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Additional Water for the San Joaquin River Agreement,
2000 – 2010 Supplemental EIS/EIR

7. AQUATIC RESOURCES

7.1 AFFECTED ENVIRONMENT

This chapter describes the aquatic resources of the Project Area and is structured in a format similar to the Meeting Flow Objectives for the San Joaquin River Agreement, 1999-2010, Final Environmental Impact Statement/Environmental Impact Report (Final EIS/EIR, Reclamation 1999). Information presented in the Final EIS/EIR forms the basis for the evaluation of potential impacts to aquatic resources by the Proposed Action of the current project and will be referenced throughout the chapter. This chapter will focus primarily on the Tuolumne and Merced river systems, the two tributaries to the San Joaquin River directly related to the Proposed Action. Because the Proposed Action is intended to aid in the restoration of Chinook salmon populations found in the San Joaquin River Basin, as well a promoting the general health of the ecosystem, the fall-run Chinook salmon along with steelhead/rainbow trout have been selected as the primary indicator species.

7.1.1 Habitats and Ecological Zones

The Project Area encompasses unique Ecological Zones (Reclamation 1999, Figure 3.5-1) characterized by their predominant physical habitats and species assemblages as defined by the Ecosystem Restoration Program Plan (CALFED 1997). These Ecological Zones relate directly to rivers, tributaries, and reservoirs of the San Joaquin River Basin and include:

• San Joaquin River Ecological Zone
• East San Joaquin Basin Ecological Zone
• West San Joaquin Basin Ecological Zone
• Sacramento-San Joaquin Delta Ecological Zone (Delta)

A detailed description of the demarcation lines of each Ecological Zone, the ecological features, major tributaries, and species assemblages is presented in the Final EIS/EIR.

The Tuolumne River Ecological Unit and the Merced River Ecological Unit of the East San Joaquin Basin Ecological Zone along with the Vernalis Station to Merced River Ecological Unit of the San Joaquin River Ecological Zone comprise the areas that will be discussed in this document. A description of these units as taken from the Final EIS/EIR are presented below.

7.1.1.1 Tuolumne River Ecological Unit

The Tuolumne River is the largest of the San Joaquin River tributaries and has an average annual unimpaired flow of approximately 1.8 million acre-feet. The Tuolumne has a series of dams diverting water for municipal and irrigation uses as well as the generation of electric power. In the 1920s, the City of San Francisco constructed the O’Shaughnessy Dam, forming the Hetch-Hetchy Reservoir, and another smaller dam, forming Lake Eleanor. Cherry Dam, forming Lake Lloyd, was completed in 1956. Flow down the lower Tuolumne is regulated at the New Don Pedro Dam operated by the Turlock and Modesto irrigation districts. New Don Pedro Reservoir has a maximum storage of approximately 2 million acre-feet.

La Grange Dam (built in 1893) is the upstream barrier to salmon migration. Spawning now takes place in the 25-mile reach below the dam, and juvenile rearing takes place throughout the lower river. The quantity and quality of habitat for salmon in the Tuolumne River have been degraded over the years by many factors, including loss of riparian habitat due to cattle grazing, instream gravel mining, reduced instream flows, and elimination of upstream sources of gravel recruitment.

In 1995, a settlement agreement was signed by federal and state agencies, local irrigation districts, the City and County of San Francisco, and local environmental groups as part of anamendment to Article 37 of the Federal Energy Regulatory Commission (FERC) license for the operation of the New Don Pedro Project (TID/MID 1996). One of the results of this agreement is increased flow releases from New Don Pedro as part of a strategy for recovery of Tuolumne River Chinook salmon. Currently, restoration activities are taking place on the Tuolumne River to improve habitat conditions for salmon.

7.1.1.2 Merced River Ecological Unit

The Merced River drains over 1,200 square miles of Sierra Nevada range, including the southern part of Yosemite National Park, and has an annual average, unimpaired runoff of approximately 1 million acre-feet per year (CALFED 1997). The unimpaired monthly flow peaks in April, May and June and then abruptly drops to flows of less than 100 cubic feet per second (cfs) from August through November. Flow is regulated by a series of dams that allow for flood control, irrigation and power production. The New Exchequer Dam, operated by the Merced Irrigation District, blocks off the higher elevations of the Merced River, creating Lake McClure with over one million acre-feet of storage capacity. Farther downstream, the McSwain Dam acts as an afterbay for New Exchequer Dam.

Habitat quantity and quality within the lower reaches of the Merced River are extensively degraded due to cattle grazing, removal of bank side vegetation, gravel mining in the river bed, agricultural return flows into the reaches used by juvenile salmon and trout, low flows resulting in siltation of the spawning gravel, and lack of recruitment of new spawning gravel. Low flows in the lower reaches of the Merced River result in significantly degraded fish rearing habitat. The Merced Falls and Crocker-Huffman agricultural diversion dams divert approximately 500,000 acre-feet per year. Six major diversions in the salmon spawning reach from Crocker-Huffman to Snelling deplete virtually all available flow (CALFED 1997). Currently, restoration activities are taking place on the Merced River to improve habitat conditions for salmon.

7.1.1.3 Vernalis Station to Merced River Ecological Unit

This 43-mile reach includes the confluence of the Merced, Tuolumne, and Stanislaus rivers, the main tributaries to the San Joaquin River, entering on the east side of the San Joaquin River Basin. Levees confine the river on both sides and have limited the extent of available floodplain, wetland, or shaded riverine habitat (CALFED 1997). On the west side, broad alluvial river channels and floodplains connect to the San Joaquin, but water from these rivers rarely reaches the San Joaquin. Virtually all land adjacent to the river is under intensive agricultural development.

7.1.2 Factors Affecting the Distribution and Abundance of Aquatic Resources in the San Joaquin River Basin and Bay-Delta Estuary

The aquatic resources of the San Joaquin River Basin and Delta are greatly reduced from their former status. Changes in distribution and abundance, and the causes of these changes, have been documented extensively (State Board 1995b). The factors associated with the decline in fishery resources include natural environmental variability, water development, introduction of nonnative aquatic organisms, food supply limitations, ocean harvest, pollution, and reservoir issues (DFG 1994; SFEP 1992). Each of these factors is described in greater detail in the Final EIS/EIR and is summarized below.

7.1.3 Indicator Species Population Trends

The two primary species being considered in this report as indicator species are the fall-run Chinook salmon and the steelhead/rainbow trout. These species were chosen not only for their unique value to the ecosystem, but also because the Proposed Action is directly intended to benefit Chinook salmon and would result in potential changes to flows in rivers they inhabit.

Central Valley steelhead were chosen because of their close association with Chinook salmon in the tributaries and because of their federal status as threatened species. Splittail are included because of their federal status as threatened species. Table 7-1 lists sensitive species found in the San Joaquin Basin.

Table 7-1
Sensitive Fish Species in the San Joaquin River Basin

Notes:

State: ST=threatened; SC=candidate for listing; SSC=special concern.
Federal: FT=threatened; FPT= proposed threatened.

7.1.3.1 Chinook Salmon

As described in the Final EIS/EIR, Chinook salmon are an anadromous species that spend most of their adult life in open ocean waters and return to freshwater inland streams to spawn. As adult salmon migrate upstream, water must be cool enough and have sufficient dissolved oxygen to avoid stressing the fish. If these conditions are not met, adult fish may delay their migration (Service 1995c). Adult Chinook salmon in the San Joaquin Basin typically spawn in upper reaches of the major tributaries. They select areas with gravel substrates and prefer loose, clean gravel about 1 to 4 inches in diameter, with preferred water depths ranging from 0.5 to 3.0 feet, and preferred water velocities of 1 to 3 feet per second (Service 1995c). For optimal development of embryos and survival of alevins (very young salmon with a yolk sac attached), water should contain high concentrations of dissolved oxygen and range in temperature from 41 to 55� F (Vogel and Marine 1991). Adult salmon typically do not feed while in freshwater, and all adult salmon die after spawning.

Fall-run Chinook salmon in the San Joaquin Basin return to their natal streams to spawn from mid-October through December, with most spawning occurring in November. Eggs are fertilized and buried in gravels where they develop for a period of 40 to 60 days. After the eggs hatch, the alevins remain in the gravels for up to 30 days prior to emerging. Most salmon fry (young salmon with yolk sac absorbed) emerge from the gravels and rear in the streams from mid-January through March prior to emigrating back to the ocean as smolts from April through early June. In high flow years, fry may be displaced downstream or begin to migrate downstream earlier than in other years. For example, during the high flows of 1998, many fall-run fry emigrated from the San Joaquin tributaries to the lower San Joaquin River and Delta in January and February, according to the National Marine Fisheries Service (NMFS). Chinook salmon from the San Joaquin Basin spend 2 to 4 years maturing at sea before returning to spawn.

Four separate races of Central Valley Chinook salmon have been identified: the fall, late-fall, winter, and spring runs, based on the timing of the upstream migration. Spring-run Chinook salmon in the San Joaquin River Basin became extinct following the construction of impassible dams on major tributaries. Currently, the entire Chinook salmon population in the San Joaquin River is made up of fall-run Chinook salmon that spawn between October and December (Service 1995b). Small numbers of spawners have been observed in the Tuolumne River as late as February. Although it has been suggested that these represent a distinct late-fall run, these late-fall salmon are more usually viewed as stragglers, or strays from other river systems (ORNL 1994; Yoshiyama and Moyle 1995).

San Joaquin fall-run Chinook are usually regarded as forming a distinct stock, on the basis of geographical distribution and life-history timing. Evidence of genetic separation between Sacramento and San Joaquin fall Chinook salmon is weak. Tag returns indicate straying from the Sacramento River system to the San Joaquin (Service 1996a). Mixing of genetic stocks has also occurred due to the initial use of Stanislaus River brood stock at the Merced River Fish Facility, and the outplanting of facility-reared smolts and yearlings in the Stanislaus, Tuolumne, and San Joaquin rivers, and in the Delta (Service 1995b).

Population Trends

As described in the Final EIS/EIR, the annual spawning escapement of fall-run Chinook salmon in the San Joaquin River Basin has been estimated for most years since 1940, but early estimates are often incomplete and based on subjective methods (Reclamation and DWR 1986). Methods for estimating the number of returning adults have improved over the last five decades. Recent spawning escapement of Chinook salmon in the Merced and Tuolumne rivers is highly variable.

Causes of decline for Chinook salmon populations have been attributed to isolation from historical spawning areas; loss of habitat; impaired conditions for smolt emigration, including decreasing flows and increased water temperatures; legal and illegal harvest; introgression with hatchery stocks; presence of pesticides and agricultural chemicals; and entrainment of smolts in State Water Project/Central Valley Project water export system (Service 1995c). All the major rivers of the San Joaquin River Basin have dams at fairly low elevations that are impassable to salmon, preventing their migration into the tributary streams of the Sierra Nevada mountains.

Streamflow is an important factor affecting the productivity of the remaining habitat in the basin. Fall flows provide access to the spawning gravels and may be important in attracting returning spawners to the San Joaquin system. Spring flows may stimulate and transport migrating smolts out of the tributaries, provide suitable conditions for migrants in the San Joaquin River, and maintain acceptable water temperatures for juveniles (State Board 1995b). Increased flows for the benefit of salmon have been negotiated on the Stanislaus River, as part of the New Melones Interim Operation Plan, and on the Tuolumne River, as part of the reevaluation of instream flows from the New Don Pedro Project by the FERC. Increased flows are also being negotiated for the Merced River (CALFED 1997).

Stream temperatures are recorded at U.S. Geological Survey and California Department of Water Resources gauging stations located in the San Joaquin Basin. In addition, the California Department of Fish and Game (DFG) is compiling a database of stream temperatures from a series of thermographs (temperature recorders) located in each ofthe major tributaries (DFG 1995). Turlock Irrigation District and Modesto Irrigation District have compiled a database of their thermograph data for the Tuolumne River and San Joaquin River. Temperature models that show predicted water temperatures under various flow conditions have also been developed, or are being developed, for each major tributary.

Since 1970, the Merced River run has been sustained in part by production of yearling fall-run salmon at the Merced River Fish Facility (DFG 1987). Because of low flows on the Merced, there has been a tendency for returning adult salmon to stray into agricultural drainage ditches, especially at Mud and Salt sloughs, and lose the opportunity to spawn. In the fall of 1991, an estimated 35 percent of the San Joaquin River salmon strayed into westside canals (DFG 1993). Since 1992, physical barriers have been installed to keep the migrating adults in the Merced River and out of the sloughs.

7.1.3.2 Steelhead/Rainbow Trout

Steelhead/rainbow trout have a broad range of life history strategies that include strains that always emigrate to the ocean and other strains that generally do not. Strains that emigrate to the sea are called steelhead, and strains that remain resident in freshwater are termed rainbow trout. Both adult steelhead and rainbow trout typically survive after spawning, though it is rare that adult steelhead will spawn more than twice. Studies have shown there to be little or no genetic differences between steelhead and rainbow trout inhabiting the same stream system (IEP 1998; NOAA 1996). Juvenile steelhead in streams are similar in appearance to juvenile rainbow trout. Adult steelhead are generally larger than adult rainbow trout and display a more uniform and silvery color upon entering fresh water.

Steelhead have a life history similar to salmon and much of their habitat requirements are also similar. The primary difference is that juveniles will remain in the tributaries for at least 1 year before smolting. The majority of spawning for winter-run steelhead occurs between December and April. Steelhead spawning can occur in water depths from 0.5 to 4 feet, water velocities from 0.75 to 4.5 feet per second, and utilizing gravels from 0.25 to 5 inches in diameter. Water temperatures between 50 to 60 degrees Fahrenheit are generally required for spawning and egg development (Wang 1986). Steelhead eggs are deposited in gravels and hatch in 30 to 90 days. Fry generally emerge during April and May, and juvenile steelhead will spend 1 to 3 years in freshwater before emigrating to the ocean, where they will spend 2 to 4 years before returning to spawn. Adults that survive spawning return to the ocean from April through June. Juveniles will usually emigrate from November through May.

Presently, winter-run steelhead are the only race found in the Central Valley and are native to the Sacramento and San Joaquin river basins (Reclamation 2000d). The major populations of Central Valley steelhead currently occur in the Sacramento River Basin. In the San Joaquin River Basin, steelhead populations have been reduced to remnant levels. Evidence of a distinct anadromous run of steelhead in the Stanislaus River is controversial and some disagreement exists as to the exact origin of these fish.   Past monitoring efforts have been inconclusive in determining the presence or absence of steelhead populations in the Tuolumne and Merced rivers, or the San Joaquin River upstream of the Stanislaus River. Resident rainbow trout can be found in the San Joaquin River, its tributaries, the Delta, and San Joaquin Basin reservoirs.

Central Valley steelhead were listed by the federal government as a threatened species in March 1998. Designated critical habitat habitat for Central Valley steelhead was established in February 2000.  Included as part of the critical habitat are all river reaches potentially accessible to steelhead in the San Joaquin River and its tributaries. Excluded are areas of the San Joaquin River upstream of the Merced River confluence. In designating critical habitat, protection is granted to essential features of the habitat including; spawning sites, food sources, water quality and quantity, and riparian vegetation. With designation of critical habitat, Federal agencies are provided with a clear indication as to which areas may require special management considerations.

Population Trends

There are a variety of indications that self-sustaining stocks of rainbow trout continue to exist in the San Joaquin River system. Evidence is not as clear, however, concerning steelhead. DFG records contain reference to a small population characterized as emigrating steelhead smolts that are captured at the DFG Kodiak trawl survey station at Mossdale on the lower San Joaquin River each year. A few ripe rainbow trout that could be large enough to be small steelhead enter the fish traps at the Merced River Fish Facility every year.

Although it is likely that steelhead once inhabited most of the streams used by Chinook salmon for spawning, they probably traveled farther upstream into smaller tributaries (Moyle et al. 1996). These passages are now blocked by dams. There is also little or no historic record of escapemen available. Current annual escapements of steelhead steelhead in the San Joaquin River Basin do not exist due to the long-term scarcity or absence of steelhead in the basin.

Because of their similarity to salmon, many of the same conditions that have caused the decline of salmon have also affected steelhead. These conditions include isolation from historic spawning areas, loss of habitat, and impaired conditions for adults and juveniles, including decreasing flows and increased water temperatures, blockages, and entrainment.

Genetic studies have shown that in general, the larger the geographic distance between populations is, the more genetic differences are shown (NOAA 1997).

Efforts using genetic sampling in the San Joaquin River Basin to determine differences or similarities  between steelhead and resident rainbow trout found in the San Joaquin River Basin to those from the Sacramento River Basin, coastal populations, and hatchery production are being developed along with comprehensive monitoring plans and habitat restoration programs to better assess the distribution and abundance of steelhead (IEP 1998).

7.1.3.3 Splittail

The splittail is a large minnow endemic to the Bay-Delta Estuary and the Sacramento and San Joaquin basins. It was listed under the federal Endangered Species Act as a threatened species in February 1999. Once found throughout low elevation lakes and rivers of the Central Valley, from Redding to Fresno, this species is now confined to the lower reaches of the Sacramento and San Joaquin rivers, the Delta, Suisun and Napa marshes, and tributaries of north San Pablo Bay. Although the splittail is generally considered a freshwater species, the adults and subadults have an unusually high tolerance for saline waters for a member of the minnow family. Therefore, the splittail is often considered an estuarine species also.

The splittail has a high reproductive capacity, can live 5 to 7 years, and generally begin spawning at 1 to 2 years of age. Spawning is triggered by increasing water temperatures and day length, and occurs over beds of submerged vegetation in slow-moving stretches of water, such as flooded terrestrial areas and dead-end sloughs. Year class strength has been highly variable over the last decade, with particularly strong year classes associated with seasonally flooded wetlands that provide optimum spawning and larval rearing habitat. Adults spawn from March through May in sloughs of the Delta, Napa Marsh, Suisun Marsh, and on the inundated floodplains of large rivers during Wet years. Hatched larvae remain in shallow, weedy areas until they move to deeper offshore habitat later in the summer. Young splittail may occur in shallow and open waters of the Delta and San Pablo Bay, but they are particularly abundant in the northern and western Delta (DFG 1992a; DWR 1992).

Splittail are benthic foragers that feed extensively on opossum shrimp (Neomysis mercedis) and opportunistically on earthworms, clams, insect larvae, and other invertebrates. They are preyed upon primarily by striped bass.

Population Trends

Population levels appear to fluctuate widely from year to year, but since 1980 splittail numbers have declined steadily, reaching their lowest recorded numbers in 1994. The overall decline in splittail numbers can be attributed to a variety of factors, including modification of spawning habitat, changed estuarine hydraulics, climatic variation, toxic substances, introduced species, predation, and exploitation (NHI 1992). Splittail have disappeared from much of their native range because dams, diversions, and agricultural development have eliminated or drastically altered much of the lowland habitat these fish once occupied. Splittail foraging and spawning habitat has been lost due to land reclamation activities (CUWA 1994; DFG 1992a). The construction of levees where floodwaters formerly inundated low lands has prevented the splittail from moving into habitat critical for its spawning and early life history.

Successful reproduction is strongly associated with high outflows preceding, during, and following spawning, as demonstrated by high correlation’s between abundance of splittail in the fall mid-water trawl survey and various monthly combinations of Delta outflow from the previous winter through early summer (DFG 1992b). The strong correlation of the abundance of young Sacramento splittail with freshwater outflows during the late winter and spring accounts, in part, for the observed decline in juvenile production during the recent drought period (NHI 1992; DFG 1992b; Hanson 1994).

7.1.4 Summary

Aquatic resources in the San Joaquin River Basin are varied and form complex interactions of species assemblages and habitats. Water development projects, the introduction of nonnative species, and the creation of dams and large reservoirs, along with many other factors, over the past century have dramatically altered the habitats and reduced the abundance of fish species such as Chinook salmon and steelhead/rainbow trout.

By characterizing the factors affecting the recovery of these indicator species within the Project Area, the potential impacts of the Project can be evaluated. Specific habitats, such as spawning, rearing, and those used for migration of anadromous species, have been identified as being vital to the species of prime importance and to those that are considered indicators of a functional ecosystem. Factors identified as manageable and that contribute to the overall ability of a species to recover include habitat restoration, streamflow, and water quality.

7.2 ENVIRONMENTAL CONSEQUENCES AND MITIGATION MEASURES

This section assesses the impacts to aquatic resources that could be affected by the Proposed Action.

7.2.1 Key Impact Issues and Evaluation Criteria

The aquatic resources within the Project Area have been defined in terms of existing habitats represented by unique Ecological Zones as described in Section 7.1.1. Riverine systems that provide spawning and rearing habitat, as well as passage into and out of the Delta for anadromous species of fish, form the basis for the impact analysis. Also considered are the reservoir habitats provided by two major reservoirs in the Project Area. The estuarine habitats of the Delta are included only to the extent that they would be impacted indirectly by the cumulative effects of the Proposed Project.

Indicator fish species that occur within the Project Area during one or more environmentally sensitive stages of their life cycle, were chosen as important representatives of aquatic ecosystem responses to changes caused by the Proposed Project. Fall-run Chinook salmon were selected as the species of prime interest because water contributed by the Proposed Project is designated to provide protection for this species in the San Joaquin River Basin. The analysis of Chinook salmon also encompasses steelhead trout, an anadromous species closely related to salmon.

The criterion used to determine the level of riverine impact associated with the implementation of the Project is the same as that used in the Final EIS/EIR. This procedure is based on the average percentage changes to streamflow as compared to base conditions. Thresholds of impact significance were established as follows:

• greater than +10 percent changeBeneficial
• less than �10 percent changeNot significant
• between -11 and -25 percent changeLess than significant
• greater than -25 percent changePotentially significant or Significant

A complete description of the criteria used can be found in the Final EIS/EIR. An updated hydrologic analysis covering the same 71-year period (1922 through 1992) used in the 1999 Final EIS/EIR was again used to assess the differences between the No Action and Proposed Action alternatives. The current minimum flow requirements, established by FERC for the Tuolumne River, and by FERC and the Davis-Grunsky contract for the Merced River, were adhered to (Reclamation 1999). The established range of water year types continue to include (1) Critically Dry, (2) Dry, (3) Below Normal, (4) Above Normal, and (5) Wet. The No Action Alternative represents the baseline conditions for comparing the Project alternatives.

7.2.2 Environmental Consequences

The Proposed Project would provide additional streamflow in the form of supplemental spring pulse flows in either the Tuolumne or Merced rivers and the San Joaquin River below the river from which the water is released. The Project would provide water through releases from reservoir storage and releases would only occur during conditions that result in "double-step years" for the Water Years 2001 through 2010. A complete description of the Proposed Project can be found in Chapter 2 of this document.

7.2.2.1 Habitats and Ecological Zones

Only portions of two of the four Ecological Zones presented in Section 7.1.1 would have the potential for impacts from the Proposed Action, and as stated in the Final EIS/EIR, no criterion exists to determine the significance of impacts across all of the habitats occurring with the zones on an ecosystem level. Therefore, assessments of impacts within these zones are made through the use of indicator aquatic species.

No Action

The No Action Alternative results in no changes to existing conditions. The No Action Alternative includes the Vernalis Adaptive Management Plan (VAMP) 31-day pulse flows during April and May, flow releases in accordance with various operating plans, settlement agreements, and FERC requirements now in place for the San Joaquin River Basin. Because No Action represents the baseline, no impacts are identified for implementation of this alternative.

Proposed Action

Of the four Ecological Zones within the Project Area, only portions of the San Joaquin River and East San Joaquin Basin zones would be directly affected by the Project. The Project would provide flows in addition to those from the base case in April or May, with either the Tuolumne River or Merced River experiencing the increases. Periodic reductions in flow during Above Normal and Wet water year types would also occur as a result of reservoir recharge. Because no criteria exist for assessing impacts to Ecological Zones, no determination of significance can be made.

7.2.2.2 Factors Affecting the Distribution and Abundance of Aquatic Resources in the San Joaquin River Basin and Bay-Delta Estuary

A list of factors that affect the distribution and abundance of aquatic resources in the Project Area was identified in Section 7.1.2 and described in the Final EIS/EIR. These factors include (1) Natural environmental variability, (2) Water development, (3) Introduced species, (4) Food supply, (5) Harvest, (6) Pollution, and (7) Reservoirs. Of these factors, only Pollution (Water Quality) and Reservoirs would be directly impacted by the Project. Changes in surface water quality are discussed in Section 4.2.2. No selected indicator species relate to reservoir issues. Impacts to reservoirs are discussed in Chapters 8, 9 and 10.

No Action

The No Action Alternative results in no changes to existing conditions.

Proposed Action

Implementation of the Proposed Action under either the April or May scenario for either the Tuolumne or Merced rivers would result in only slight benefits to water quality due to small increases in flow at Vernalis and would, therefore, not adversely affect aquatic resources.

7.2.2.3 Indicator Species

The indicator fish species provide a link between effects on individual organisms and consequences at the population, community, and aquatic ecosystem or "ecological unit" (see Section 7.1.1) levels of biological organization. The assessment of impacts to selected indicator species is based on the amount of change in streamflow. Changes in flow relate directly to the amount and quality of available physical habitat for various life stages of the indicator species and hence to its population distribution, numbers, and dynamics (change in distribution and numbers through time). To transform the magnitude of change in flow to impacts, threshold values were identified for beneficial, not significant, less-than-significant, and potentially significant changes (see Section 7.2.1). Table 7-2 shows the average monthly percent change in flow (cfs) by water year type for the Tuolumne and Merced rivers along with a specific reach of the San Joaquin River. Table 7-2 was created by first calculating the percentage of the change in flow from base conditions, represented by the No Action Alternative, to the various April and May scenarios for the Tuolumne and Merced rivers representing the Proposed Action, using results from the 71-year hydrologic analysis. These percentages were then averaged by water year type.

The selection criteria is based on the average percent change in flow between No Action and Proposed Action and is tightly linked to individual flow measurements and their relative accuracy. Statistically, the differences between meaningfully paired comparisons (i.e., Proposed Action minus No Action) have a distribution similar to the original data which can be characterized by a variance and a mean. This transformation of the data (the process of calculating differences) preserves the information contained in the original data set. Consequently, the average percent change in flow is chosen as the criterion to assess impacts. This choice maintains the close, meaningful relationship between the selected assessment criteria and individual flow measurement (Reclamation 1999).

Table 7-2 - Average Percent Changes in cfs for Rivers with April/May Project Compared with Base Case by Water Year Type
Table 7-2 (continued)
Table 7-2 (concluded)

Optional releases are not permitted to fall below established minimum flow requirements. The streamflow changes associated with the Proposed Action generally occur during periods of high flow water year types. For more discussion of the assessment methodology, see Reclamation (1999), Appendix H, Response 11 to Comment 11 by NMFS.

Table 7-3 shows the individual changes in flow predicted from the hydrologic analysis under the various scenarios of the Proposed Action when compared to No Action. These flows are provided for information purposes only and have not been used in the determination of impacts. Note that the percentage difference between the individual flow changes listed in Table 7-3 are used in the calculation of the average percent change in flows listed in Table 7-2.

Chinook Salmon

As described in the Final EIS/EIR, various life stages of fall-run Chinook salmon can be present in the San Joaquin River Basin during all months of the year, although the number of individuals may vary considerably by stream and by year.

Pulse flows can mimic natural storm events that increase streamflow and stimulate emigration of Chinook salmon smolts. Pulse flows usually result in increased turbidity and lower water temperatures. Both of these factors serve to reduce the impact of predation on emigrating smolts. Additionally, pulse flows may provide the necessary means to increase the survival of Chinook salmon smolts by moving them out of tributaries and through the Delta in years when water temperature increases during the summer months result in elimination or reduction of suitable rearing habitat. The VAMP is an experimental study to determine the proper level for the pulse flows.

No Action. The No Action Alternative represents existing conditions. The No Action Alternative includes fall attraction flow and spring pulse flow releases in accordance with VAMP as described in the Final EIS/EIR, along with the various operating plans, settlement agreements, and FERC requirements now in place for the San Joaquin River Basin. These flows are intended to benefit adult and smolt life stages of Chinook salmon. Because No Action represents the baseline, no impacts are identified for implementation of this alternative.

Proposed Action. Analysis of the Proposed Action can be subdivided into effects that occur under (1) supplemental water from the Tuolumne River in April/May, or (2) supplemental water from the Merced River in April/May. Results for the Tuolumne River, Merced River, and San Joaquin River (from Vernalis to the Merced River confluence) show no significant changes in flow as a result of implementing the Proposed Action (Table 7-2). The Merced River shows beneficial flow increases in April in Dry water year types when supplemental releases occur in the Merced River during April, and in May in Below Normal water year types when supplemental releases occur in the Merced River during May. The increases shown under these conditions are viewed as beneficial to fall-run Chinook salmon smolts emigrating out of the river towards the Delta.

Decreases in flow as a result of reservoir recharge for the Tuolumne, Merced, and San Joaquin rivers (from Vernalis to the Merced River confluence) are also shown as not significant. These decreases would occur primarily in Above Normal and Wet water year types during the months of December through March, with the exception of the Merced

Table 7-3

Predicted Changes in Flow for the Tuolumne and Merced Rivers from a 71-Year Hydrologic Model Analysis of VAMP Conditions

Table 7-3 (concluded)

River, in which some decreases would also occur during January and February of Dry water years (Table 7-2).

The generally small average percentage changes in flow shown in Table 7-2 reflect the relatively low frequency of occurrence and magnitude of the supplemental releases.

The inherent possibility for rapid increases and decreases in river height (stage) associated with implementing pulse flows and potentially impacting salmon by stranding juveniles or dewatering of redds (spawing gravels) is mitigated for in the Final EIS/EIR by development of ramping guidelines governing the release of pulse flows to ensure and maximize the protection of salmon. The same ramping rates would apply to the supplemental water.

Note that the effects analysis considers effects only when supplemental water is delivered through either the Tuolumne or Merced river system. While this scenario serves to demonstrate the extreme, other release patterns using a combination of the two rivers may result in diminished individual flow changes for any one river while still meeting VAMP requirements.

Steelhead/Rainbow Trout

The presence of a distinct anadromous steelhead population in the San Joaquin River Basin is controversial, but in general , steelhead are thought to occur mainly as a small, remnant population in the Stanislaus River. Genetic sampling of rainbow trout populations in the Stanislaus, Tuolumne, and Merced rivers is currently being developed in an attempt to determine the origin of these fish and compare them with known steelhead populations from the Sacramento River Basin and other areas. Designated critical habitat has been established for Central Valley steelhead and includes the Stanislaus, Tuolumne and Merced rivers (Federal Register 2000).

Steelhead populations that may occur in the Stanislaus River are excluded from analysis because of the low frequency of occurrence involving operational releases in the Stanislaus under the Proposed Action. Only one instance is shown over the 71-year hydrologic model analysis (for either the Tuolumne (May) source or Merced (April) source that requires additional release/refill from the Stanislaus River for the purpose of meeting water quality objectives at Vernalis. The Proposed Action is predominately achieved through releases on either the Tuolumne River or Merced River.

Due to the designation of critical habitat for steelhead in the Tuolumne and Merced rivers and the potential for steelhead populations to exist there, an impact analysis for steelhead in these river systems is provided.

Steelhead use habitat in much the same way as fall-run Chinook salmon. The main differences between steelhead and fall-run Chinook are: (1) adult steelhead begin their spawning migration slightly later than Chinook and, therefore, stages of development for the eggs and juveniles will be approximately one month later than Chinook; (2) adult steelhead will not necessarily die after spawning, resulting in some adults remaining in the rivers through June; and (3) young steelheadwould likely remain in the rivers throughout their first summer. Because of these traits, juvenile steelhead are less likely to be influenced to emigrate by spring pulse flows and are more likely to be influenced by summer flows.

No Action. The No Action Alternative results in no changes to existing conditions. The No Action Alternative includes fall attraction flow and spring pulse flow releases in accordance to VAMP as described in the Final EIS/EIR, along with the various operating plans, settlement agreements, and FERC requirements now in place for the San Joaquin River Basin. The No Action Alternative includes flow releases for the Stanislaus River in accordance with the New Melones Interim Plan of Operation. Because No Action represents the baseline, no impacts are identified for implementation of this alternative.

Proposed Action. Analysis of the Proposed Action can be subdivided into effects that would occur under (1) supplemental water from the Tuolumne River in April/May, or (2) supplemental water from the Merced River in April/May. Results for the Tuolumne River, Merced River, and San Joaquin River (from Vernalis to the Merced River confluence) show no significant changes in flow as a result of implementing either scenario of the Proposed Action (Table 7-2). Decreases in flow as a result of reservoir recharge are also shown as not significant and occur primarily in Above Normal and Wet water year types during the months of December through March, with the exception of the Merced River when some decreases also occur during January and February of Dry eater years (Table 7-2). No changes in flow conditions during summer months (June, July, August) are shown with the exception of minor decreases in the Merced River during August in Above Normal water years.

The Merced River shows small beneficial flow increases in April in Dry water year types when supplemental releases occur in the Merced River during April, and in May in Below Normal water year types when supplemental releases occur in the Merced River during May. The increases shown under these conditions are viewed as beneficial to juvenile steelhead rearing in the river.

The generally small average percentage changes in flow shown in Table 7-2 reflect the relatively low frequency of occurrence and magnitude of the supplemental releases.

The inherent possibility for rapid increases and decreases in river height (stage) associated with implementing pulse flows and potentially impacting steelhead by stranding juveniles or dewatering redds would be mitigated for in the Final EIS/EIR by development of ramping guidelines governing the release of pulse flows to ensure and maximize the protection of both salmon and steelhead. The same ramping rates would apply to the supplemental water.

Note that the effects analysis considers effects only when supplemental water is delivered through either the Tuolumne or Merced river system. While this scenario serves to demonstrate the extreme, other release patterns using a combination of the two rivers may result in diminished individual flow changes for any one river while still meeting VAMP requirements.

Splittail

Splittail may enter the San Joaquin River Basin to spawn during the winter and spring months. They require shallow, near shore areas or inundated floodplains for spawning and juvenile rearing. The young then continue to rear in these areas for a period of a few weeks up to 1 year (Sommer et al. 1997). This native species is found in the lower reaches of the San Joaquin River and its major tributaries and also occurs in the Delta and the Sacramento River Basin.

No Action. The No Action Alternative results in no changes to existing conditions. The No Action Alternative includes fall attraction flow and spring pulse flow releases in accordance to VAMP as described in the Final EIS/EIR, along with the various operating plans, settlement agreements, and FERC requirements now in place for the San Joaquin River Basin with no specific management of flows to benefit splittail. Because No Action represents the baseline, no impacts are identified for implementation of this alternative.

Proposed Action. The Tuolumne River, Merced River, and San Joaquin River (from Vernalis to the Merced River confluence) would show no significant changes in flow as a result of implementing the Proposed Action (Table 7-2). The Merced River shows beneficial flow increases in April in Dry water year types when supplemental releases occur in the Merced River during April, and in May in Below Normal water year types when supplemental releases occur in the Merced River during May. The increases shown under these conditions are viewed as potentially beneficial to splittail spawning in the river.

Decreases in flow as a result of reservoir recharge are also shown as not significant and would occur primarily in Above Normal and Wet water year types during the months of December through March, with the exception of the Merced River when some decreases would also occur during January and February of Dry water years (Table 7-2).

The generally small average percent changes in flow shown in Table 7-2 reflect the relatively low frequency of occurrence and magnitude of the supplemental releases.

7.2.3 Impact Summary and Mitigation of Impacts

7.2.3.1 Habitats and Ecological Zones

Proposed Action

• No criteria exist for assessing impacts to Ecological Zones, so no determination of significance can be made. Assessment of impacts within these zones are made through the use of indicator species. No mitigation is proposed.

7.2.3.2 Factors Affecting the Distribution and Abundance of Aquatic Resources in the San Joaquin Basin and Bay-Delta Estuary

Proposed Action

The only factor that would be directly impacted by the Project is water quality. Implementation of the Proposed Action would have no significant impact on water quality and would, therefore, not adversely affect aquatic resources. No mitigation is required.

7.2.3.3 Indicator Species

Chinook Salmon

Proposed Action

The Proposed Action could result in flow changes for the Tuolumne River, Merced River, and portions of the San Joaquin River that are not considered to be significant. No mitigation is required.

Beneficial impacts to fall-run smolts emigrating out of the river towards the Delta are shown for the Merced River in April during Dry water year types with supplemental releases in the Merced River during April, and in May during Below Normal water year types with supplemental releases in the Merced River during May.

Steelhead/Rainbow Trout

Proposed Action

• The Proposed Action could result in flow changes for the Tuolumne River, Merced River, and portions of the San Joaquin River that are not considered to be significant. No mitigation is required.
• Beneficial impacts to juvenile steelhead rearing in the river are shown for the Merced River in April during Dry water year types with supplemental releases in the Merced River during April, and in May during Below Normal water year types with supplemental releases in the Merced River during May.

Splittail

Proposed Action

• The Proposed Action could result in flow changes for the Tuolumne River, Merced River, and portions of the San Joaquin River that are not considered to be significant. No mitigation is required.
• Potential beneficial impacts to splittail spawning are shown for the Merced River in April during Dry water year types with supplemental releases in the Merced River during April, and in May during Below Normal water year types with supplemental releases in the Merced River during May.