Whole-body samples of bluegills (Lepomis macrochirus) and common carp (Cyprinus carpio) from the San Joaquin River and two tributaries (Merced River and Salt Slough) were analyzed to determine if the concentrations of any of nine elements were elevated as a result of exposure of the fish to agricultural subsurface (tile) drainage water. Highest concentrations (μg/g dry weight) detected were as follows (first number in each pair applies to bluegills and the second to carp): arsenic (As), 0.97 and 1.5; boron (B), 14 and 20; cadmium (Cd), 0.14 and 0.27; chromium (Cr), 2.7 and 2.2; mercury (hg), 3.3 and 2.9; molybdenum (Mo), 2.8 and 3.6; nickel (Ni), 0.87 and 2.2; lead (Pb), 0.26 and 2.3; and selenium (Se), 3.2 and 5.5. The lowest concentrations were below the levels of detection, except for Hg (0.15 in bluegills and 0.12 in carp) and Se (0.43 and 0.56). As judged by comparisons with data from the National Contaminant Biomonitoring Program and other published surveys, the concentrations of B, Hg, Mo, and Se were moderately elevated in fish from several sites in the San Joaquin Valley. However, only the Se concentrations were positively correlated with water quality variables (e.g., total alkalinity, conductivity, and turbidity) known to be influenced by irrigation return flows. Historical data from one site (Salt Slough), where trace elements in whole fish have been measured since 1969, indicated that Se concentrations increased more than twofold between 1973 and 1977, but thereafter remained near 3.0 μg g−1 (dry weight basis), presumably due to the continuing practice of disposing seleniferous tile drainage water into the most convenient stream channel.