. The discussion in this section explains how the NMFS calculated the long-term flow levels that it believed were necessary to avoid the likelihood of jeopardy to the coho. The agency determined that the species could withstand a 20 percent reduction in habitat from what it would have received under an unimpaired flow regime, and calculated the flows that must be provided to achieve this quantity of habitat. The agency also determined that in summer months, flows of less than 1000 cfs would threaten coho in the main stem with dangerously high water temperatures, and required maintenance of flows of 1000 cfs or greater. F. The Proceedings Below The litigation below began with an unsuccessful request by Pacific Coast for a temporary restraining order in response to interim measures initiated before the BiOp was finalized. The NMFS completed the final BiOp on May 31, 2002. After 33,000 chinook, coho, and steelhead salmon died in an unexplained fish kill in the Klamath River between September 20 and 27, 2002, Pacific Coast filed an amended complaint against the federal defendants. The parties filed cross-motions for summary judgment, on which the district court ruled on July 14, 2003. The district court overturned a significant aspect of the RPA, finding the requirement that the BOR provide only 57 percent of the long-term flows to be arbitrary and capricious. The court concluded that the NMFS had inappropriately considered the effects of actions that were not “reasonably certain to occur” when it determined that the coho would receive 100 percent PACIFIC COAST v. BUREAU OF RECLAMATION 14307 of the flows through a collaborative process. The federal defendants do not appeal this ruling, nor does Pacific Coast challenge the long-term flow levels established for Phase III. At issue in this appeal is the district court’s determination that Phases I and II of the RPA, or the short-term measures, were not arbitrary and capricious. Pacific Coast challenged the flow levels established in Phases I and II, arguing that the Phase I flows were the same flows rejected by the NMFS as insufficient in its review of the BOR’s biological assessment and that the Phase II flows provided only 57 percent of the flows that the NMFS recognized the coho required. The court acknowledged that the RPA “does not explicitly engage in an analysis of what effect the water flows in Phases I and II, with the addition of the available water from the water bank, will have on the coho salmon or their critical habitat.” However, the court found that the NMFS had determined that providing less water during the short-term would not jeopardize the coho. The court reasoned: [T]he statements by the NMFS do not reflect a con- clusion that it is necessary to consistently provide 100% of the long-term target flows throughout each phase of the program in order to avoid jeopardy to the salmon. In fact, implicit in the RPA’s phased approach is the ultimate conclusion that maintaining a percentage of the long-term flow rates with the additional water provided by the water bank during Phase I and II will not jeopardize the salmon or adversely modify their critical habitat, provided that the long-term flow rates are eventually met by Phase III of the program. The court ordered the NMFS to revise its BiOp to address the deficiencies identified in Phase III of the RPA, but specified that the BiOp and the RPA would remain in effect until a revised BiOp was issued. Pacific Coast timely filed the instant appeal. The federal defendants initially cross-appealed 14308 PACIFIC COAST v. BUREAU OF RECLAMATION the decision to strike down Phase III, but voluntarily dismissed the appeal prior to briefing.