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B. BIOLOGY

District activities under the SMP would affect salt and brackish marsh habitat in tidal areas and freshwater wetland, riparian forest and woodland, ruderal/non-native grassland, and open water habitat in non-tidal areas. The District's proposed 20 year work program would temporarily remove an estimated cumulative total of 146 acres of jurisdictional wetlands: 30 acres in tidal areas, and 116 acres in non-tidal areas. Implementation of vegetation management under the SMP would also remove an estimated cumulative total of 78 acres of in-stream woody riparian vegetation. An additional, unquantified amount of riparian vegetation would be removed for bank protection, which will impact approximately one linear mile of bank per year. The direct and cumulative impacts of sediment removal, vegetation management, and bank protection would be mitigated by implementing BMPs and providing compensatory mitigation. Compensatory mitigation would include tidal wetland restoration, freshwater wetland creation, stream and watershed protection, and control of giant reed.

1. Environmental Setting

a. Description of Habitats in the Project Area

This discussion describes those habitats that may be affected by the program, rather than giving a broader description of all of the vegetation or habitat types found in Santa Clara County. Within the description of the habitats below, regional differences between the north, south, and east portions of the county occur due to slope, exposure, climate, and rainfall. The cooler and wetter sites are in the higher elevations of the Santa Cruz Mountains (the west slopes of Santa Clara County); the warmer, drier sites are on the valley floor and in the eastern and southern sections.

District sediment removal and vegetation management in tidal areas would affect salt and brackish marsh habitats. In non-tidal areas, sediment removal, vegetation management, and bank protection work may affect freshwater wetland, riparian forest and woodland, ruderal/non-native grassland, or open water habitats, depending on the site. Where not otherwise cited, information in this section was prepared by Thomas Reid Associates and District staff.

1) Tidal salt marsh

Salt marsh occupies the intertidal zone in the lower, tidal reaches of the creeks surrounding south San Francisco Bay. Salt marsh vegetation is generally found immediately adjacent to the Bay or its major sloughs where the water is relatively saline. Very little salt marsh is in the areas where the project work would occur.

In San Francisco Bay in general, the lower salt marsh supports monotypic stands of California cordgrass (Spartina foliosa), while the mid to upper elevations are dominated by pickleweed (Salicornia virginica). Other native and non-native peripheral halophytes (salt tolerant plants) including spearscale (Atriplex triangularis), alkali heath (Frankenia salina), salt grass (Distichlis spicata), and brass buttons (Cotula coronopifolia) are occasionally present, especially at the wetland/upland interface.

Distribution of salt marsh species along local creeks may be patchy, and development of the typical salt marsh plant zonation pattern is often incomplete. In this photo of San Francisquito Creek just downstream of Highway 101, a narrow strip of pickleweed occurs at the base of a sediment bar. Two weedy species, curly dock (Rumex crispus) and smilo grass (Piptatherum milaceum), are intermixed with the pickleweed. The aggressive, invasive species smooth cordgrass (Spartina alterniflora) occurs in several locations in the county, but is currently more abundant to the north in San Mateo and Alameda Counties.

Tidal salt marshes provide habitat for several special-status species, including California clapper rails (Rallus longirostris obsoletus), Alameda song sparrows (Melospiza melodia pusilla), salt marsh harvest mice (Reithrodontomys raviventris raviventris), and salt marsh wandering shrews (Sorex vagrans halicoetes).

Fish species occurring in the salt marshes are not well known but may include Pacific herring (Clupea pallasi) and striped bass (Morone saxatilis), as well as anadromous fish (steelhead [Oncorhynchus mykiss] and Chinook salmon [O. tshawytscha]) in the spring and fall. Amphibians tend to be absent from salt marsh habitats due to their requirement of fresh water. Gopher snakes (Pituophis melanoleucus) and other reptiles forage on the levees within the salt marshes but generally not in the salt marsh habitat itself. Introduced Norway rats (Rattus norvegicus) and red foxes (Vulpes vulpes) do forage within the salt marsh habitat, and are important clapper rail predators.

Numerous aquatic, semiaquatic, and terrestrial birds, including grebes, cormorants, herons, ducks, raptors, rails, plovers, sandpipers, gulls, and songbirds inhabit South Bay salt marshes. Commonly observed species include western grebes (Aechmophorus occidentalis), double-crested cormorants (Phalacrocorax auritus), snowy egrets (Egretta thula), northern pintails (Anas acuta), mallards (A. platyrhynchos), ruddy ducks (Oxyura jamaicnesis), northern harriers (Circus cyaneus), American coots (Fulica americana), black-bellied plovers (Pluvialis squatorola), black-necked stilts (Himantopus mexicanus), American avocets (Recurvirostra americana), willets (Catoptrophorus semipalmatus), western sandpipers (Calidris mauri), dunlins (C. alpina), long-billed dowitchers (Limnodromus scolopaceus), long-billed curlews (Numenius americanus), whimbrels (N. phaeopus), greater yellow-legs (Tringa melanoleuca), Forster's terns (Sterna forsteri), western gulls (Larus occidentalis), Bonaparte's gulls (L. philadelphia), marsh wrens (Cistothorus palustris), and song sparrows (Melospiza melodia).

2) Tidal brackish marsh

Brackish marshes occur in tidal reaches of leveed streams upstream of salt marsh areas, where freshwater inflow markedly reduces the salinity of the incoming tidal water. Tidal influence in the South Bay generally does not extend upstream of U.S. Highway 101. For the SMP, the estimated limits of tidal influence were determined based on features such as stream water salinity and elevation (Rankin 2000). The more saline brackish marshes are dominated by alkali bulrush (Scirpus robustus). California bulrush (Scirpus californicus) often occupies a narrow strip in the lower marsh, adjacent to the low-flow channel. Lower-salinity brackish marshes are dominated by California bulrush and cattails (Typha spp.). Perennial pepperweed (Lepidium latifolium; also known as peppergrass), an invasive, non-native species, is sometimes a significant or even dominant component of brackish marshes. In some areas, fresher brackish marshes are dominated by a suite of lower-stature species, rather than cattails and bulrush. A variety of species may be present, including marsh pepper (Polygonum punctatum), marsh primrose (Ludwigia peploides ssp. peploides), cocklebur (Xanthium strumarium), tall cyperus (Cyperus eragrostis) and curly dock (Rumex crispus). These areas often correspond to areas treated with herbicides.

Brackish marshes support several special-status wildlife species including saltmarsh common yellowthroat (Geothlypis trichas sinuosa) and some of the species also found in salt marshes, such as Alameda song sparrows.

Many wildlife species that are found in either or both freshwater wetland and salt marsh habitats also occur in brackish marshes. Most amphibian and reptile species tend to be absent from brackish marshes, with the exception of bullfrogs (Rana catesbeiana), western aquatic garter snakes (Thamnophis atratus), western terrestrial garter snakes (T. elegens), and western pond turtles (Clemmys marmorata). Common bird species typically found in brackish marshes include pied-billed grebes (Podilymbus podiceps), black-crowned night herons (Nycticorax nycticorax), mallards, American widgeon (Anas americana), American coots, California gulls (Larus californicus), western gulls, common tern (Sterna hirundo), Forster's terns, black phoebes (Sayornis nigricans), and barn swallows (Hirundo rustica). Mammals commonly found in brackish marshes include native species such as California vole (Microtus californicus) and non-native species such as feral house cats (Felis felis), red foxes, Norway rats, and muskrats (Ondatra zibethinus). The first three species non-native species all are significant predators of native birds.

3) Freshwater wetland

Freshwater wetlands occupy earthen and sediment-covered concrete channel beds in non-tidal reaches of District streams. The greatest extent of in-stream freshwater wetlands is found in modified, rather than natural channels, as the straightening and flattening of channels and removal of overhanging riparian vegetation results in conditions that support wetland vegetation. Wetlands are particularly abundant in modified streams that are supplied with water throughout the summer. Streams not subject to these modifications contain smaller, patchy areas of freshwater wetland and tend to support riparian forest and woodland instead.

There are three general categories of vegetation within the freshwater wetlands in District-jurisdiction channels, as defined by dominant vegetation. These are categorized as 1) erect emergents, 2) creeping emergents, and 3) non-native/annual mix types. Erect emergent and creeping emergent categories are described by Rejmankova (1992). The dominant species vary between these types, but species from each category are often non-dominant components of the other categories.

These three vegetation types often co-occur on sites, with their distribution apparently related to water availability and channel bottom topography. Both of these features, and the resulting distribution of wetlands, can change from year to year in response to natural disturbance, such as scouring and sediment deposition by storm flows, human disturbance such as stream maintenance, and variable rainfall. The wetlands variously comprise small to medium patches a few feet across, narrow strips of vegetation that fringe low-flow channels, or dense stands of vegetation that occupy almost the entire channel bed. Vegetation cover within the wetlands is generally high.

Broad-leaved cattails (Typha latifolia) typically dominate erect emergent vegetation, but other tall, rhizomatous, grass-like species, such as tule (Scirpus acutus var. occidentalis), California bulrush, narrow-leaved cattail (Typha angustifolia) and broad-fruited bur-reed (Spaganium eurycarpum ssp. eurycarpum) are sometimes present or dominant. This vegetation type often forms very dense, almost monotypic stands. Small amounts of lower-stature species that occur in the other two vegetation types are usually restricted to stand edges. Most of the dominant species are natives.

Creeping emergent vegetation is dominated by lower-stature plants with floating stems that root at the nodes. These species can tolerate varying hydrologic regimes and can expand by flotation into deep water not available to other rooted plants (Pierce 1994). Locally, the vegetation may be absent or sparse in spring and early summer, depending on the amount of rainfall and scouring flows during the previous rainy season. Where surface water is available, the vegetation continues to expand, often forming dense continuous mats in the channel bottom by the end of summer. In local streams, this vegetation type usually occupies the wettest part of the vegetated channel bed.

Creeping emergent vegetation is common and abundant within the District's jurisdiction and project work area. The majority of component species are native, but some of these native species, like water primrose, are considered to be weedy (Jepson 1993). Watercress (Rorippa nasturtium-aquaticum) and water primrose are the most abundant species. They each form extensive, dense, almost monotypic vegetation mats in some locations. Other typical native and non-native components include water smartweeds (Polygonum punctatum, P. lapathifolium, P. hyrdopiperoides), common willow-herb (Epilobium ciliatum ssp. ciliatum), tall cyperus, and water speedwell (Veronica anagallis-aquatica).

The non-native/annual mix vegetation is dominated by a variety of weedy, non-native annual and perennial grasses and forbs such as dallis grass (Paspalum dilatatum), barnyard grass (Echinochloa crus-galli), rabbitfoot grass (Polypogon monspeliensis), Italian ryegrass (Lolium multiflorum), cocklebur (Xanthium strumarium), prickly ox-tongue (Picris echioides), lady's thumb (Polygonum persicaria), and marshpepper (Polygonum hydropiper). Non-native/annual mix vegetation is usually located in drier areas in the channels, such as on sediment benches and bars above the summer water level, in summer-dry channels, and along the wetland-upland interface. Compared to the two other vegetation types, the species mix consists of more upland and facultative species (species that typically occur in both wetlands and uplands). The erect emergent and creeping emergent types primarily comprise obligate and facultative wetland species (species that are almost always found only in wetlands rather than uplands).

The species composition of the in-stream freshwater wetlands may be indicative both of the disturbed nature of the habitat in which the wetland occurs, and the fact that such habitat has likely not been a long-term feature of the local natural environment. Component species are not specific either to this type of wetland, or to the local area. Most of the wetland species, including the native species, are widely distributed, with few endemic to California. Three of the most abundant species provide examples of this widespread distribution: watercress occurs in temperate areas worldwide, water primrose is found in Oregon, Texas, and South America, and broad-leaved cattail occurs throughout temperate North America, South America, Eurasia, and Africa (Jepson 1993).

Rejmankova (1992) studied the ecology of five creeping emergents that commonly occur in nutrient rich pools, sloughs, and irrigation and drainage canals of Central and Southern California. Watercress and water primrose, both of which are abundant in Santa Clara County, were among the species studied. She made several observations relevant to understanding the dynamic and disturbed nature of local in-stream freshwater wetlands. She observed that in undisturbed habitats, creeping macrophytes (plants) are fairly inconspicuous, occupying transitional areas between littoral (shoreline) and terrestrial zones. These species seem to benefit from human impact on watercourses, however, and their behavior changes in disturbed habitats. For example, once they get established in fertile, nutrient-rich environments, they grow very vigorously, developing extensive dense mats. If left undisturbed, they are usually slowly out-competed by erect emergents (e.g., cattails and tules). The disturbance that maintains their dominance often is represented by periodic dredging and/or water level fluctuations.

McNaughton (1966) states that "probably no native community is as ubiquitous and as lacking in floristic complexity as the Typha (cattail) community." Like creeping emergents, cattails are common in disturbed environments and are considered to be weedy under certain circumstances due to their tendency to invade human-disturbed habitats such as irrigation canals, drainage ditches, rice fields, and farm ponds (Grace and Harrison 1985). However, cattails can also be abundant in less-disturbed environments. Broad-leaved cattail, the most abundant erect emergent plant locally, tolerates a broad range of hydrologic conditions, growing almost anywhere the soil remains wet or saturated during most of the growing season. Broad-leaved cattail and other cattail species occur in early to late successional stages of many wetland types, including marshes, lake shores, estuaries, roadside ditches, and bogs. Cattail vegetation, like creeping emergent vegetation, is highly productive (i.e., produces substantial biomass over the growing season) (McNaughton 1966, Rejmankova 1992).

Freshwater wetlands are used by a variety of special-status wildlife species for breeding, foraging, and as a source of water for drinking. California red-legged frogs (Rana aurora draytonii), western pond turtles, San Francisco garter snakes (Thamnophis sirtalis tetra taenia), and tricolored blackbirds (Agelaius tricolor) are some of the special-status wildlife species that inhabit freshwater wetlands.

A wide variety of common native and introduced species inhabit freshwater wetlands. Fish include prickly sculpin (Cottus asper), carp (Cyprinus carpio), threespine stickleback (Gasterosteus aculeatus), and tule perch (Hysterocarpus traski). Amphibians and reptiles include bullfrogs, Pacific tree frogs (Hyla regilla), western toads (Bufo boreas), common garter snakes (Thamnophis sirtalis), terrestrial garter snakes, and western aquatic garter snakes. Birds include pied-billed grebes, great egrets (Ardea alba), great blue herons (A. herodias), snowy egrets, Canada geese (Branta canadensis), mallards, gadwalls (Anas strepera), American coots, common moorhens (Gallinula chloropus), Forster's terns, ring-billed gulls (Larus delawarensis), black phoebes, song sparrows, marsh wrens, common yellowthroats, and barn swallows. Mammals include red foxes, raccoons (Procyon lotor), and muskrats. Species requiring year-round water of adequate depth, such as fish, and the fish-eating diving birds, such as pied-billed grebes and Forster's terns, can only utilize the drier wetland sites when adequate water is present. On the other hand, seasonal wetlands are important breeding habitat for common amphibians such as California newts (Taricha torosa) due to the absence of fish predators.

4) Riparian Forest and Woodland

Riparian forests and woodlands occur adjacent to freshwater reaches of watercourses throughout Santa Clara County. Riparian habitats comprise the transition between the stream and the upland portion of the watershed. Natural riparian habitats are characterized by variable gradients of moisture and light, lush vegetation, and very high biological diversity (Goals Project 1999). Riparian forests along District streams tend to be long and narrow, either intergrading into adjacent upland habitat, such as oak woodlands, ornamental landscaping, and other habitat, or constrained by adjacent land uses.

The District attempted to determine the amount of riparian forest and woodland adjacent to Santa Clara County streams using existing data from previous mapping efforts. Riparian forest and other plant communities associated with Santa Clara County streams were mapped during the mid-1990s by a consultant for the City of San Jose and the County of Santa Clara. The scale of the aerial photographs used was 1:6,000 or 1:24,000. Between the two studies, the City of San Jose, some of the unincorporated areas of the county, and some of the incorporated cities were included. Due to the nature of these studies, and differences in data sources and scales, riparian forest and woodland could not be reliably distinguished from other forest and woodland types. Therefore, all forest and woodland types were included in the District analysis. These data were re-analyzed for the SMP in 2000 to estimate the acreage of riparian or other types of forest or woodland within or adjacent to District streams. Based upon this GIS analysis, the District estimates that 8,000 to 20,000 acres of riparian forest or woodland, associated urban forest, and upland woodlands occur adjacent to the 828 miles of stream within the District's jurisdiction. These rough acreage estimates are based upon forest and woodland vegetation occurring within 100 feet or 500 feet from the centerline of the channel, respectively. In general, most of this vegetation occurs adjacent to natural streams with relatively little adjacent to concrete channels.

Vegetation

Deciduous cottonwood-willow riparian forest occurs primarily in the middle to lower watersheds where the water table is high or there is year-round flow. On drier sites, oak or oak-sycamore riparian forest or woodland may dominate. Although evergreen and deciduous oak species such as coast live oak (Quercus agrifolia) and valley oak (Q. lobata) dominate the drier sites rather than cottonwoods and willows, there is much overlap in species with the cottonwood-willow forest type. Where hillside open space adjoins a riparian corridor, riparian forest often intergrades with adjacent upland forest, woodland, or scrub, increasing its habitat value by providing increased plant diversity and community structure. Numerous non-native species including northern California black walnut (Juglans californica var. hindsii), eucalyptus (Eucalyptus spp.), and tree-of-heaven (Ailanthus altissimus) are locally abundant and occur throughout riparian habitats in the District.

The riparian vegetation mix in the upper watersheds is different from the lower watersheds of the valley floor. These differences are related to factors such as slope, channel morphology, flow, and the ability of plants to withstand periodic flooding.

The upper watersheds are in steeper terrain where flooding rarely occurs. The upper reaches of Stevens and Penitencia Creeks in the Santa Clara basin and Little Arthur Creek in the Pajaro River basin are typical examples. Here, the more deeply incised channels and upper reaches of creeks on steep hillsides support upper floodplain and canyon species such as coast live oak, valley oak, and California laurel (Umbellularia californica). White alder (Alnus rhombifolia), blue elderberry (Sambucus mexicana), big-leaf maple (Acer macrophyllum), western sycamore (Platanus racemosa), and California buckeye (Aesculus californicus), as well as a shrubby understory of native and non-native species such as toyon (Heteromeles arbutifolia), Himalayan blackberry (Rubus discolor), California blackberry (R. ursinus), and poison oak (Toxicodendron diversilobum) may also be present or common. Riparian vegetation in the upper watersheds has generally not been impacted by urbanization.

The lower watersheds are flatter with relatively frequent flooding. Although these channels historically generally had fairly gently sloping channel banks and broad floodplains, many of them have been channelized or have otherwise become deeply incised between steep banks. Those with riparian vegetation tend to be dominated by Fremont cottonwood (Populus fremontii), willows (e.g., arroyo [Salix lasiolepis], sandbar [S. exigua], and red [S. laevigata]), box elder (A. negundo californicum), western sycamore, coast live oak, and valley oak. Other typical tree species include California black walnut and blue elderberry. The non-tidal reaches of Coyote Creek in the Santa Clara Basin and Llagas Creek in the Pajaro River Basin are typical examples. There may be an understory of shrubs such as California rose (Rosa californica), blackberries, poison oak, and creeping snowberry (Symphoricarpos mollis).

Wildlife

Healthy, stratified riparian forest (i.e., having differing layers of vegetation) supports the greatest wildlife diversity of any of the habitats within the District's jurisdiction. The layering of trees, shrubs, and herbaceous and aquatic vegetation creates a complexity of micro habitats used for breeding, foraging, and movement by wildlife (Goals Project 1999). Riparian habitats and adjacent woodlands provide habitat for many special-status species, including white-tailed kites (Elanus leucuras), Cooper's hawks (Accipiter cooperi), sharp-shinned hawks (A. striatus), California yellow warblers (Dendroica petechia brewsteri), and San Francisco dusky-footed woodrats (Neotoma fuscipes annectens).

Fish commonly found in streams associated with riparian habitat include native species such as California roach (Hesperoleucus symmetricus), Sacramento sucker (Catostomus occidentalis), threespine stickleback, rainbow trout, prickly sculpin, and riffle sculpin (Cottus gulosus), and introduced fishes such as green sunfish, largemouth bass (Micropterus salmoides), and mosquitofish (Gambusia affinis). In addition to the amphibians described above that are also found in freshwater wetlands, such as Pacific tree frogs, amphibians such as arboreal salamanders (Aneides lugubris) are generally found only in forested habitats.

Common riparian birds include green herons (Butorides striatus), mallards, wood ducks (Aix sponsa), red-shouldered hawks (Buteo lineatus), belted kingfishers (Ceryle alcyon), downy woodpeckers (Picoides pubescens), Nuttall's woodpeckers (P. nuttallii), spotted towhees (Pipilo maculatus), Swainson's thrush (Catharus ustulatus), hermit thrush (C. guttatus), Bewick's wrens (Thryomanes bewickii), yellow-rumped warblers (Dendroica coronata), Wilson's warblers (Wilsonia pusilla), American robins (Turdus migratorius), house finches (Carpodacus mexicanus), Stellar's jays (Cyanocitta stelleri), mourning doves (Zenaida macroura), European starlings (Sturnus vulgaris), brown-headed cowbirds (Molothrus ater), Bullock's orioles (Icterus bullockii), black-headed grosbeaks (Pheucticus melanocephalus), Pacific-slope flycatchers (Empidonax difficilis), black phoebes, chestnut-backed chickadees (Poecile refescens), bushtits (Psaltriparus minimus), and ruby-crowned kinglets (Regulus calendula).

Birds and other animals associated with different types of riparian habitats can be somewhat distinct. The few studies (e.g., Knopf 1985, Finch 1989) that have examined the relationship between elevation, riparian vegetation, and bird diversity have shown that the low elevation vegetation is normally more complex, and the birds associated with it are more diverse and different from the species associated with the higher elevation riparian habitats. In the project area, however, species such as the Swainson's thrush and Wilson's warbler are rare on the valley floor and more abundant in the upper watersheds, likely due to decline of valley floor riparian habitat (Rottenborn, pers. comm.).

Mammalian species that use riparian areas include those listed above using freshwater wetland habitat and additional species such as Virginia opossums (Didelphis virginiana), Trowbridge's shrews (Sorex trowbridgii), broad-footed moles (Scapanus latimanus), western red bats (Lasiurus blosevillii), hoary bats (L. cinerius), Yuma myotis (Myotis yumanensis), deer mice (Peromyscus maniculatus), house mice (Mus musculus), California voles (Microtus californicus), Norway rats, fox squirrels (Sciurus niger), gray fox (Urocyon cinereoargenteus), and bobcats (Lynx rufus).

Vegetation that grows at the interface of the stream and adjacent riparian habitat and shades the water is known as shaded riverine aquatic habitat (SRA). The SRA vegetation is composed of overhead cover and instream cover. The overhead cover comprises overhanging riparian vegetation, and the instream cover comprises woody debris, such as roots and trunks, and aquatic plants. Large boulders and undercut banks also contribute to shading. The SRA shades the water and contributes leaf litter and insects to the stream. Stream shading is generally a critical component of healthy riparian corridors within the District. The shadows from SRA help maintain cooler water temperatures, which in turn maintain higher oxygen levels in the water and reduce evaporation. Higher oxygen levels benefit salmonids and other native fish and invertebrates, and reduced evaporation results in increased flow for a greater portion of the year. SRA also provides escape cover in the shadows and in between the woody debris that accumulates at the edge of the channel. This cover benefits fish, amphibians, and invertebrates. The plant material and insects that fall into the water off of the SRA vegetation can be an important part of the food chain, especially in streams that do not otherwise support abundant aquatic plant production. Although large boulders in and along the channel, including large rip rap, can contribute some of the benefits of overhanging vegetation (e.g., escape cover, shading), they cannot contribute plant material to the food chain.

District Channel Types

The Santa Clara Basin has 71% and the Pajaro River Basin has 29% of the 828 total miles of stream channel within District jurisdiction (see SMP Table 5-1 and Table IV-B-1). The SMP divides channels within District jurisdiction into three broad categories: 1) Natural (+/-), Mixed, and Concrete Natural (+/-) channels may have some modification to the flood plain but have no modification of the stream channel or stream banks. The (+/-) thus stands for more or less natural. Mixed channels are engineered or otherwise modified streams where the stream bottom is earthen, but the banks have a variety of conditions, including excavated earth, earth levees, rock, gabions, sack concrete, or flood walls. Concrete channels have a concrete bottom and may have either concrete or earthen banks. The majority of the channel miles in both basins that are categorized as to channel type are Natural (+/-). The District has not recorded the channel type for 306 miles of streams within its jurisdiction, which are thus not categorized. Data has not been recorded on these uncategorized streams because they do not have engineered designs, and the District does not systematically collect information on non-engineered streams. The District estimates that the majority of these unrecorded stream miles are Natural (+/-).

Sub-regional differences exist between the basins related to rainfall and temperature. The Pajaro River basin (South County) is generally drier and hotter than the Santa Clara Basin (North County). The eastern side of both basins tends to be drier, whereas the western side receives the most rainfall. Riparian vegetation characteristics vary with respect to these environmental gradients.

The Santa Clara Basin has 399 miles (76%) of the total District channel miles for which channel type is known. Residential, industrial, and commercial development has occurred extensively throughout the Santa Clara Basin. Much of this development encroaches right up to the top of the streambanks and levees, in some cases within former riparian habitat. Nonetheless, mature riparian forest habitat, including cottonwoods, oaks, and sycamores, remains in the Santa Clara Basin. In lowland areas these habitats typically occur in a narrow band between the stream and the levee. Avian species that are more tolerant of nearby development, such as yellow warblers, warbling vireos (Vireo gilvus), and black-headed grosbeaks, have persisted in these lowland riparian habitats of the Santa Clara Basin. They are rare in the Pajaro basin, however, where the taller cottonwoods are generally absent (Rottenborn, pers. comm.). In some suburban areas of the Santa Clara Basin, the remaining native riparian habitat blends into dense ornamental landscaping, creating a broader band of forested, albeit heavily disturbed, cover. Likewise, the upper reaches of many Santa Clara Basin streams, such as upper Adobe Creek and Stevens Creek, are less disturbed and adjacent to broader bands of oak woodland. The lower reaches of many Santa Clara Basin streams are tidal and thus have salt water marsh without adjacent riparian vegetation.

Table IV-B-1
Estimated Existing Channel Type by Basin

Channel conditions provided in miles and percent of categorized and total miles for each basin, channel type, and all District channel miles.
Channel Type	Santa Clara Basin				Pajaro River Basin			Total
	Miles	% Categ- orized Basin1	% All Basin2	% Chan. Type3	Miles	% Categ- orized Basin	% All Basin	% Chan. Type	Miles	% All Categ- orized Miles	% All District Miles
Natural (+/-)	205	52%	35%	67%	103	83%	43%	33%	308	59%	37%
Mixed	115	29%	20%	85%	20	16%	8%	15%	135	26%	16%
Concrete	78	20%	13%	99%	1	1%	<1%	1%	79	15%	10%
Total Categorized	398	100%	68%	76%	124	100%	52%	24%	522	100%	63%
Not Categorized	190	n/a	32%	62%	116	n/a	48%	38%	306	n/a	37%
Total	588	n/a	100%	71%	240	n/a	100%	29%	828	n/a	100%
Canals	37	n/a	100%	90%	4	n/a	100%	10%	41	n/a	100%
Source: SMP 3/01 Note: All numbers are rounded. 1 Percent of categorized stream miles in the basin for each channel type category. 2 Percent of all stream miles in the basin for each channel type category. 3 Percent of miles of each channel type category contained within each basin.

The Pajaro River Basin has 124 miles (24%) of the total District channel miles for which the channel type is known (Table IV-B-1). Some stream reaches in the Pajaro River watershed, as well as the southern part of the Coyote Creek watershed (e.g., Fisher Creek), are characterized by dense willow thickets. In contrast to the Santa Clara Basin, the majority of stream-miles in the Pajaro River Basin are immediately adjacent to agricultural fields. Although less impervious surface encroaches upon these channels, the riparian bands are nonetheless generally narrow. In some places, such as along Llagas Creek between Masten and Buena Vista Avenues, eucalyptus trees along with scattered oaks and sycamores create a thin corridor of trees along banks that are otherwise mostly lined with non-native grasses. Other streams in the Pajaro River Basin have dense riparian vegetation, although it is generally confined to a narrow band along the channel. Uvas-Carnadero Creek at Bloomfield Avenue, for example, has a well-developed, diverse riparian canopy with a mix of native and non-native species. Llagas Creek, in the same general area, is lined with dense stands of mature willows growing up to the edge of the levee slopes. From Bloomfield to Buena Vista Avenues, the District has planted many of the levee slopes and top of bank areas with riparian and oak woodland plants as mitigation for the Lower Llagas Creek flood control project.

Valley floor riparian: A remnant community

Little direct information, such as early maps or written accounts, exists describing the extent of lowland riparian vegetation in Santa Clara County prior to European settlement. Anecdotal information suggests that the lowland riparian community was once more abundant and widespread than it is today, although the corridors were generally narrow (Clarke 1959). The decline of riparian habitat is illustrated by the accounts of bird species that used to be abundant in Santa Clara County but are now rare or have been extirpated. Compared to other vertebrates, birds are the most significant indicators of riparian habitat quality because many bird species-unlike most mammals, reptiles, or amphibians-are strictly found in riparian habitats (forest, woodland, or scrub) in California.

Yellow-billed cuckoos (Coccyzus americanus), little willow flycatchers (Empidonax traillii brewsteri), and yellow-breasted chats (Icteria virens) historically nested in the South Bay but no longer do so. All of these species nested in the dense, extensive willow thickets along South Bay streams. Yellow-breasted chats remain as breeders along some Pajaro River Basin streams. While the extirpation of willow flycatchers was probably exacerbated by brood parasitism by brown-headed cowbirds, the decline of these species was probably a direct result of the loss of the dense, extensive willow thickets along South Bay streams (Rottenborn 1997, B. Bousman in RipariaNews 1997).

The start of commercial agriculture in the Santa Clara Valley in the 1850's, which required irrigation and vegetation clearing, also started the decline of the valley floor riparian forests. Since that time, riparian habitat in the lower watersheds continued to decline in quality and quantity as a result of human activities, including vegetation removal for levee construction and bank protection, flow regulation, groundwater pumping, channel modification (straightening, armoring, sediment removal), encroachment of urban land uses, habitat fragmentation, and introduction of invasive exotic species.

Urban encroachment on the floodplains and terraces right up to the edge of the natural creek channels has resulted in downcutting of the channel beds and erosion and over-steepening of the banks. Armoring channels with hard materials may leave a rim of mature riparian vegetation at the top that persists for a while, but the riparian species on the rim will likely eventually disappear, perhaps within a few decades, because of two major factors: (1) the downcut channel has a lowered water table compared to the original channel, so that the roots of the trees may no longer reach to the water table during the summer months; (2) the natural succession of the riparian community from its regenerative stages to its more mature stages has been interrupted by the downcutting process, bank steepening, and channel straightening. Stream maintenance contributes to this effect by removing young saplings from stream channels. Therefore, the mature riparian trees at the top of bank are probably not being replaced once they die. These trees and the forest corridor are likely to disappear over time (see, e.g., Howe and Knopf 1991).

One of the factors causing a decline of the cottonwood-willow type riparian vegetation within the valley floor is likely the lack of sites for regeneration (see, e.g., Rottenborn 1997). Studies have shown that regeneration of the lowland (cottonwood-willow) riparian forest depends on establishment of seedlings along gravel point bars (Strahan 1984; McBride and Strahan 1984). Willows and cottonwoods depend on fresh surfaces such as point bars for seed germination and establishment of viable seedlings. The bars form each year when sufficient sediment accumulates above summer low-water levels. As the bar builds higher as more sediment is deposited, the bar is flooded less frequently and eventually supports first a mature cottonwood/willow forest and then an understory of shade-tolerant species as well. When a large enough flood occurs the new influx of sediment provides locations for cottonwood and willow regeneration.

Straightening and widening creeks, sediment removal activities, and modified flood flows have reduced the point bars created by naturally meandering streams and thus interfered with this on-going regeneration process. Without the periodic formation of new, open gravel bars along stream meanders, the riparian forest succession may occur, but replacement of older riparian trees with new seedlings is reduced. Stream maintenance keeps channels open for purposes of maintaining flood capacity. This results in conditions conducive to seedling establishment; however, the seedlings need to be repeatedly removed to maintain the flood capacity. Without replacement of the older trees by these seedlings, the tree canopy could eventually become fragmented and much of it could be lost (Rottenborn 1997). When the tree canopy is lost, the area may become a riparian scrub community, which is often dominated by mulefat (Baccharis salicifolia), coyote brush (B. pilularis), and shrubby willows (Salix spp.).

Flow regulation from reservoirs and water diversions to offstream percolation ponds may also have played some role in riparian forest decline, but the effects are complex. Dams typically modify the timing and intensity of flood flows, the extent of flooding, the manner in which flood waters recede, and the sediment load. Such changes can greatly affect riparian flora and fauna. For example, controlled releases may occur too late for successful reproduction of cottonwoods and willows, restrict necessary moisture during the crucial establishment period, or be of such long duration that native vegetation drowns (Ohmart 1994, Rood and Heinz-Milne 1989, Fenner et al. 1985, Strahan 1984). Dams can reduce formation of alluvial seedbeds due to the reduced suspended sediment flows and the reduction in lateral channel migration, which would otherwise build point bars (Strahan 1984, Fenner et al. 1985). By limiting the amount of floodwaters that reach the remaining undeveloped floodplain, dams can also lower water tables, putting stress on cottonwoods and willows (Ohmart 1994, Fenner et al. 1985) and eventually reducing the height and density of riparian forests (Rood and Heinz-Milne 1989, Ohmart 1994).

None of the cited studies occurred in systems that mirror District operations, and thus conclusions regarding the effects of District-operated dams are harder to draw. Unlike systems operated for flood control, hydroelectric power, water supply diversion, or navigation, District dams are largely operated to enhance groundwater storage through instream percolation. The dams collect winter and early spring flows, which are then released into District channels and off-stream percolation ponds in the late spring and summer. This system does reduce flow intensity during winter and spring storms, thus reducing the timing and magnitude of floods. Spring and summer releases, especially in channels that naturally would be dry in the summer, may enable establishment of riparian trees.

As with flow regulation, the effects of groundwater pumping on riparian forests are complex. Past pumping, primarily for agriculture, lowered water tables in the Santa Clara Valley substantially. Roughly half of the District's water supply is used for groundwater recharge to prevent subsidence from groundwater pumping. Since the groundwater recharge program was accelerated in the late 1960's, groundwater overdraft has been reversed and the level of the groundwater in the basins has been rising. The recharge is generally to deeper aquifers, however, and does not increase the groundwater available to riparian vegetation. On the other hand, over half of the input into the groundwater sub-basins in Santa Clara County now comes from imported water and is not water that would otherwise have been in the channels. Furthermore, some of this imported water is stored in reservoirs and then flows down specific sections of stream to allow percolation into the groundwater basin. Some of this water, both within the channel and in the immediate vicinity of the percolation site, presumably reaches vegetation and thus may result in different riparian habitat than would occur under the natural flow regime.

5) Ruderal/Non-native grasslands

Upland areas likely to be affected by SMP activities are largely located on channel banks, modified floodplains, fields adjacent to streams, along access roads, and along levees upslope of salt and brackish marshes and freshwater wetlands. Sparse ruderal vegetation can occasionally also be found in channels on sediment benches and bars. Those areas that are devoid of riparian forest or scrub generally consist of ruderal/non-native grassland habitat. Wild oats (Avena fatua), ripgut brome (Bromus diandrus), soft chess (Bromus hordeaceus), Italian ryegrass (Lolium multiflorum), smilo grass (Piptatherum miliaceum), black mustard (Brassica nigra), wild radish (Raphanus sativus), star thistle (Centaurea solstitialis), English plantain (Plantago lanceolata), and sweet fennel (Foeniculum vulgare) are a few of the weedy species typical of this habitat. Riparian scrub species are sometimes sparsely distributed within these areas.

Although these non-native habitats are generally not as high in wildlife values as native habitat, many special-status wildlife species do use ruderal and non-native grassland habitats, including California horned lizards (Phrynosoma coronatum frontale), white-tailed kites (Elanus caeruleus), burrowing owls (Athene cunicularia), loggerhead shrikes (Lanius ludovicianus), and California horned larks (Eremophila alpestris actia).

Ruderal and non-native grassland habitats in Santa Clara County support numerous wildlife species, especially if the habitat is extensive, relatively well vegetated, or adjacent to other high-quality habitat (such as riparian). Western toads are found in these habitats, and reptiles using these habitats include western fence lizards (Sceloporus occidentalis), western skinks (Eumeces skiltonianus), gopher snakes, racers (Coluber constrictor), common garter snakes, and common kingsnakes (Lampropeltis getula). A limited number of bird species, such as western meadowlarks (Sturnella neglecta) and Savannah sparrows (Passerculus sandwich ensis), nest within ruderal and non-native grassland habitats, but many other species that breed in adjacent riparian habitats will forage in these more open areas. Such species include American kestrels (Falco sparverius), red-tailed hawks (Buteo lineatus), ash-throated flycatchers (Myiarchus cinerascens), northern flickers (Colaptes auratus), and western scrub-jays (Aphelocoma californica). The burrows of many small mammals found in these habitats, such as California ground squirrels (Spermophilus beecheyi), California voles, and Botta's pocket gophers (Thomomys bottae) also provide refuge for many of the reptiles described above. Other mammals found in ruderal/non-native grassland habitats include opossums, pallid bats (Antrozous pallidus), black-tailed hares (Lepus californicus), deer mice, coyotes, striped skunks (Mephitis mephitis), and black-tailed deer.

6) Open water

Seasonal, perennial, and tidal flows within channels comprise open water habitat. During summer and fall, beds of seasonal streams and high-flow benches in perennial streams are exposed, consisting of dry sediments, sand, and gravel bars. During low tides, mudflats, sediment benches, and channel bottoms can also be exposed in tidal areas.

Open water provides aquatic habitat for the many fish and amphibian species described above in salt marsh, brackish marsh, freshwater wetland, and riparian forest, such as steelhead, chinook salmon, threespine stickleback, Pacific tree frogs, western pond turtles, and muskrats. Waterfowl and wading birds, such as great egrets, mallards, and American coots, use open water habitats for foraging.

b. Fisheries and the Aquatic Environment

1) Existing Fish Habitat and Fisheries

The streams of Santa Clara Valley can be loosely classified into eight categories according to their fish species compositions and potential habitat values for fish (categories 7 through 0 in declining order of overall value). These categories, which are described in detail below, are: Trout (7), Steelhead (6), Potential Trout (5), Warm Native (4), Mixed; Spawning (3), Native/Introduced (2), Limited (1), and No Regular Value (0) (See Figure IV-B-1, Table IV-B-2). Adequate data on fish and habitat conditions exists to allow assignment of these fish categories to approximately 344 miles of the 828 miles of stream within the District's jurisdiction.

Table IV-B-2
Fish Habitat by Basin

Fish habitat category provided in miles and percent of total miles of channel with recorded fish habitat category.
Fish Habitat Category	Santa Clara		Pajaro River		Total
	Miles	%	Miles	%	Miles	%
Trout (7)	20	6%	0	0%	20	6%
Steelhead (6)	30	9%	11	3%	41	12%
Potential Trout (5)	23	7%	8	2%	31	9%
Warm Water Native (4)	18	5%	4	1%	22	6%
Mixed; Spawning (3)	24	7%	0	0%	24	7%
Native/Introduced (2)	51	15%	11	3%	62	18%
Limited (1)	71	21%	19	6%	90	26%
No Value (0)	11	3%	43	13%	54	16%
Subtotal	248	72%	96	28%	344	100%
No Habitat Category Data	339	n/a	144	n/a	484	n/a
Total Miles	587	71%	240	29%1	828	100%1
Source: SCVWD 2001; Jerry Smith 2001 Note: Numbers are rounded from calculations of category miles. Total District miles = 828. 1Percent total District miles; all other percentages represent percent of miles with recorded fish habitat category.

The "No Habitat Category Data" category in Table IV-B-2 is assigned to stream reaches where not enough information is available to assign a category relative to fish habitat. Most of the remaining stream miles occur in small or urbanized streams; many of these probably have relatively low values for fish. These habitat designations are for assessing general program impacts only, not for accurately assessing impacts of individual stream maintenance activities.

Descriptions of the fish habitat categories with example streams follow, presented in declining order of overall value based upon presence of significant fisheries, habitat rarity, sensitivity to impact, or impact to species of limited. population distribution. Significant fisheries are present if priority species (rainbow trout, steelhead, chinook salmon) use, or potentially could use, the habitat for spawning or rearing. Significant fisheries also exist where native warm-water fish presently, or potentially, dominate the fish community (categories 3-7). Even lower quality habitats (categories 1-2) can be considered to have significant fisheries values if they provide migration passage for native juvenile and adult fish. Some of these lower quality stream reaches also have the potential to be restored in the future for use by priority species or native warm-water fish. Species compositions within these categories are summarized in Table IV-B-3.

Resident Trout (7)

Upstream of barriers to steelhead spawning migrations, resident rainbow trout can be present in the cooler, permanent streams. This category includes most headwater streams, except those in the dry southeast portion of the county, and accounts for about 6% of District stream miles with recorded fish habitat categories. In smaller streams with natural barriers, habitats are generally steep and well-shaded. These streams, including upper Bodfish Creek, a tributary to Uvas Creek, contain only rainbow trout and riffle sculpin. In larger streams or flatter streams, the upstream migration barriers are more likely to be man-made (dams, flood control drop structures). Other species usually present with the trout and riffle sculpins in these streams are California roach and often Sacramento suckers; typical streams include Stevens and Uvas Creeks upstream of their reservoirs, and Saratoga Creek within and upstream of the town of Saratoga. Most resident trout habitat is upstream of Lexington, Guadalupe, Almaden, and Anderson Reservoirs in streams subject to District jurisdiction, but where stream maintenance generally does not occur. The upstream habitats of the resident trout (7), steelhead (6), and undisturbed warm-water native fish (4) categories are those most likely to still contain California red-legged frogs. In more disturbed, downstream communities, red-legged frogs have usually been replaced by introduced bullfrogs.

Steelhead (6)

These streams provide regular or frequent access for spawning steelhead and regularly provide rearing conditions for juvenile steelhead (about 12% of District stream miles with recorded fish habitat categories). Streams are usually well-shaded and cool (San Francisquito, Bodfish, Little Arthur, and Tar Creeks), or else have substantial augmented flows from reservoir releases (Uvas Creek from the dam downstream to Highway 152 and Stevens Creek from the dam downstream to Fremont Road). In addition to steelhead, other species present include those listed for resident trout streams and also, in some cases, threespine stickleback and Sacramento pikeminnow (Ptychocheilus grandis).

In Stevens Creek downstream of the reservoir and Upper Penitencia Creek within and immediately downstream of Alum Rock Park, resident rainbow trout occur with anadromous steelhead. Difficult steelhead access in some years probably prevents complete replacement of resident trout by steelhead. In Guadalupe, Alamitos, Arroyo Calero, and Coyote Creeks downstream of their reservoirs, recent laddering of barriers (Blossom Hill drop structure and Metcalf Dam) allows steelhead and chinook salmon access to what has been resident trout habitat.

Warm-water Native Fish/Potential Steelhead or Trout(5)

In warmer (greater than 70 degrees), relatively natural, less-shaded streams, native warm-water fish usually dominate; abundant species include California roach, Sacramento sucker, Sacramento pikeminnow, and, downstream of reservoirs, hitch (Lavinia exilicauda). Abundant summer streamflows in wetter years, however, especially from reservoir releases for percolation, provide potential fast-water feeding habitat for juvenile steelhead. The fast-water habitat allows for potentially good densities and growth by juvenile steelhead or resident rainbow trout, despite the increased food demands from higher metabolic rates due to the warmer water. Chinook salmon may also use these habitats for spawning, with juvenile fish out migrating prior to warm summer temperatures. These habitats include middle or lower reaches of Stevens, Saratoga, Guadalupe, Alamitos, Upper Penitencia, and Coyote Creeks, accounting for about 9% of District stream miles with recorded fish habitat categories. Pacheco and Llagas Creeks downstream of Pacheco and Chesbro Reservoirs provide periodic steelhead habitat, although steelhead outmigrant passage due to low spring streamflows is a problem on both streams.

Warm-water Native Fish (4)

About 6% of stream miles with recorded fish habitat categories support predominantly native warm-water fishes. The warmer, downstream portions of Alamitos, Uvas, Llagas, and Pacheco Creeks, downstream of their reservoirs, cannot support steelhead because of low flows and/or warm-water, but do support large populations of native fish, including California roach, Sacramento suckers, and often hitch, Sacramento squawfish, and Sacramento blackfish (Orthodon microlepidotus). Prickly sculpin and threespine stickleback are also commonly present. In wetter years, non-native reservoir fishes (largemouth bass, bluegill [Lepomis macrochirus], goldfish [Carassius auratus], threadfin shad [Dorosoma petenense]) may enter these stream sections due to reservoir spilling, but they usually do not reproduce or persist long. Upper Silver Creek is a small, natural, generally unshaded stream with perennial flow (it runs in the Silver Creek Fault Zone). It contains only native threespine stickleback and California roach and is one of the few area streams that is both depauperate in native species and lacking introduced species.

Mixed Introduced/Native with Salmon Spawning (3)

Chinook salmon presently use the lower portions of Coyote Creek, the Guadalupe River, and occasionally Los Gatos Creek for spawning, accounting for about 7% of District stream miles with recorded fish habitat categories. Summer water temperatures and/or water quality are usually not suitable for summer salmonid rearing because of unshaded conditions, urban runoff, and low streamflows. However, juvenile chinook salmon may outmigrate to the Bay in spring before conditions deteriorate. Lowered water quality (high temperature, low dissolved oxygen, and turbidity) and abundant slow pools in these lower stream reaches usually shift species composition towards non-native species. Native Sacramento sucker and California roach and/or hitch are usually found at the salmon spawning sites. Likely introduced fishes include carp, goldfish, and mosquitofish. In Coyote Creek, the introduced and very adaptive red shiner (Notropis lutrensis) and fathead minnow (Pimephales promelas) are often the most abundant fish.

Table IV-B-3
Fish, Amphibian, and Reptile Species Compositions In Fish Communities of Santa Clara Valley

Species	Fish Habitat Categories
	Trout (7)	Steel-head (6)	PotentialTrout (5)	Warm Native (4)	Mixed; Spawning (3)	Native/ Introduced (2)	Limited (1)
NATIVE
Resident Rainbow Trout	RP	OP	OP	--	--	--	--
Steelhead	--	RP	RP	--	--	--	OP1
Riffle Sculpin	UP	UP	OP	--	--	--	--
Pacific Lamprey	OP	OP	OP	--	OP	--	--
California Roach	UP	UP	UP	UP	OP	OP	OP
Sacramento Sucker	UP	UP	RP	UP	UP	UP	OP
Threespine Stickleback	OP	OP	OP	UP	OP	--	--
Chinook Salmon	--	--	OP	--	RP	--	--
Sacramento Pikeminnow	--	OP	OP	UP	OP	--	--
Prickly Sculpin	OP	OP	OP	UP	UP	OP	--
Hitch	--	--	OP	OP	OP	UP	OP
Sacramento Blackfish	--	--	--	OP	OP	OP	--
Red-legged Frog	UP	UP	OP	OP	--	OP	OP
Yellow-legged Frog	--	--	--	OP	--	--	--
Western Pond Turtle	--	--	OP	UP	OP	OP	OP
INTRODUCED2
Green Sunfish	--	OP	OP	OP	OP	OP	OP
Goldfish	--	--	OP	OP	OP	UP	OP
Carp	--	--	--	OP	OP	OP	OP
Mosquitofish	--	--	--	OP	OP	UP	OP
Sunfish, other than green	--	--	--	OP	--	OP	--
Largemouth Bass	--	--	--	OP	--	OP	--
Fathead Minnow	--	--	--	--	OP	OP	OP
Red Shiner	--	--	--	--	OP	OP	OP
Bullfrog	--	--	OP	OP	UP	UP	--
Source: Jerry Smith 2001 Key: RP = indicator species, regularly present in community; UP = usually present; OP = often present. 1 Migration only. 2 List of introduced species is not complete but provides a representative sample of introduced species.

Mixed Native/Introduced Fish (2)

Introduced fish species are likely to be at least as abundant as native species in about 18% of District streams with recorded fish habitat categories. This species composition is especially common where water quality is impaired (Lower Llagas Creek and the Pajaro River in south county or Lower Penitencia, Lower Matedero, and Lower San Francisquito Creeks in the north county). Fisheries values are also relatively low where the habitat has been severely modified (channelized, with no pools or riparian vegetation), even if flows are perennial and water quality is not impaired (Canoas Creek). Since most of the introduced species prefer slower water, they are also likely to become dominant where percolation ponds provide abundant source populations from which these species disperse into streams. The effect is probably greatest where ponds usually remain in place for several years (Almaden Lake, Metcalf Pond, and Penitencia Creek Percolation Ponds) rather than where the ponds are removed annually (such as the formerly utilized seasonal percolation ponds on the Guadalupe River and Los Gatos Creek). Seasonal percolation ponds (which are not currently being used by the District) on streams without reservoirs (Saratoga Creek) or without substantial channel modifications (Stevens Creek) remain dominated by native fish species (categories 5 and 7).

Limited Fish Resources (1)

Many valley streams, especially smaller ones in urbanized areas or those in the drier southeast portion of the county, have been channelized and generally have only seasonal surface water; these habitats constitute about 26% of the stream miles in the District with recorded fish habitat categories. Some stream sections (lower Los Gatos Creek and Coyote Creek between Tully Road and Hellyer Park) serve as potential migration pathways for chinook salmon and steelhead. Others (most of Calabazas, Golf, and San Tomas Aquino Creeks) have limited fish values because they go dry in the summer of most years. They may provide habitat for fast-developing amphibians such as toads or tree frogs.

No Regular Value (0)

Some streams have surface flow only during storm events (Randol Creek and some of the tributaries to Little Llagas Creek). Such streams account for 16% of the stream miles in the District with recorded fish habitat categories. They do not provide habitat for fish or even for amphibians in most years.

Table IV-B-4 quantifies fish habitat Categories 0-7 by channel type: Natural (+/-), Mixed, and Concrete (see "District Channel Types" above, and Table IV-B-1 for channel type definitions). The fish habitat type is not known for 178 miles of channels that have been categorized by channel type. Natural (+/-) channels, which include the majority of District channels with recorded channel type conditions, contain most of the known fish habitat of all categories mapped within the District. About 98% of the steelhead habitat and almost 100% of the resident trout habitat occur in such channels.

Table IV-B-4
Fish Habitat by Channel Type

Fish habitat category provided in miles and percent of total miles for each habitat category.
Fish Habitat Type	Natural (+/-)		Mixed		Concrete		No Channel Type Data		Total Miles
	Miles	%	Miles	%	Miles	%	Miles	%
Trout (7)	20	100%	0	0%	<1	<1%	0	0%	20
Steelhead (6)	40	98%	1	2%	0	0%	0	0%	41
Potential Trout (5)	23	74%	7	23%	1	3%	0	0%	31
Warm Water Native (4)	20	95%	<1	<1%	1	5%	0	0%	21
Mixed; Spawning (3)	7	29%	16	67%	1	4%	0	0%	24
Native/ Introduced (2)	20	32%	31	49%	12	19%	0	0%	63
Limited (1)	46	51%	20	22%	25	27%	0	0%	91
No Value (0)	33	61%	15	28%	6	11%	0	0%	54
No Habitat Category Data	99	20%	34	7%	45	9%	306	63%	484
Total	308	37%	123	15%	91	11%	306	37%	829
Source: SCVWD 3/01; Jerry Smith 2001 Note: Numbers are rounded from calculations of habitat type miles. Total District miles = 828..

2) Aquatic Microorganisms and Invertebrates

In general, Santa Clara Valley streams become larger, flatter, sunnier, and warmer downstream. In addition, flatter streams tend to have fine sand or silt substrate, rather than the boulder, cobbles and gravels of headwater streams. These changes in habitat conditions determine plants, invertebrates and food chain patterns within valley streams.

Organisms in steep and fast streams must attach, root, burrow, or hide in crevices to prevent being washed away in winter. Attached diatoms and filamentous algaes are the predominant source of primary production. Higher aquatic plants (such as emergent cattails or rooted aquatic plants like pond weeds) are usually scarce because of the difficulty of rooting in coarse substrates and because of damage during winter floods. Single celled phytoplankton are absent from the water column because the current is too strong most of the year to allow them to become abundant; phytoplankton are important only in the slowest downstream or tidal reaches or in percolation ponds. In fast streams algae is scraped from rocks by larval mayflies (Order Ephemeroptera) and cased caddisflies (Trichoptera). In addition, fragments of algae and other fine particulate organic matter are filtered ("collected") from the water by blackfly larvae (Diptera) and net-spinning caddisflies. If algae is abundant enough, midge larvae are usually abundant as grazers within the algal mats. Stoneflies (Plecoptera) and hellgramites (Neuroptera) are often important insect predators in steep streams.

The most important large invertebrate is the non-native signal crayfish (Pacifasticus leniusculus), which is omnivorous and requires rock substrates and cooler, oxygenated water. All of the Santa Clara Valley crayfish are introduced; they are absent from some streams, such as Upper Penitencia Creek, because they have not yet been introduced or dispersed to the stream. Recent studies have indicated that crayfish, and probably the recently introduced mitten crab (Eriocheir sinensis), are important predators on eggs and larvae of frogs and salamanders. Mitten crab burrows are common in tidally influenced areas with steep banks that are high in clay content and lined with vegetation. The lower Guadalupe River has an abundant population of mitten crabs, and the species has been reported as far as 30 miles upstream from the mouth of Coyote Creek (San Francisco Estuary Project 1997).

Dissolved oxygen levels are high in steeper streams, and many invertebrates in such areas have large gills and require abundant dissolved oxygen. A byproduct of the large gill surface is rapid uptake and extreme sensitivity to toxic substances. Headwater species, such as cased caddisflies, stoneflies, hellgramites, and some of the mayflies, are good indicators of cool, oxygenated, contaminant-free conditions.

In slow stream reaches, plant detritus from upstream and from higher aquatic plants tends to accumulate on the bottoms of pools, providing both a potential food source and potentially depleting dissolved oxygen levels. Phytoplankton can be abundant and support small open water zooplankton (crustaceans, such as water fleas (Cladacera) and copepods). Larger shrimp, such as Neomysis, can be abundant in tidal reaches. Because of their small size (and large relative gill surface area), small zooplanton tend to be very sensitive to toxins. Insects that are abundant in slow water include many true bugs (Hemiptera), such as water boatmen (Corixidae) and water striders (Gerridae), and damsel and dragonflies (Odonata). Some of these slow water insects live on the surface (water striders) and breathe air or carry air bubbles down with them for breathing; lacking gills, these species can be abundant even where the water has inadequate oxygen for most gill breathers. The most likely crayfish in slow, muddy-bottomed downstream areas is the non-native, burrowing, swamp crayfish (Procambarus clarkii), which as its common name indicates, is tolerant of poor water quality.

Sunlit streams support abundant plant production from higher aquatic plants, attached algaes, or water column phytoplankton. In heavily shaded streams or those which are very turbid (muddy), however, light penetration may be limited to shallow water or the surface or pools, and aquatic plant production may be scarce. In heavily shaded streams the base of the food chain may instead come from leaves and twigs, dropped from the riparian plants coarse particulate organic matter, CPOM). In streams bordered by deciduous trees, such as alders, maples and willows, light may be available in winter and spring to support some aquatic plant growth. Evergreen borders (redwoods and evergreen oaks and bays) never permit much plant growth in narrow streams. The CPOM is processed by shredders, such as stoneflies and cased caddisflies, and their partially processed feces become an important food source for collectors, such as blackflies and netspinning caddisflies. The quality, as well as the quantity, of leaves affects insect abundance. Alders are nitrogen fixers, and their leaves are high in protein. Deciduous leaves are soft and easily processed and lack the hard structure and protective toxins (California bay and eucalyptus) and tanins (redwoods) of most of the evergreen leaves. Even though organic input from evergreens may be heavy, insects may be scarce compared to those produced from deciduous leaf food chains.

3) The Effects of Watershed Development on Fish Habitat

Ongoing stream maintenance is only one of numerous developments within Santa Clara County watersheds that affects fisheries. Development in Santa Clara Valley has altered flow regimes and the extent, species composition, and density of riparian corridors (Clarke 1959, Rottenborn 1997). Upstream habitats once supported resident rainbow trout and steelhead (categories 7 and 6), and downstream habitats supported warm-water fishes (categories 4 and 5). Many of the streams were small or shallow, and sites with only warm-water fishes contained only sculpins, California roach, and Sacramento suckers. Slow, permanent, deepwater habitats were confined to lower Coyote Creek and to the Pajaro River and its larger tributaries (Leidy 1984). Coyote Creek and the Pajaro River system are still the only streams in Santa Clara County that contain Sacramento pikeminnow and Sacramento blackfish. Tule perch, Sacramento perch, and possibly thicktail chub (Gila crassicauda) and splittail (Pogonichthys sp.) were present in both Coyote Creek and the Pajaro River, but the latter three species are now gone from the county, and tule perch may be gone as well (Leidy 1984). Similar losses occurred statewide; thicktail chub is extinct and Sacramento perch and splittail are rare in California.

Agricultural pumping drastically lowered groundwater levels by the 1930's, eliminating most artesian wells and summer flow for valley floor streams. Dam construction in the 1930's through 1950's resulted in reservoirs on Los Gatos Creek (Lexington and Vasona), Stevens Creek (Stevens Creek Reservoir), Guadalupe Watershed (Calero, Almaden, and Guadalupe), Coyote Creek (Coyote and Anderson), and the Pajaro watershed (Pacheco, Chesbro, and Uvas). Water was not (and mostly still is not) used directly from the reservoirs, but was percolated in streambeds and pumped from wells for agricultural and municipal use. In-channel and near-channel percolation ponds were later developed to increase percolation capacity, primarily in the Coyote Creek and Guadalupe River Watersheds. The combined results of heavy groundwater pumping and reservoir/percolation operations have been to reduce winter runoff intensity, reduce summer flow in many stream sections, and greatly increase summer flow in stream sections downstream from most of the reservoirs or used for percolation.

Construction of reservoirs blocked steelhead access to much of their former spawning and rearing habitat. None of the dams has a fish ladder, although the water right for Uvas Reservoir calls for providing fish passage (by fish ladder or trapping and trucking) if fish are unable to ascend the impassable spillway.

Beginning in 1965, imported (Delta) water was brought into the valley, and an extensive system of pipelines was constructed to distribute water among the watersheds. Additional water could then be percolated in streams without reservoirs (Saratoga and Calabazas Creeks) or with small reservoirs (Stevens and Upper Penitencia Creeks). Only Uvas Reservoir presently has a year-round minimum release requirement as a stated part of its water right. In the remainder of the valley, reservoir and pipeline operations are currently primarily controlled by water supply concerns.

Downstream of the reservoirs the bottom releases in early to midsummer are cooler than historical flows. However, draining down the reservoirs, especially the smaller ones, by late summer often results in warmer water temperatures in late summer and fall. Fish species composition has been changed by the altered temperature patterns below some of the dams. The reduced winter flows have also allowed current-intolerant fish (such as native hitch and Sacramento blackfish) to expand upstream.

Urbanization of the valley has increased impervious surfaces, resulting in exaggerated flood peaks for frequent events. The need for flood protection has resulted in channel excavations and realignments and levee construction. Drop structures, constructed in many stream channels to flatten and stabilize channel grade, act as barriers to fish movement (Saratoga, San Tomas, Calabazas Creeks). Even where fish ladders are constructed at drop structures (e.g., Stevens Creek), fish passage may be limited.

4) Fish Utilization of Reservoirs and Percolation Ponds

Although reservoirs and percolation ponds are not included in the SMP project area, these facilities are a significant habitat component of streams within the District's jurisdiction. They provide habitat for both native and non-native species and a source from which many species may disperse into project area streams.

The artificial habitats provided by reservoirs and percolation ponds have provided warm-water lake conditions, a habitat type originally rare in California. Most of the native fishes require running water for reproduction, and few (exce