A survey of trace element and synthetic organic compound concentrations in botton materials was conducted on the Apalachichola River in northwest Florida in 1979-80 as part of the Apalachicola River Quality Assessment. Substances analyzed included trace elements (predominantly heavy metals), organochlorine insecticides, organophosphorus insecticides, chlorinated phenoxy-acid herbicides, and polychlorinated biphenyls (PCBs). Three kinds of materials were surveyed: fine-grained sediments, whole-body tissue of the Asiatic clam Corbicula manilensis, and bottom-load organic detritus. No hazardous levels of any of the substances were found. Concentrations in the fine-grained sediments and clams were generally at least ten times lower than maximum limits considered safe for biota of aquatic systems. A comparison of trace-substance data from the Apalachicola River with data from Lake Seminole (upstream) and Apalachicola Bay (downstream) showed lower concentrations in riverine clams. Sediment concentrations in all parts of the system were comparable. Most trace substances in the Apalachicola River enter the river from the upstream part of the basin (the Chattahoochee and Flint Rivers in Georgia and Alabama) and from nonpoint sources throughout the basin. There are no major point discharges along the Apalachicola. Trend analysis was limited by the scope of the study, but did not reveal any spatial or temporal trends in concentrations of any of the substances analyzed. Concentrations of organic compounds and most metals in Corbicula manilensis did not correlate with those in sediments.