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3.4.4.4 Fall-run/late-fall-run Chinook Salmon (Oncorhynchus tshawytscha) Fall-run/late-fall-run Chinook salmon are anadromous with spawning and juvenile rearing occurring within freshwater rivers and streams and juvenile and adult rearing occurring within coastal marine waters. Adult fall-run Chinook salmon migrate from the coastal marine waters upstream through San Francisco Bay and the Delta during late summer and early fall (approximately late July - early December). Adult fall-run Chinook salmon migrate upstream to areas characterized by suitable spawning conditions, which include the availability of clean spawning gravels, cold water (considered be less than 56º F) and relatively high water velocities. Fall-run Chinook salmon spawning is similar to that described for other Chinook salmon with the creation of redds where eggs are deposited and incubate. Fall-run Chinook salmon spawning occurs between October and December with the greatest spawning activity occurring typically in November and early December. The success of fall-run Chinook salmon spawning is dependent, in part, on seasonal water temperatures. After incubating and hatching, the young salmon emerge from the gravel redd as fry. A portion of the fry population migrate downstream soon after emergence, where they rear within the lower river channels, Delta, and estuary during the spring months. The remaining portion of juvenile salmon continue to rear in the upstream stream systems through the spring months, until they are physiologically adapted to migration into saltwater (smolting), which typically takes place between April and early June. A small proportion of the fall-run Chinook salmon juveniles may, in some systems, rear through the summer and fall months migrating downstream during the fall, winter, or early spring as yearlings. The juvenile and adult Chinook salmon rear within coastal marine waters, foraging on fish and macroinvertebrates (e.g., northern anchovy, Pacific herring, squid, krill, etc.), until they reach maturation. Adult Chinook salmon, spawn at ages ranging from approximately two to five-years-old with the majority of adult fall-run Chinook salmon returning at age three. Chinook salmon, unlike steelhead, die after spawning. A variety of environmental and biological factors have been identified that affect reproductive success, mortality, and population dynamics of fall-run and late fall-run Chinook salmon. The loss of access to historic spawning and juvenile rearing areas as a result of the construction of dams and reservoirs on many of the Central Valley river systems is a factor affecting population abundance. In addition, exposure to seasonal water temperatures during both the upstream migration of adults and downstream migration of juveniles, changes in instream flows resulting from reservoir operations, degradation of the quality and availability of suitable spawning habitat and juvenile rearing areas, and the effects of hatchery operations on Chinook salmon have been identified as important factors affecting abundance. Juvenile Chinook salmon are also susceptible to entrainment at unscreened water diversions, losses resulting from salvage and handling at the SWP and CVP export facilities, predation mortality by non-native fish species, interannual variability in hydrologic conditions within the streams and river systems, and variability in ocean rearing conditions have also been identified. Contaminant exposure, impediments and barriers to upstream and downstream migration, ocean commercial and recreational angler harvest, and inland recreational harvest have also been identified as factors affecting population abundance. Management changes have occurred to regulate commercial and recreational angler harvest, improve instream flow conditions, improve water temperature management downstream of reservoirs, improve quality and availability of spawning and juvenile rearing habitat, and improve fish passage facilities at a number of existing migration impediments and barriers. The life history and factors affecting abundance of late fall-run Chinook salmon are similar to those described for fall-run Chinook salmon. Fall-run and late fall-run Chinook salmon primarily migrate upstream and downstream within the mainstem Sacramento River in the vicinity of the Proposed Project. Adult and juvenile fall-run and late fall-run Chinook salmon migrate from the Sacramento River through the Delta and San Francisco Bay during their downstream migration during the late winter and spring migration period. The project reach of the Sacramento River serves as a migration corridor for upstream and downstream migration by adult and juvenile fall-run and late fall-run Chinook salmon. Fall-run/late-fall-run Chinook salmon do not spawn within the Sacramento River in the vicinity of the Proposed Project. Fall-run and late fall-run Chinook salmon habitat quality and availability within the upper Sacramento River and tributaries has been affected by a variety of factors including construction and operation of water storage impoundments and water diversions, changes in the magnitude and seasonal timing of instream flows, hatchery operations, and barriers and impediments to adult and juvenile migration. Fall-run Chinook salmon have also been affected by predation by pikeminnow and striped bass and other species, commercial and recreational angler harvest, changes in land use, channelization and stabilization using riprap of the mainstem river and tributaries, reductions in flood plain habitat and instream cover, and a variety of other factors. Chinook salmon are also vulnerable to mortality as a direct and indirect result of SWP and CVP water diversion operations, operation of the Red Bluff Diversion Dam, operation of the Delta cross-channel, and entrainment into unscreened diversions. Reduction in the availability and quality of spawning gravel downstream of dams has also been identified as a factor affecting the species. Fall-run Chinook salmon are the most abundant species of Pacific Salmon inhabiting the Sacramento and San Joaquin river systems. Fall-run Chinook salmon are not listed for protection under either the California or Federal ESAs. In addition to fall-run Chinook salmon, the group of Pacific Salmon is comprised of late fall-run Chinook salmon (which are not listed under either the California or Federal ESAs), spring-run Chinook salmon and winter-run Chinook salmon, which are discussed above. Although fall-run and late fall-run Chinook salmon are not listed for protection under the ESA they are included in this assessment since the Proposed Project would be located within the area identified as EFH for Pacific salmon. In 1998 NOAA Fisheries proposed that Central Valley fall-run and late fall-run Chinook salmon be listed under the Federal ESA as a threatened species. Based upon further analysis, and public comment, NOAA Fisheries decided that fall-run and late fall-run Chinook salmon did not warrant listing but rather remain as a candidate species for further analysis and evaluation. The MSCS "R" goal for these races is for resource agencies to cooperatively develop restoration goals for "Viable Salmonid Populations" in a process separate from NOAA Fisheries recovery planning. Management changes have also occurred to address concerns regarding contaminant exposure, the success of fish handling and salvage at the SWP and CVP export facilities, and a number of water diversions located on both the Sacramento and San Joaquin river systems have been equipped with positive barrier fish screens designed to reduce or eliminate juvenile salmon entrainment mortality. These management changes, in combination with favorable hydrology and ocean rearing conditions in recent years, have contributed to an increasing trend in adult fall-run Chinook salmon abundance within the ocean and Central Valley river systems. In summary, there is migration and limited foraging habitat in the Action Area for fall-run and late fall-run Chinook salmon. No spawning habitat exists in the Action Area. The Sacramento River has been identified as essential fish habitat for Pacific salmon including fall-run and late fall-run Chinook salmon. 3.4.4.5 Essential Fish Habitat The Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA), as amended by the Sustainable Fisheries Act of 1996, established procedures designed to identify, conserve, and enhance EFH. The EHF mandate applies to all species managed under a Federal Fishery Management Plan (FMP). In California, the FMP for Pacific Salmon (Pacific Fisheries Council 1999) designates the mainstem Sacramento River as EFH. The project reach of the mainstem Sacramento River contains three components of EFH:
The Amendment 14 of the Pacific Salmon FMP identifies and describes mechanisms by which various factors may influence EFH and salmonids. Specifically, habitat requirements are identified and potential habitat concerns are listed. The requirements/concerns applicable to EFH in the Action Area are summarized below:
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