(i) Trace element concentrations in soft tissue of the benthic bivalve, Corbicula fluminea, from the San Joaquin River and its major tributaries were examined during the primary irrigation season in relation to the spatial variation in concentrations of major, minor and trace constituents in riverwater and sediments. (ii) Selenium concentrations in Corbicula from perennial flow reaches of the San Joaquin River and its major tributaries varied directly with the solute (??? 0.45 ??m) Se concentrations of riverwater. Elevated concentrations occurred in clams from sites with substantial discharge originating as subsurface drainage and irrigation return flows. Both tissue and solute Se concentrations declined from June through the end of the primary irrigation season. (iii) Arsenic concentrations in Corbicula from perennial flow reaches of the San Joaquin River varied directly with the HNO3-extractable (pH 2) As:Fe ratio of suspended matter, providing evidence that sorption to oxyhydroxide surfaces is an important control on the biological availability of As. However, Corbicula from several tributaries draining alluvium derived from the Sierra Nevada had lower As concentrations than would be predicted by the relation developed for perennial flow sites of the San Joaquin River. Arsenic concentrations in Corbicula from the Tuolumne and Merced Rivers and upstream reaches of the San Joaquin River were higher than in clams from the downstream perennial flow reaches of the San Joaquin River. Concentrations of As in clams from downstream perennial flow reaches of the San Joaquin River increased from June through the end of the primary irrigation season. (iv) Mercury concentrations in Corbicula were elevated in upstream reaches of the San Joaquin River, in the Merced and Tuolumne Rivers, and in tributaries draining the Coast Ranges. Mean Cd and Cu concentrations in Corbicula were elevated in the Merced and Tuolumne Rivers, Orestimba Creek and a perennial flow reach of the San Joaquin River which receives water directly from the Delta Mendota Canal. Concentrations of Ni in clams from the San Joaquin River decreased downstream of the Delta Mendota Pool. (v) Boron and Mo were not accumulated by Corbicula despite high solute concentrations (means as high as 2960 ??g B l-1 and 9 ??g Mo l-1) in riverwater during the primary irrigation season. This bivalve may not be an appropriate bioindicator of B and Mo enrichment. Concentrations of Cr, Pb, Ag, V and Zn in Corbicula exhibited little geographic variability in the drainage. (vi) Regression analysis revealed no clear evidence of synergistic or antagonistic interactions among As, Cd, Cu, Hg, Ni and Se in their uptake by Corbicula.