Human activities, including development of water resources, agriculture, and urbanization in the San Joaquin-Tulare Basins, have been accompanied by large-scale changes in aquatic ecosystems. Populations of anadromous salmon have declined, along with other migratory and resident native species. Though there are likely many reasons for the decline, the roles of water chemistry and habitat degradation have not been assessed on a basin-wide scale. Fish communities were sampled in the San Joaquin-Tulare Basins to determine their status and whether they provided useful indications of water chemistry and habitat conditions.
Assessments of fish communities were made at 32 sites during August and September from 1993 to 1995. Fish were collected and identified to species, and habitat and water-chemistry data were collected at each site (Meador and others, 1993a,b). A total of 34 species of fish were collected. Twelve species were native to California and 22 species were introduced from outside California. Native species were generally more abundant at higher elevation sites in the valley, the foothills, and the Sierra Nevada. Introduced species were generally more abundant at lower elevation sites on the valley floor. High percentages of introduced species are considered an indication of impaired water chemistry and habitat conditions (Hughes and Gammon, 1987; Karr, 1991).
Using the fish data collected, groups of sites with similar relative abundances of fish species were defined using statistical techniques. This analysis was done twice: once for the 20 low-elevation sites most likely to be affected by human activities, and once for all of the 32 sites sampled.
The 20 low-elevation sites were all in the lower San Joaquin River drainage, downstream from the major foothills reservoirs. Four groups of sites were identified on the basis of fish communities, water chemistry, and habitat quality: a San Joaquin Main Stem group, a Lower Tributary group, a Stanislaus River group, and an Upper Tributary group.
At the 20 lower elevation sites, fish communities, habitat, and water chemistry varied significantly among the site groups. (SC - Specific conductance; CF - Cover for fish; AL - Agricultural land).
The San Joaquin Main Stem group was characterized by high percentages of introduced species tolerant of harsh environmental conditions, particularly the fathead minnow, red shiner, threadfin shad, and inland silverside (all referred to as the San Joaquin Main Stem species). The San Joaquin Main Stem group included eight sites on the main stem of the San Joaquin River and on small western and southern tributary streams. Specific conductance (an indicator of salinity), which was highest at these sites, is a good indicator of general water chemistry and of the influence of irrigation return flows in the San Joaquin River drainage. Fish cover--the percentage of area that provides cover from predators--was lowest at these sites. Environmental degradation, as indicated by increased specific conductance and decreased fish cover, was related to human activities such as agricultural land use. The Lower Tributary group was characterized by high percentages of introduced largemouth bass, redear sunfish, and white catfish. These sites were located in the lower and middle reaches of the Merced and Tuolumne Rivers, but only the farthest downstream site on the Stanislaus River. Values of specific conductance, fish cover, and agricultural land use were intermediate between the Upper Tributary and San Joaquin Main Stem groups.
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Riparian and instream habitats are good at Orestimba Creek, but because water chemistry is poor and fluctuations in flow are substantial, the site had a high percentage of introduced fish species (photograph by Larry R. Brown, U.S. Geological Survey).
The Upper Tributary group included the farthest upstream site on the Stanislaus and Merced Rivers, and the two farthest upstream sites on the Tuolumne River. These sites were characterized by high percentages of the native species: Sacramento squawfish, hardhead, Sacramento sucker, and prickly sculpin. Specific conductance and agricultural land use were lowest at these sites, and fish cover was highest.
The two middle sites on the Stanislaus River formed a separate group characterized by high percentages of introduced smallmouth bass and native tule perch. Water chemistry and habitat were similar to the Upper Tributary sites.
The second analysis, which was based on the fish data from all 32 sites, also resulted in four groups of sites: a San Joaquin Main Stem group, a Foothill group, a Lower Tributary group, and a Sierra Nevada group. The San Joaquin Main Stem group was identical and the Lower Tributary group very similar to the groups obtained using 20 sites. The Foothill group included all but one site in the previously defined Upper Tributary group, the Stanislaus River group, and additional sites located upstream from the foothill reservoirs. These sites were characterized by native Sacramento squawfish, hardhead, tule perch, sculpins, and introduced smallmouth bass. The Sierra Nevada group was dominated by native rainbow trout and introduced brown trout. Water chemistry and habitat conditions were very different among site groups, as would be expected in a study that included small, cold, high-elevation streams and large, warm, low-elevation rivers. Thus, these groups are most indicative of large-scale, natural gradients and less related to environmental impairment than the groups obtained from the analysis of 20 low-elevation sites.
Overall environmental quality is reflected by fish communities: native species are common at the least altered sites, and tolerant introduced species are common at the most altered sites. However, the influences of water chemistry and habitat on fish communities could not be separated because both sets of variables were related to land use (Brown and others, in press). Additional variables may also contribute to this pattern. Dissolved pesticide concentrations sometimes reached levels toxic to some invertebrates, primarily at sites in the San Joaquin Main Stem group. Similarly, concentrations of organochlorine insecticides in sediments and tissues of biota were highest at sites in the San Joaquin Main Stem group (Brown, 1997). The dominance of tolerant introduced species at the San Joaquin main stem sites is consistent with these patterns.
Environmental degradation due to human activities may have been stressful to resident fish as indicated by the high incidence of external abnormalities, such as parasites and lesions, at the Lower Tributary sites (21 percent) and San Joaquin main stem sites (17 percent). The incidence of abnormalities was much lower at the Stanislaus River (3 percent) and Upper Tributary sites (3 percent). In other areas of the country, an incidence of external abnormalities greater than 2 percent is considered an indicator of impaired conditions (Hughes and Gammon, 1987; Karr, 1991).
The rarity of native fishes at the Lower Tributary and San Joaquin main stem sites may not be irreversible. High discharges in 1995 in the Merced and Tuolumne Rivers were accompanied by higher percentages of resident and migratory native species. Statistical analysis of data from sites sampled in more than one year indicated that fish communities in 1993 and 1994 were very similar, but in 1995 were very different from the other years. Also, the greater abundance of native species in the Stanislaus River, particularly tule perch, at downstream sites compared with the other eastern tributaries, suggests that the higher summer flows favor native species. Further monitoring during different flow conditions could help determine conditions necessary to reestablish native fish communities.
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This site on the Stanislaus River has good riparian habitat, instream habitat, and water chemistry (photograph by Larry R. Brown, U.S. Geological Survey).