A synoptic reconnaissance survey was performed over a five-day period in August 1988 to assess benthic habitat quality throughout Narragansett Bay, Rhode Island, using REMOTS® sediment-profile photography and analysis in combination with measurements of the levels ofClostridium perfringens spores (a fecal indicator) in sediments. Three main areas of degraded benthic habitat quality related to either excessive organic enrichment or physical disturbance were identified based solely on the REMOTS® analysis: the Providence River Reach, Greenwich Bay and its associated coves and harbors, and an area located along the southwest side of Prudence Island. Sediments at many stations in these areas exhibited shallow apparent redox-potential discontinuity (RPD) depths, high apparent oxygen demand, and low-order benthic successional stages. ElevatedClostridium perfringens spore counts in surface sediments were attributed to inputs from wastewater treatment facilities. The highest spore counts occurred at the head of the bay, where wastewater treatment discharges and associated combined sewer overflows are numerous. Using data from the REMOTS® analysis and the sediment inventory ofC. perfringens spores, a distinction was made between organic enrichment of the bottom from sewage, versus nonsewage enrichment or physical disturbance. The combination of techniques employed in this investigation could be used to design more efficient monitoring programs to assess eutrophication effects in estuaries and determine the effectiveness of regulatory or management initiatives to reduce organic overenrichment of benthic habitats.