Concern about degradation in estuarine water quality has prompted a search for indicators that can be used to predict and reconstruct estuarine health. We are examining the utility of dinoflagellate cysts (or hypnozygots produced by dinoflagellates, which can be preserved in sediments) as high-resolution indicators of environmental conditions in estuaries. We measured chemical contamination and analyzed dinoflagellate cyst assemblages in surface sediments collected from three neighboring embayments of Buzzards Bay, Massachusetts. Characteristics of cyst assemblages reflect variations in salinity and nutrient status of embayment waters, as well as sediment chemistry. We found a significant negative relationship between dinoflagellate cyst diversity and sediment concentrations of copper and organic carbon. Sedimentary cyst concentrations, serving as a proxy of dinoflagellate production, were lowest in the heavily polluted sites of New Bedford Harbor. Principal component analysis, based on proportions of cyst taxa, indicates that cyst assemblages gradually change when moving away from sources of nutrient pollution, and sewage outfalls in particular. Quantitative and qualitative analyses of dinoflagellate cyst assemblages demonstrate that cysts do reflect environmental conditions such as levels of pollution, nutrients and salinity in estuarine systems, and thus can be sensitive indicators of those conditions.