The San Joaquin River is the main artery of California’s second largest river system. The river originates high in the Sierra Nevada mountains, on mountain peaks southeast of Yosemite National Park, and then tumbles westward out of the mountains and into the trough of the Central Valley. Near the city of Mendota, the River turns abruptly north for the final stretch of its several hundred mile journey, picking up the Merced, Tuolumne, Stanislaus, Mokelumne, Calaveras, and Cosumnes Rivers as major tributaries on the way. It finally merges with the Sacramento River to form the San Francisco Bay-Delta estuary.

Historically, the San Joaquin River supported substantial populations of Chinook salmon, including both a fall and a spring run (Decl. of Peter Moyle, Exh. F, at 16). Chinook are distinguishable from other species of Pacific salmon by their large size and unique markings. They are an anadromous species, which means that they emerge and rear in freshwater tributaries, migrate to the ocean as juveniles, and return to their natal waters to spawn two to four years later. The San Joaquin River’s adult spring-run Chinook historically returned to the River mostly during the months of March through June, and spent the summer holding in deep pools above and below the existing location of Friant Dam. Spring-run would then spawn in the early fall, and their offspring would migrate out to the sea the following year, generally from January to March. Historically, the adult fall-run Chinook returned to the river mostly between September and December, and spawned soon thereafter. Fall-run juveniles would emerge in late winter and migrate out to the sea primarily in the months of March through May.

Salmon on the San Joaquin River were abundant prior to the closure of Friant Dam (Moyle Decl., ¶ 1; Decl. of Amy Macaux, Exh. F, at 16). The river’s spring run was one of the largest Chinook runs anywhere on the Pacific Coast and has been estimated at several hundred thousand fish (Moyle Decl., ¶ 20; Macaux Decl., Exh. G, at 9; Macaux Decl., Exh. F, at 8). The historical fall run is conservatively estimated to have numbered 50,000 to 100,000 fish. So many salmon migrated up the San Joaquin River during the spawning season that some people who lived near the present site of Friant Dam compared the noise to a waterfall. Some residents even said that they were kept awake nights by the myriad salmon heard nightly splashing over the sand bars in the River. One observer reported that salmon were so plentiful that ranchers trapped the fish and fed them to hogs. A fisherman who lived downstream recalls that, in the 1940s, the salmon were still â??so thick that we could have pitch-forked them. One almost could have walked across the River on the backs of the salmon when they were running.â? (Decl. of John Banks, ¶ 5).

The upper San Joaquin River contained Chinook habitat both above and below the location of Friant Dam, including some of the best spring-run habitat anywhere in California. This included a mixture of deep pools for holding and gravelly riffles for spawning, over which cold water ran. (Moyle Decl., ¶ 19). Much of that habitat still survives in the River below Friant Dam. ( Id.) Other anadromous fish, including Pacific lamprey and steelhead, once lived on the San Joaquin River below Friant Dam as well. (Moyle Decl., ¶ 22; Macaux Decl., Exh. G, at 1,9; Wall Decl., Exh. B., at 29-32). Collections of fish made in the vicinity of Friant in 1898 and 1934 indicate that the River supported diverse native fish that included rainbow trout, splittail, hitch, hardhead, and Kern brook lamprey, all species of conservation interest today. The river’s flow into the Delta also helped support that important ecosystem’s water quality and habitat. In 1999, the National Marine Fisheries Service designated the San Joaquin River between Friant Dam and the Merced as â??essential fish habitatâ? for Chinook salmon, pursuant to the Magnuson-Stevens Fishery Conservation and Management Act, 16 U.S.C. §§ 1801-83 (Decl. of Michael E. Wall, Exh. A; RJN, Exh. A).

The Bureau built Friant Dam across the upper San Joaquin River, northwest of Fresno, in the early 1940s as part of the Central Valley Project. Construction began in 1939 and was largely completed by the mid-1940’s. The Dam stores the river’s flow in Millerton Lake, the reservoir behind the Dam, and diverts water for irrigation and other purposes into two canals. The first of these, the Madera Canal, was completed in 1945. The second, the Friant-Kern Canal, began delivering water by 1949. Since that time, the Bureau has operated Friant Dam to maximize the quantity of water diverted to its Friant Division contractors, including the non-federal defendants.

Friant Dam blocked upstream access to a portion of the San Joaquin River’s spawning habitat for salmon and steelhead; however, it was not the construction of the Dam that terminated the salmon runs. For several years after Friant Dam was in place, the Bureau released sufficient water to sustain the salmon fishery. Chinook salmon are a remarkably resilient species, and although Friant Dam blocked passage to upstream habitat, during the first years after the Dam was built, spring-run Chinook successfully held in pools below Friant Dam during the summer months, adults successfully spawned in habitat below the Dam, and juveniles continued to migrate downstream. In one of these years, 1945, an estimated 56,000 spring-run returned to spawn below Friant Dam. While the upper San Joaquin’s salmon runs were not as strong as they once were, Professor G.H. Clark, of Stanford University, reported that the fish themselves were â??in excellent shapeâ? in 1942 (Decl. of Adam Wolf, Exh. F).

By the late 1940s, however, the Bureau’s operation of Friant Dam had caused long stretches of the River to dry up. (Macaux Decl., Exh. F, at 18). In the spring of 1948, the California Division of Fish and Game responded with a dramatic fish rescue in an attempt to save the River’s spring-run Chinook salmon. About 2,000 up-migrating Chinook were trapped in the lower portion of the River, hauled by truck around the dewatered stretch of the River, and released at a point from which they could migrate upstream to deep pools just below Friant Dam. These salmon were able to hold over the summer in these pools, and to spawn successfully below Friant Dam in the fall, but their offspring perished in early 1949 when they attempted to out-migrate through the dried-up River bed.

With the completion of the Friant-Kern Canal, the Bureau in 1949 further increased diversions, leaving even less water for the San Joaquin River. (Moyle Decl., ¶ 31; Macaux Decl., Exh. J, at 6). The last of the upper San Joaquin River’s fall-run Chinook salmon were reported in a pool below Mendota Dam in 1949. (Loudermilk Decl., Exh. K). Spring-run Chinook salmon disappeared from the San Joaquin River after unsuccessful salmon rescue attempts in 1949 and 1950. (Moyle Decl., ¶ 39; Macaux Decl., Exh. F., at 18; Macaux Decl., Exh. G, at 9). For most of the last 50 years, the Bureau has diverted virtually all of the River’s flows. (Macaux Decl., Exh. J, at 6; Macaux Decl., Exh. K, at 3; Moyle Decl., ¶¶ 22-28, 31; Loudermilk Decl., ¶ 2). While salmon continued to return and spawn until 1949, after that, â??the San Joaquin chinook was extirpated in its southernmost range.â? (Macaux Decl., Ex F, at 18).

Some sixty miles of the River upstream of its confluence with the Merced now lie continuously dry, except during rare flood events. (Macaux Decl., Exh. E, at 7; Macaux Decl., Exh. K, at 3; Wall Decl., Exh. B, at 43; Loudermilk Decl., ¶ 2). The spring-run Chinook-once the most abundant race of salmon in the Central Valley-appear to have been extirpated from the length of the River. (Wall Decl., Exh. B, at 36, 42, 48; Macaux Decl., Exh. H, at 9). Small populations survive only in the Sacramento River system. (Moyle Decl., ¶ ¶ 26, 29). The fall-run Chinook, too, were eliminated from the upper San Joaquin River, although reduced populations of fall-run Chinook survive on downstream tributaries, principally the Merced, Tuolumne, and Stanislaus Rivers. (Moyle Decl., ¶ 27; Wall Decl., Exh. B, at 36, 42, 48; Macaux Decl., Exh J at 6). In the words of the Department of the Interior, Friant Dam’s operations have been a â??disasterâ? for Chinook salmon. United States Dep’t of the Interior, The Relationship Between Instream Flow, Adult Immigration, and Spawning Habitat Availability for Fall-Run Chinook Salmon in the Upper San Joaquin River, California at 6 (Sept.1994) (Macaux Decl., Exh. J).

Despite the upper San Joaquin River’s degraded habitat and long stretches of normally dry river bed, salmon and Pacific lamprey have returned to the upper San Joaquin River in wet years, even after Friant Dam began full storage and diversion operations. Part of Chinook salmon’s natural behavior includes establishing or re-establishing themselves in new streams and rivers by â??strayingâ? from their natal waters. (Moyle Decl., ¶ 33). In some years, salmon have made it to the base of Friant Dam. (Moyle Decl., ¶ 33; Macaux Decl., Exh. G, at 10). Adequate flows of water have not been released from Friant Dam for these up-migrating salmon to spawn, however, or for their offspring to migrate back to the sea. (Moyle Decl., ¶ 33; Loudermilk Decl., ¶ 2; Wall Decl., Exh. B, at 29, 35-36).

The Bureau’s operation of Friant Dam has also contributed significantly to declines in other native fish throughout the San Joaquin River system. (Moyle Decl., ¶ 22, 31; Macaux Decl., Exh. G, at 1-2; Wall Decl., Exh. B, at 42-43). Following the construction of Friant Dam, ten of the sixteen species of native fish disappeared from the area. (Moyle Decl., ¶ 22; Macaux Decl., Exh. G, at 1-2). They were replaced, in the reaches where enough water for any fish still exists, primarily by a variety of non-native fishes. (Moyle Decl., ¶ 22; Macaux Decl., Exh. E, at 6-7).

Waters from the upper San Joaquin had been critical to providing habitat for fish species many miles below the Dam. (Moyle Decl., ¶ 31; Macaux Decl., Exh. G, at 1). San Joaquin River flows are needed to help attract adult salmon to their spawning grounds, to provide habitat for young and juvenile salmon, to move juvenile salmon downstream in the spring through the lower San Joaquin River, and to provide sufficient dilution of toxic and saline drainage to maintain a minimum level of water quality. (Moyle Decl., ¶ 31; Macaux Decl., Exh. E, at 10). Failure to release water from Friant Dam has rendered many miles of fish habitat unusable, especially in the stretch between the Dam and the river’s confluence with the Merced, and has also adversely affected water quality along the whole course of the river. (Moyle Decl., ¶ 31; Macaux Decl., Exh. G, at 1, 2; Wall Decl., Exh. B, at 44, 46). Today, the first several miles of the San Joaquin River deep water ship channel, near Stockton, experience dissolved oxygen levels that are so low during summer and fall months that they do not meet the state water quality objective. (Wall Decl., Exh. C, at 1). Low dissolved oxygen in these reaches poses a danger to fish generally, and a migration barrier to anadromous fish, including salmon in particular. Id.

Reduced flows in the San Joaquin below Friant Dam have diminished the area available for fish, increased the temperature of the water that is available, reduced the ability of the river to assimilate agricultural runoff and other pollutants, and substantially degraded riparian vegetation. (Moyle Decl., ¶ 31; Wall Decl., Exh. B, at 46; Macaux Decl., Exh. G, at 6). Native fishes such as hitch, splittail, tule perch, and pikeminnow, have largely disappeared from the River and have been replaced by exotic fishes tolerant of warm polluted water. PSUF 66. The present warm-water fishery that exists on portions of the San Joaquin River between Mendota Pool and the San Joaquin’s confluence with the Merced River is small and erratic. (Moyle Decl., ¶ 32). Many of the fish in this reach are contaminated with pesticides and other agricultural contaminants. (Moyle Decl., ¶ 31; Wall Decl., Exh. B., at 35). From Mendota Pool to Sack Dam, the river is basically used to convey irrigation water, and from Sack Dam to the river’s confluence with the Merced River, the river is dewatered for forty miles until agricultural drain water provides a small flow that is a *912 highly degraded environment for fish. (Moyle Decl., ¶ 31; Macaux Decl., Exh. G, at 6). Surveys by the U.S. Geological Survey indicate that the fish in this polluted section of the river are almost entirely pollution-tolerant non-native fishes, such as common carp, red shiners, bluegill, and mosquito fish (Macaux Decl., ¶ 32). The native fish have largely disappeared.