A survey of the toxicity of sediments was performed by NOAA's National Status and Trends (NSandT) Program throughout the Hudson-Raritan Estuary. The objectives of the survey were to determine the spatial patterns of toxicity, the spatial scales (magnitude) of toxicity, the severity (frequency) of toxicity, and the relationships among measures of toxicity and chemical substances in the sediments. This survey was conducted as a part of a nationwide program supported by NOAA's Coastal Ocean Program and the NSandT Program, in which the biological effects of toxicants are determined in selected estuaries and bays. The survey was conducted in two phases: 117 samples were collected throughout the entire estuary during 1991 (Phase 1) and an additional 57 samples were collected in Newark Bay and vicinity during 1993 (Phase 2). Relatively sensitive toxicity tests were performed under controlled laboratory conditions with portions of each sample. During Phase 1, three independent tests were performed: (1) a 10-day, acute survival test of solid-phase sediments with the amphipod Ampelisca abdita; (2) a 48-hour liquid phase test of elutriates with the embryos of the bivalve Mulinia lateralis in which both percent survival and normal embryological development were recorded; and (3) a 15-minute microbial bioluminescence test (Microtoxtm) of organic solvent extracts. Only the amphipod tests were performed on the samples collected during Phase 2. Chemical analyses of selected samples were performed and the concentrations of trace elements, polynuclear aromatic hydrocarbons (PAHs), chlorinated pesticides and other hydrocarbons were reported. Also, during Phase 2 the concentrations of numerous chlorinated dioxins and furans were determined.