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Status Definitions Federal FE = listed as endangered under the Federal Endangered Species Act FT = listed as threatened under the Federal Endangered Species Act FC = Candidate for listing under the Federal Endangered Species Act FSC = Federal special concern species FSLC = Federal species of local concern EFH = Essential Fish Habitat for this species has been described for the project reach of the Sacramento River D = Delisted -- = no designation
SE = listed as endangered under the California Endangered Species Act ST = listed as threatened under the California Endangered Species Act CSC = California Species of Special Concern -- = no designation Although there is potential for some of the special-status birds listed above to fly over various portions of the project area, the project will not affect birds in flight or a significant portion of the thousands of acres of potential foraging area for birds which may land and forage in agricultural fields. In areas adjacent to Boyers Bend, Howells Landing, and Tyndall Mound, some foraging activity by species such as rufous hummingbird may occur during migration. In addition, white-tailed kite, oak titmouse, Lawrence's goldfinch, Vaux's swift, Nuttall's woodpecker, Lewis's woodpecker, and loggerhead shrike could use treed areas of the levees for nesting, but work to remove existing facilities in these areas will occur during periods of low flow which will occur following the nesting period. In addition, in these areas, the Proposed Project will occur entirely on lands that are currently disturbed by routine operation and maintenance activities. Because the project will not create disturbance substantially in excess of the current levels during the 7 to 14 day facility removal period, there is no mechanism by which the project would affect post-nesting incidental use of these areas by the special-status birds listed on Table 3-2. Based on this analysis, a list of special-status species with potential to occur in the Action Area was developed (Table 3-3). The list on Table 3-3 includes all special-status species for which there may be a potential mechanism for the project to have effects, both adverse and beneficial, but it does not address the nature or biological significance of these effects. Table 3-3. Special-status species potentially occurring within the RD108 Combined Pumping Plant and Fish Screen Project action area.
Status Definitions Federal FE = listed as endangered under the Federal Endangered Species Act FT = listed as threatened under the Federal Endangered Species Act FSC = Federal special concern species EFH = Essential Fish Habitat for this species has been described for the project reach of the Sacramento River -- = no designation
ST = listed as threatened under the California Endangered Species Act CSC = California Species of Special Concern -- = no designation 3.4.4 Baseline Conditions for Species 3.4.4.1 Chinook Salmon Adult Chinook salmon migrate from the Pacific Ocean upstream within the Sacramento River to spawning areas. The river reach adjacent to the project reach serves as a migratory corridor for adult upstream migration. The timing of adult upstream migration for each of the four races typically occurs during the winter, spring, fall, and late-fall (the seasonal timing of adult upstream migration corresponds with the designation for each of the four races of Chinook salmon). The most abundant of the four races are fall-run Chinook salmon. The general seasonal timing of migration and spawning by each of the races is shown in Figure 17 based on observations of fish passage upstream at the Red Bluff Diversion Dam and other fishery monitoring within the Sacramento River (Vogel and Marine 1991). Spawning by adult Chinook salmon has not been observed or documented in the area of the Proposed Project. Adult salmon migrate upstream past the project site, with subsequent migration by juvenile salmon during their emigration from the Sacramento River to the Pacific Ocean. Results of fishery sampling at the RD 108 Wilkins Slough diversion over the period from 1993 through 1996 provides useful information on the seasonal distribution and length frequencies of juvenile Chinook salmon in the project reach of the river. Results of these surveys are consistent in showing that juvenile Chinook salmon are present in greatest abundance during the spring (April - June) and during the winter (November - January). Although not included in the RD108 monitoring period, juvenile Chinook salmon also migrate downstream in the Sacramento River during the late winter (February-March). Results of monitoring at the Wilkins Slough diversion show a seasonal distribution pattern for juvenile Chinook salmon which is consistent with that observed in the CDFG monitoring at Knights Landing and USFWS monitoring at Sacramento. Habitat conditions within the Sacramento River in the vicinity of the Proposed Project, including channelized riprap stabilized levees, sand and silt substrate, and lack of shallow-water aquatic habitat limit habitat quality and availability for various lifestages of Chinook salmon. No suitable sized gravel is known to occur within the project area that would support salmon spawning or egg incubation. There is no evidence from fishery surveys that spawning by either Chinook salmon or steelhead occurs in the project area. The area of the Sacramento River would, however, provide foraging opportunities for juvenile salmon during their downstream migration. Within the project area, as well as along a majority of the Sacramento River reach, there is very little structural habitat cover or shallow-water areas for juvenile rearing. The Sacramento River in the project vicinity serves as a migratory corridor for both the upstream migration of adult salmonids and downstream migration of juveniles and to a lesser extent foraging habitat for juvenile emigrating salmon. The area is thus included in EFH for Pacific salmon. Suitable spawning and juvenile rearing habitat does occur within areas of the mainstem Sacramento River and tributaries upstream of the project site. Therefore, the river corridor serves an important function as a migratory pathway between coastal marine waters and spawning and juvenile rearing habitat located upstream of the reach. Size criteria have been established for the Sacramento River Chinook salmon races in an effort to differentiate the four races of salmon inhabiting the river (i.e. winter-run, spring-run, fall-run, and late-fall-run Chinook salmon). Although the majority of juvenile salmon collected in the RD 108 Wilkins Slough fishery monitoring were classified as fall-run, juveniles of other salmon races were also collected. Winter-run sized salmon were predominantly collected during winter sampling (November - January). Juvenile fall-run Chinook salmon, and other races, were collected predominantly during the spring (April - mid-June). 
Figure 17. Diagram of presence of the seasonal occurrence of salmonids in the Sacramento River (Source: Vogel and Marine 1991). Juvenile Chinook salmon emigrating downstream past the project reach typically range in length from approximately 27 to 150 mm. Length frequencies typically reflect three juvenile lifestages including fry (approximately 30 - 50 mm), smolts (approximately 60 - 90 mm), and yearlings (up to 150 mm). The largest numbers of juvenile salmon collected in the area have been in the smolt-size class that may reflect, in part, an artifact of the seasonality in sampling effort. Fishery sampling was not conducted as part of the RD 108 Wilkins Slough studies (Demko et al. 1994; Hanson 1996; Hanson and Bemis1997) during the late winter or early spring (e.g., mid-January - March) when salmon fry would be expected to by most abundant in the river. Although fall-run and late fall-run Chinook salmon inhabit a number of watersheds within the Central Valley for spawning and juvenile rearing, the largest populations occur within the mainstem Sacramento River, Feather River, Yuba River, American River, Mokelumne River, Merced River, Tuolumne River, and Stanislaus River. Fall-run Chinook salmon, in addition to spawning in these river systems, are also produced in fish hatcheries located on the Sacramento River, Feather River, American River, Mokelumne River, and Merced River. Hatchery operations are intended to mitigate for the loss of access to upstream spawning and juvenile rearing habitat resulting from construction of dams and reservoirs within the Central Valley in addition to producing fall-run Chinook salmon as part of the ocean salmon enhancement program to support commercial and recreational ocean salmon fisheries. Fall-run Chinook salmon also support an inland recreational fishery. 3.4.4.2 Winter-run Chinook salmon (Oncorhynchus tshawytscha) (CE/FE) Winter-run Chinook salmon are an anadromous species spending 1-3 years within the ocean before migrating upstream into the Sacramento River to spawn. The majority of adult winter-run Chinook salmon returning to spawn are three-year-olds; however, the adult population also includes two-year-old and four-year-old Chinook salmon. Adult winter-run salmon migrate upstream through San Francisco Bay and Delta during the winter and early spring months with peak migration occurring during March (Moyle 2002). Adult winter-run Chinook salmon migrate upstream within the Sacramento River with the majority of adults spawning in the reach upstream of Red Bluff. Winter-run Chinook salmon spawn within the mainstem of the Sacramento River in areas where gravel substrate, water temperatures, and water velocities are suitable. Spawning occurs during the spring and summer (mid-April through August; Moyle 2002). Egg incubation continues through the fall months. Juvenile winter-run Chinook salmon rear within the Sacramento River throughout the year, feeding primarily on aquatic insects. Juvenile winter-run salmon (smolts) migrate downstream through the lower reaches of the Sacramento River, Delta, and San Francisco Bay during the winter and early spring (December through May) as they migrate from the freshwater spawning and juvenile rearing areas into the coastal marine waters of the Pacific Ocean. The migration timing of juvenile winter-run Chinook salmon varies within and among years in response to a variety of factors including increases in river flow and turbidity resulting from winter storms. The Sacramento River mainstem in the vicinity of the Proposed Project is the primary upstream and downstream migration corridor for winter-run Chinook salmon. Within this reach of the river, winter-run Chinook salmon require relatively cool water throughout their juvenile residence, good water quality, and foraging/cover areas. With the construction of Shasta and Keswick dams winter-run salmon no longer had access to historic spawning habitat within the upper watersheds. As a result of migration blockage, spawning and juvenile rearing habitat for winter-run Chinook is limited to the mainstem Sacramento River downstream of Keswick Dam. During the mid-1960s adult winter-run Chinook salmon returns to the Sacramento River were relatively high (approximately 80,000 returning adults). However, the population declined substantially during the 1970s and 1980s. The population decline continued until 1991 when the adult winter-run Chinook salmon population returning to Sacramento River was estimated to be less than 200 fish. As a result of the substantial decline in abundance the species was listed as endangered under both the California and Federal ESAs. During the mid- and late 1990s the numbers of adult winter-run salmon returning to Sacramento River gradually increased and the trend of increasing abundance continues to present. Approximately 8200 adult winter-run salmon returned to the river to spawn in 2001, 7400 in 2002, and 8200 in 2003. As with other Chinook salmon stocks, NOAA Fisheries is continuing to evaluate the status of the winter-run Chinook salmon population and the effectiveness of various management actions implemented within the Sacramento River, Delta, and ocean to provide improved protection and reduced mortality for winter-run salmon, in addition to providing enhanced habitat quality and availability for spawning and juvenile rearing. Winter-run Chinook salmon are listed as an endangered species under both the California and Federal ESAs. The Sacramento River, including the proposed Action Area, has been designated as critical habitat for winter-run Chinook salmon by NOAA Fisheries. NOAA Fisheries has prepared a draft recovery plan for winter-run Chinook salmon. A variety of environmental and biological factors have been identified that affect the abundance, mortality, and population dynamics of winter-run Chinook salmon. One of the primary factors that have affected population abundance of winter-run Chinook salmon has been the loss of access to historic spawning and juvenile rearing habitat within the upper reaches of the Sacramento River and its tributaries as a result of the migration barrier caused by Shasta and Keswick dams. Operation of the Red Bluff Diversion Dam, which impedes adult upstream migration and vulnerability of juvenile winter-run Chinook salmon to predation mortality, has been identified as a factor affecting mortality within the river. In recent years, changes to Red Bluff Diversion Dam gate operations have been made to provide improved access for upstream and downstream migrating winter-run Chinook salmon. Water temperatures within the mainstem Sacramento River have also been identified as a factor affecting incubating eggs, holding adults, and growth and survival of juvenile winter-run Chinook salmon rearing in the upper Sacramento River. Modifications to Shasta Reservoir storage and operations and water temperature management have been implemented in recent years to improve water temperature conditions within the upper reaches of the Sacramento River. Juvenile winter-run Chinook salmon are also vulnerable to entrainment at a large number of unscreened water diversions located along the Sacramento River and within the Delta in addition to entrainment and salvage mortality at the SWP and CVP export facilities. Changes in habitat quality and availability for spawning and juvenile rearing, exposure to contaminants and acid mine drainage, predation mortality by Sacramento pikeminnow, striped bass, and other predators, and competition and interactions with hatchery-produced Chinook salmon have all been identified as factors affecting winter-run Chinook salmon abundance. In addition, subadult and adult winter-run Chinook salmon are vulnerable to recreational and commercial fishing, ocean survival is affected by climatic and oceanographic conditions, and adults are vulnerable to predation mortality by marine mammals. In recent years a number of changes have been made to improve the survival and habitat conditions for winter-run Chinook salmon. Modifications have been made to reservoir operations for instream flow and temperature management, modifications been made to Red Bluff Diversion Dam gate operations, and several large previously unscreened water diversions have been equipped with positive barrier fish screens. Changes to ocean salmon fishing regulations, and modifications to SWP and CVP export operations have also been made to improve the survival of both adult and juvenile winter-run Chinook salmon. These changes in management actions, in combination with favorable hydrologic and oceanographic conditions in recent years, are thought to have contributed to the trend of increasing abundance of adult winter-run Chinook salmon returning to the upper Sacramento River to spawn since the mid-1990s. In the immediate Action Area, recovery efforts have been focused on reductions in mortality for emigrating juveniles, through screening of large agricultural diversions. Adult and juvenile winter-run Chinook salmon utilize the river in the vicinity of the project primarily to migrate upstream and downstream within the mainstem Sacramento River. Juvenile winter-run Chinook salmon migrate from the Sacramento River through the Delta and San Francisco Bay during their downstream migration during the winter and early spring migration period. Winter-run Chinook salmon do not spawn within the Sacramento River in the vicinity of the Proposed Project. The Sacramento River has been designated by NOAA Fisheries as critical habitat for winter-run Chinook salmon. 3.4.4.3 Spring-run Chinook salmon (Oncorhynchus tshawytscha) (CT/FT) Spring-run Chinook salmon are an anadromous species, spawning in freshwater and spending a portion of their life cycle within the Pacific Ocean. Adult spring-run Chinook salmon migrate upstream into the Sacramento River system during the spring months, but are sexually immature. Adult spring-run Chinook salmon hold in deep cold pools within the rivers and tributaries over the summer months prior to spawning. Spawning occurs during the late summer and early fall (late August through October) in areas characterized by suitable spawning gravels, water temperatures, and water velocities. Eggs incubate within the gravel nests (redds) emerging as fry during the late fall and winter. A portion of the fry appear to migrate downstream soon after emerging where they rear within the lower river channels, and potentially within the Delta estuary, during winter and spring months. After emergence a portion of the spring-run Chinook salmon fry remain resident in the creeks and rear for a period of approximately one year. The juvenile spring-run Chinook salmon that remain in the creeks migrate downstream as yearlings primarily during the late fall, winter and early spring with a peak yearling migration occurring in November (Hill and Weber 1999). The downstream migration of both spring-run Chinook salmon fry and yearlings during the late fall and winter typically coincides with increased flow and turbidity associated with winter stormwater runoff. A variety of environmental and biological factors have been identified that affect the abundance, mortality, and population dynamics of spring-run Chinook salmon. One of the primary factors that have affected population abundance of spring-run Chinook salmon has been the loss of access to historic spawning and juvenile rearing habitat within the upper reaches of the Sacramento River and its tributaries and San Joaquin River as a result of the migration barriers caused by construction of major dams and reservoirs. Operation of the Red Bluff Diversion Dam, which impedes adult upstream migration and vulnerability of juvenile spring-run Chinook salmon to predation mortality, has been identified as a factor affecting mortality within the river. Water temperatures within the rivers and creeks have also been identified as a factor affecting incubating eggs, holding adults, and growth and survival of juvenile spring-run Chinook salmon. Juvenile spring-run Chinook salmon are also vulnerable to entrainment at a large number of unscreened water diversions located along the Sacramento River and within the Delta in addition to entrainment and salvage mortality at the SWP and CVP export facilities. Changes in habitat quality and availability for spawning and juvenile rearing, exposure to contaminants, predation mortality by Sacramento pikeminnow, striped bass, and other predators, and competition and interactions with hatchery-produced Chinook salmon have all been identified as factors affecting spring-run Chinook salmon abundance. In addition, subadult and adult spring-run Chinook salmon are vulnerable to recreational and commercial fishing, ocean survival is affected by climatic and oceanographic conditions, and adults are vulnerable to predation mortality by marine mammals. Spring-run Chinook salmon were historically widely distributed and abundant within the Sacramento and San Joaquin river systems (Yoshiyama et al. 1998). Spring-run Chinook salmon historically migrated upstream into the upper reaches of the mainstem rivers and tributaries for spawning and juvenile rearing. Construction of major dams and reservoirs on these river systems eliminated access to the upper reaches for spawning and juvenile rearing and completely eliminated the spring-run salmon population from the San Joaquin River system. Spring-run Chinook salmon abundance has declined substantially and the geographic distribution of the species within the Central Valley has also declined substantially. Spring-run spawning and juvenile rearing currently occurs on a consistent basis within only a small fraction of their previous geographic distribution, including populations inhabiting Deer, Mill, and Butte creeks, the mainstem Sacramento River, several other local tributaries on an intermittent basis, and the lower Feather River. Recent genetics studies have shown that spring-run like Chinook salmon returning to lower Feather River are genetically similar to fall-run Chinook salmon. Hybridization between spring-run and fall-run Chinook salmon, particularly on the Feather River where both stocks are produced within the Feather River hatchery, is a factor affecting the status of the spring-run salmon population. Spring-run Chinook salmon are listed as a threatened species under both the California and Federal ESAs. NOAA Fisheries is in the process of developing a recovery plan for Central Valley spring-run Chinook salmon. The MSCS goals for the species would be derived from this recovery plan. The Proposed Project would contribute directly to the improved protection and recovery of the species. In recent years a number of changes have been made to improve the survival and habitat conditions for spring-run Chinook salmon. Several large previously unscreened water diversions have been equipped with positive barrier fish screens. Changes to ocean salmon fishing regulations, and modifications to SWP and CVP export operations have also been made to improve the survival of both adult and juvenile spring-run Chinook salmon. Improvements in fish passage facilities have also been made to improve migration and access to Butte Creek. These changes and management actions, in combination with favorable hydrologic and oceanographic conditions in recent years, are thought to have contributed to the trend of increasing abundance of adult spring-run Chinook salmon returning to spawn in Butte Creek in recent years. Adult and juvenile spring-run Chinook salmon primarily migrate upstream and downstream within the mainstem Sacramento River in the vicinity of the Proposed Project. Adult and juvenile spring-run Chinook salmon migrate from the Sacramento River through the Delta and San Francisco Bay during their downstream migration during the late-fall, winter and early spring migration period. Spring-run Chinook salmon do not spawn within the Sacramento River in the vicinity of the Proposed Project. The Sacramento River is included in proposed critical habitat for spring-run Chinook salmon currently being evaluated by NOAA Fisheries. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||