The 1985-88 study period included hydrologic extremes throughout most of central California. Except for an 11-month period during and after the 1986 flood, San Joaquin River streamflows during 1985-88 were generally less than median for 1975-88. The Merced Tuolumne, and Stanislaus Rivers together comprised 56 to 69 percent of the annual San Joaquin River flow, Salt and Mud Sloughs together comprised 6 to 19 percent, the upper San Joaquin River comprised 2 to 25 percent, and unmeasured sources from agricultural discharges and ground water accounted for 13 to 20 percent. Salt and Mud Sloughs and the unmeasured sources contribute most of the dissolved-solids load. The Merced, Tuolumne, and Stanislaus Rivers greatly dilute dissolved-solids concentrations. Suspended-sediment concentration peaked sharply at more than 600 milligrams per liter during the flood of February 1986. Concentrations and loads varied seasonally during low-flow conditions, with concentrations highest during the early summer irrigation season. Trace elements present primarily in dissolved phases are arsenic, boron, lithium, molybdenum, and selenium. Boron concentrations exceeded the irrigation water-quality criterion of 750 micrograms per liter more than 75 percent of the time in Salt and Mud Sloughs and more than 50 percent of the time at three sites on the San Joaquin River. Selenium concentrations exceeded the aquatic-life criterion of 5 micrograms per liter more than 75 percent of the time in Salt Slough and more than 50 percent of the time in Mud Slough and in the San Joaquin River from Salt Slough to the Merced River confluence. Concentrations of dissolved solids, boron, and selenium usually are highest during late winter to early spring, lower in early summer, higher again in mid-to-late summer, and the lowest in autumn, and generally correspond to seasonal inflows of subsurface tile-drain water to Salt and Mud Sloughs. Trace elements present primarily in particulate phases are aluminum, chromium, copper, iron, manganese, nickel, and zinc, none of which cause significant water-quality problems in the river.