Summary of Major Issues and Findings -

This report summarizes the major findings of the National Water-Quality Assessment (NAWQA) for the San Joaquin-Tulare Basins, California. The brief statements of the major findings that follow are expanded on later in this report (p. 6-19). Comparisons of data within this Study Unit with data from all 20 Study Units nationwide are given in descriptive (p. 20-23) and tabular (p. 26-31) formats. Additional information on the methods, approaches, and findings of all the investigations of the San Joaquin-Tulare Basins NAWQA studies is available in the technical reports listed on pages 32-33. Though this report is an integral part of a national study, it also is intended to serve as a stand-alone resource for anyone interested in water quality in California.

A wide variety of pesticides occur in the San Joaquin River and its tributaries, some at concentrations high enough to adversely impact aquatic life.

• Forty-nine pesticides were detected in the San Joaquin River and three subbasins, 22 of which were detected in more than 20 percent of the samples. Available drinking-water standards were not exceeded, but the concentrations of seven pesticides exceeded the criteria for the protection of aquatic life.
• Pesticide occurrence is related to the timing and spatial distribution of pesticide application; the most frequent occurrence and highest concentrations generally coincide with the time of heaviest agricultural application.
• Crop type and basin characteristics affect spatial and seasonal variability of pesticide occurrence.
• The main source of organophosphate insecticides is the application to dormant orchards. Concentrations of organophosphate insecticides in runoff are high, and highly variable, during winter storms. Peak diazinon concentrations in Orestimba Creek, in the Merced and the Tuolumne Rivers, and in the main stem of the San Joaquin River frequently exceeded levels that can be acutely toxic to some aquatic life.
• Diazinon and other pesticides were also found to be transported to the Tuolumne River in stormwater runoff from the Modesto urban area.

Long-banned organochlorine insecticides, such as DDT, are bound to soil particles in areas of past application. The soils and associated bound pesticides are transported to streams by soil erosion during natural or irrigation-related runoff. Once in the stream, organochlorine insecticides are taken up by organisms and bioaccumulated through the food chain. These compounds have been shown to be harmful to wildlife and humans that consume them. (p. 10-11)

Long-banned organochlorine insecticides continue to be transported to streams by soil erosion of contaminated agricultural fields, resulting in contamination of suspended sediment, bed sediment, and aquatic organisms.

• Concentrations of organochlorine insecticides, such as DDT, toxaphene, and chlordane, in tissues of clams and fish from the San Joaquin River and its western tributaries, were high relative to national values obtained in the 1970s and 1980s.
• Concentrations of DDT compounds in fine-grained bed sediments and tissue samples are correlated, suggesting that bioaccumulation is taking place.
• Most whole-water concentrations of p,p´-DDT, chlordane, dieldrin, and toxaphene exceeded chronic criteria for the protection of freshwater aquatic life.
• Runoff from winter storms will continue to deliver a substantial load of sediment-bound organochlorine insecticides to the San Joaquin River, even if irrigation-induced soil erosion is reduced.

Designated beneficial uses for the San Joaquin River include drinking water and the aquatic ecosystem. Nitrate and ammonia criteria have been set by USEPA to protect these beneficial uses. The San Joaquin River Basin has many sources of nitrate and ammonia: fertilizer and manure, subsurface agricultural drains, dairies, and wastewater- treatment plants. (p. 12-13)

Some nitrate and ammonia concentrations exceed criteria in some small tributaries, but generally do not limit beneficial uses in the main stem of the San Joaquin River.

• Mud and Salt Sloughs account for only about 10 percent of the streamflow but contribute nearly half the nitrate load in the San Joaquin River.
• Nitrate concentrations in the San Joaquin River have been increasing over the last 40 years, but concentrations are still well below the drinking-water standard.
• Ammonia criteria were frequently exceeded in Turlock Irrigation District lateral 5, and occasionally in Orestimba Creek and Spanish Grant Drain. None of the samples collected in the main stem of the San Joaquin River exceeded criteria during 1993-95.

Development of water resources in the San Joaquin River drainage, including the Sacramento-San Joaquin Delta, has been accompanied by large-scale changes in the aquatic ecosystems, including fish populations. Anadromous salmon have declined, along with other migratory and resident native fish species. Though there are likely multiple reasons for declines in native fish species, the roles of water chemistry and habitat degradation have never been addressed on a basinwide basis. (p. 14-15) 

Fish communities in the San Joaquin River and its tributaries change in response to water chemistry and habitat quality in a pattern suggesting that human activities, including agriculture, are important factors in controlling the distribution and abundance of fish species. Fish communities in the lower San Joaquin River were highly degraded compared with other NAWQA Study Units, as was stream habitat at some sites.

• Introduced fish species outnumber native fish species by almost 2 to 1.
• In the lower San Joaquin River drainage, four groups of sites can be defined on the basis of fish communities. Native species were most common near the foothill dams and were gradually replaced by different groups of introduced species in downstream areas where land use is dominated by agriculture and other human activities.
• The Stanislaus River appeared to provide the best habitat for native species of the three major tributaries studied, possibly because of the way flow is managed in the Stanislaus River compared with that of the Tuolumne and Merced Rivers.
• Fish communities provide a useful assessment of overall stream health of San Joaquin Valley streams. Though the analysis cannot separate the individual effects of water chemistry (including toxicity) and habitat quality, both appear to be important.

Ground water is the primary source of drinking water for the majority of the population in the eastern San Joaquin Valley. Millions of pounds of pesticides and fertilizer have been used on agricultural land in the valley. Prior data have shown ground-water contamination by agricultural nonpoint sources. (p. 16-19)

Nitrate concentrations in ground water frequently exceeded drinking water standards; however, pesticide concentrations rarely exceeded drinking-water standards, with the notable exception of 1,2,-dibromo-3-chloropropane (DBCP).

• Nitrate concentrations in ground water in the eastern San Joaquin Valley exceeded the U.S. Environmental Protection Agency (USEPA) drinking-water standard in about one fourth of the domestic water-supply wells sampled.
• Nitrate concentrations in shallow ground water were related to the overlying agricultural land-use setting; concentrations varied among different agricultural land-use settings and were linked to fertilizer application, physical characteristics of the sediment, and biochemical processes in ground water.
• Nitrate concentrations in ground water have increased since the 1950s. From 1950 to 1980, the largest source of nitrate--nitrogen fertilizer--also increased from 114 to 745 million pounds per year.
• Pesticides were detected in about two-thirds of the ground-water samples collected from domestic water supply wells, but concentrations of most pesticides were low--less than 0.1 microgram per liter (µg/L).
• DBCP concentrations exceed the USEPA drinking-water standard of 0.2  g/L in 20 percent of the domestic water supply wells sampled. Data from monitoring wells show that DBCP concentrations generally decrease with depth and are highly variable near the water table.
• Pesticide concentrations in ground water generally have not increased in the last decade on the basis of a small number of wells sampled (19) during 1986-87 and again in 1995. Direct comparison of the data is difficult because of changes in detection limits.