A study was conducted in 1992 to assess the effects of anthropogenic activities and land use on the water quality of the San Joaquin River and its major tributaries. This study focused on pesticides and organic contaminants, looking at distributions of contaminants in water, bed and suspended sediment, and the bivalve Corbicula fluminea. Results indicated that this river system is affected by agricultural practices and urban runoff. Sediments from Dry Creek contained elevated concentrations of polycyclic aromatic hydrocarbons (PAHs), possibly derived from urban runoff from the city of Modesto; suspended sediments contained elevated amounts of chlordane. Trace levels of triazine herbicides atrazine and simazine were present in water at most sites. Sediments, water, and bivalves from Orestimba Creek, a westside tributary draining agricultural areas, contained the greatest levels of DDT (1,1,1-trichloro-2-2-bis[p-chlorophenyl]ethane), and its degradates DDD (1,1-dichloro-2,2-bis[p-chlorophenyl]ethane), and DDE (1,1-dichloro-2,2- bis[p-chlorophenyl]ethylene). Sediment adsorption co efficients (K(oc)), and bioconcentration factors (BCF) in Corbicula of DDT, DDD, and DDE at Orestimba Creek were greater than predicted values. Streams of the western San Joaquin Valley can potentially transport significant amounts of chlorinated pesticides to the San Joaquin River, the delta, and San Francisco Bay. Organochlorine compounds accumulate in bivalves and sediment and may pose a problem to other biotic species in this watershed.