The Hudson-Raritan Estuary is one of several United States coastal areas where chemical data have suggested a potential for contaminant-related biological effects, and multiyear intensive bioeffects surveys have been conducted by the National Oceanic and Atmospheric Administration. The severity and spatial patterns in sediment toxicity were determined in an estuary-wide survey during spring 1991 using amphipods, bivalve larvae, and luminescent bacteria as test organisms. Spatial patterns in toxicity corresponded to the distributions of a number of toxic chemicals in the sediments. Areas that exhibited the greatest sediment toxicity included the upper East River, Arthur Kill, Newark Bay, and Sandy Hook Bay. The lower Hudson River adjacent to Manhattan Island, upper New York Harbor, lower New York Harbor off Staten Island, and parts of western Raritan Bay generally showed lower toxicity. Supporting chemical analyses of the sediments, including acid-volatile sulfide and simultaneously-extracted metals, suggested that metals were generally not the cause of the observed toxicity, with the possible exception of mercury. Among all contaminants analyzed, toxicity was most strongly associated with polynuclear aromatic hydrocarbons, which were substantially more concentrated in toxic samples than in nontoxic samples, and which frequently exceeded sediment quality criteria.