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

6. TERRESTRIAL BIOLOGY

6.1 Affected Environment

This section describes the existing vegetation and wildlife in San Joaquin Valley with emphasis on biological communities along the San Joaquin River and its tributaries. Sensitive resources such as wetlands and special-status species are specifically addressed. Information for this section is primarily derived from the Meeting Flow Objectives for the San Joaquin River Agreement, 1999-2010, Final Environmental Impact Statement/Environmental Impact Report (Final EIS/EIR, Reclamation 1999).

6.1.1 Vegetation Types

A wide variety of vegetation types occur along the margins of the San Joaquin River and its tributaries. The species composition and architecture of these riparian vegetation types are a function of substrate and the hydrology. The relationship between vegetation and hydrology has been previously described in detail in the Final EIS/EIR (Reclamation 1999) and is not repeated here.

The Proposed Project could release up to 47,000 acre-feet of supplemental water into the San Joaquin River. This water would originate from either the Tuolumne River or the Merced River. These releases would only affect vegetation within the immediate area of the rivers and are not expected to have any effects on vegetation growing outside the riparian corridor. The boundary limiting the evaluation scope is defined according to the limits described in the Final EIS/EIR (Reclamation 1999). These limits are defined as the channel area below the floodplain called the bankfull channel.

Riparian vegetation types along the San Joaquin, Tuolumne, and Merced rivers are identified in this section based on Holland’s classifications (Holland 1986). The following riparian vegetation types are identified:

• Coast and Valley freshwater marsh
• Great Valley willow scrub
• Great Valley cottonwood-willow riparian forest
• Great Valley cottonwood riparian forest
• Great Valley mixed riparian forest
• Great Valley oak riparian forest
• Southern willow scrub
• Southern cottonwood-willow riparian forest
• Buttonbush scrub

The Coast and Valley freshwater marsh community includes most of the riparian vegetation types dominated by herbaceous species. Typical species of this vegetation type include cattail (Typha spp.), bulrush (Scirpus spp.), duckweed (Lemna spp.), mosquito fern (Azolla filiculoides), and pondweed (Potamogeton spp.). Riparian vegetation types dominated by trees and shrubs are included in the Great Valley willow scrub, Great Valley cottonwood-willow riparian forest, Great Valley cottonwood riparian forest, Great Valley mixed riparian forest, Great Valley oak riparian forest, southern willow scrub, southern cottonwood-willow riparian forest, and buttonbush scrub communities. Typical tree and shrub species include Fremont cottonwood (Populus fremontii), arroyo willow (Salix lasiolepis), Goodding’s black willow (Salix gooddingii), narrowleaf willow (Salix exigua), shining willow (Salix lucida ssp. lasiandra), box elder (Acer negundo), Oregon ash (Fraxinus latifolia), white alder (Alnus rhombifolia), buttonbush (Cephalanthus occidentalis var. californicus), and valley oak (Quercus lobata).

6.1.2 Wildlife

Riparian vegetation types are important breeding, foraging, roosting, and resting habitat for many birds, reptiles, small mammals, and amphibians. Representative bird species include waterfowl associated with the Pacific Flyway that overwinter in valley wetlands, upland game birds such as doves, pheasant, quail, and chukar, and shorebirds such as terns, plovers, sandpipers, egrets, and gulls. Riparian vegetation provides nesting and foraging habitat for raptors such as Swainson’s hawks, red-tailed hawks, bald eagles, prairie falcons, and owls and passerines such as warblers, blackbirds, sparrows, flycatchers, and swallows.

Reptiles and amphibians that utilize riparian vegetation types include turtles, snakes, frogs, and salamanders. Many of these species are aquatic or semiaquatic and lay open, nonshelled eggs in water or very moist areas provided by rotting logs or dense leaf litter in riparian areas. Many of reptile and amphibian species depend on riparian areas for dispersal corridors and linkages between populations.

A number of mammals are transient between upland and riparian habitats along the San Joaquin River and its tributaries. These species include the red bat, the Brazilian free-tailed bat, Virginia opossum, Botta’s pocket gopher, raccoon, striped skunk, and bobcat. Muskrats are abundant in riparian areas, especially in freshwater marsh communities. Muskrats are mainly herbivorous and prefer roots and basal stems of plants but also consume crayfish, mollusks, turtles, and fish.

6.1.3 Special-Status Species

A number of rare, threatened, and endangered species were historically associated with riparian areas along the San Joaquin, Tuolumne, and Merced rivers. These special-status species are listed below:

• Valley elderberry longhorn beetle (Desmocerus californicus dimorphus)
• California red-legged frog (Rana aurora draytonii)
• Giant garter snake (Thamnophis couchi gigas)
• Western pond turtle (Clemmys marmorata)
• Bald eagle (Haliaeetus leucocephalus)
• Bank swallow (Riparia riparia)
• California yellow warbler (Dendroica petechia brewsteri)
• Cooper’s hawk (Accipiter cooperii)
• Greater sandhill crane (Grus canadensis tabida)
• Loggerhead shrike (Lanius ludovicianus)
• Sharp-shinned hawk (Accipiter striatus)
• Swainson’s hawk (Buteo swainsoni)
• Western least bittern (Ixobrychus exilis hesperis)
• White-tailed kite (Elanus leucurus)
• Willow flycatcher (Empidonax traillii brewsteri)
• Riparian woodrat (Neotoma fuscipes riparia)
• Riparian brush rabbit (Sylvilagus bachmani riparius)

Table 6-1 summarizes the current status of these species under the federal and state Endangered Species Acts.

6.2 Environmental Consequences and Mitigation Measures

This section evaluates and describes potential impacts to riparian vegetation, associated wildlife species, and terrestrial special-status species. Mitigation measures are not required because there are no potentially significant impacts. The discussion of impact is divided into three sections: riparian vegetation, wildlife species, and special-status species.

6.2.1 Key Impact Issues and Evaluation Criteria

Impact issues and evaluation criteria are based on the California Environmental Quality Act guidelines for biological resources, state and federal laws that regulate impacts to special-status species and wetlands, and are consistent with the Final EIS/EIR (Reclamation 1999). Impacts to terrestrial biological resources are assessed as "significant," "potentially significant," "less than significant," and "no impact."

6.2.1.1 Riparian Vegetation

Key issues for riparian vegetation are those that cause a positive or negative change to riparian vegetation health or survival. Where possible, impacts of stress are differentiated from impacts causing mortality to riparian vegetation. Adverse impacts on riparian vegetation (including wetlands) are considered significant if the Proposed Project would:

• Disturb a substantial portion of the vegetation type within a local region, and natural or enhanced regeneration could not restore this vegetation to its preconstruction condition within 3 to 5 years.

Table 6-1

Special-Status Wildlife Species that May Occur in the Project Area

Table 6-1 (continued)

Table 6-1 (concluded)

Notes: Status

Federal

E = Listed as endangered under the federal Endangered Species Act
T = Listed as threatened under the federal Endangered Species Act
PE = Proposed for federal listing as endangered under the federal Endangered Species Act
C = Candidate for listing under the federal Endangered Species Act
SC = U.S. Fish and Wildlife Service species of concern
-- = No status

State

E = Listed as endangered under the California Endangered Species Act
T = Listed as threatened under the California Endangered Species Act
SSC = California Department of Fish and Game species of special concern
P = Fully protected in California
-- = No status

• Result in the long-term (more-than-5-year) substantial reduction or alteration of unique, rare, or special concern vegetation types or natural communities.
• Lead to the expanded range of existing invasive exotic weed species or soil pests so that they interfere with successful revegetation of natural communities.
• Fill or alter a wetland, resulting in long-term change in hydrology, soils, or the composition of vegetation.

6.2.1.2 Wildlife

Potential wildlife impacts would be limited to species that utilize riparian vegetation types. Changes in vegetation and associated wildlife habitat may result in a shift of species presence within the riparian system. The significance criteria for evaluation of impacts to wildlife species are:

• Temporary or permanent removal, filling, grading, or disturbance of wetlands and riparian vegetation
• Substantial decrease in the area of important wildlife habitats or use areas in the San Joaquin, Merced, and Tuolumne river systems
• Substantial fragmentation or isolation of wildlife habitats or movement corridors, especially riparian or wetland habitats

6.2.1.3 Special-Status Species

Adverse impacts to listed species are considered significant if the Proposed Project would result in:

• A reduction in the number of individual listed plants, fish, or wildlife
• Long-term or permanent loss or alteration of habitat important for one or more listed species
• Temporary loss or alteration of habitat important for one or more listed species that could result in increased mortality or lowered reproductive success

Adverse impacts to candidate or sensitive species are considered significant if Project construction or operation results in the following:

• Direct or indirect impacts on candidate or sensitive species population, or habitat that would contribute to or result in the federal or state listing of the species, e.g., by substantially reducing species numbers, or by resulting in the permanent loss of habitat essential for the continued existence of a species

6.2.2 Environmental Impacts and Mitigation

All identified impacts are considered to be not significant adverse impacts. Potential impacts to riparian vegetation, wildlife, and special-status species are discussed below.

6.2.2.1 Riparian Vegetation

Potential impacts to riparian vegetation as a result of the two release options of the Proposed Project in comparison to the No Action Alternative are evaluated below.

No Action Alternative

This alternative represents the existing hydrology of the Merced, Tuolumne, or San Joaquin rivers including the San Joaquin River Agreement (SJRA) flows and existing riparian vegetation in the Project Area.

Proposed Action on the Tuolumne River

Release of supplemental water into the Tuolumne River during April or May could occur approximately once in every 10 years based on historical data for the period 1922 through 1992 (Appendix A). Based on this same data, supplemental water could need to be released into the Tuolumne River during consecutive April and May periods only once every 20 years. During the period of 1922 to 1992, flows on the San Joaquin River at Vernalis exceeded the required "double-step" flows approximately once every 3 to 4 years. Therefore, the proposed supplemental releases would not substantially change the existing hydrologic parameters for maintenance and establishment of riparian vegetation along the Tuolumne River. It is possible that higher flows during this period may promote dispersal and germination of seeds for some riparian plant species that disperse seeds during this period such as Fremont cottonwood, Arroyo willow, and Goodding’s black willow.

Releases of supplemental water from the Tuolumne River would not cause a significant adverse impact to riparian vegetation along the Tuolumne or San Joaquin rivers. To the extent that supplemental flows enhance the establishment and survival of riparian plant species, the Proposed Project may have a minor beneficial impact on riparian vegetation along the Tuolumne and San Joaquin rivers.

Proposed Action on the Merced River

Impacts to riparian vegetation would be the same as those described for the Tuolumne River. Supplemental releases to the Merced River are not likely to cause a significant adverse impact to riparian vegetation along the Merced or San Joaquin rivers. To the extent that supplemental flows enhance the establishment and survival of riparian plant species, the Proposed Project may have a minor beneficial impact on riparian vegetation along the Merced and San Joaquin rivers.

6.2.2.2 Wildlife

Potential impacts to wildlife are discussed below.

No Action Alternative

This alternative would not alter the existing riparian wildlife habitats of the Merced, Tuolumne, or San Joaquin rivers.

Proposed Action on the Tuolumne River

As discussed above for riparian vegetation, supplemental water released from the Tuolumne River would not have a significant impact on riparian vegetation. Therefore, this alternative would not impact wildlife species that utilize riparian habitats along the San Joaquin River or the Tuolumne River.

Proposed Action on the Merced River

As discussed above for the Tuolumne River, supplemental water released from the Merced River would not have a significant impact on riparian vegetation. Therefore, this alternative would not impact wildlife species that utilize riparian habitats along the San Joaquin or Merced rivers.

6.2.2.3 Special-Status Species

Several special-status plants and animals used riparian habitats along the lower San Joaquin and tributary rivers such as the Tuolumne, Stanislaus, and Merced rivers. Potential impacts to these special-status species are evaluated below.

No Action Alternative

The No Action Alternative represents existing conditions with the SJRA flows for terrestrial special-status species in the Project Area.

Proposed Action on the Tuolumne River

Releasing supplemental water from the Tuolumne River would result in higher peak flows in April and/or May approximately 1 out of every 10 years (Appendix A). Historic data for the San Joaquin River between 1922 and 1992 demonstrate that the river has typically experienced even higher flows, greater than the "double-step" supplemental releases proposed under this alternative. Therefore, it is not likely that this alternative would have a significant adverse impact on special-status species that use riparian habitats along the Tuolumne and San Joaquin rivers.

Proposed Action on the Merced River

This alternative is not likely to have a significant adverse impact on special-status species that use riparian habitats along the Merced or San Joaquin rivers. This conclusion is based on the historic hydrologic data previously discussed for the Tuolumne River.

6.2.3 Impact Summary and Mitigation of Impacts

The Proposed Project on either the Tuolumne or Merced rivers is not likely to impact riparian vegetation, wildlife, or terrestrial special-status species. Therefore, no mitigation is proposed.