Analysis of the spatial distribution of the dinoflagellate cyst assemblages in 19 surface sediment samples collected from 3 Buzzards Bay (Massachusetts, USA) embayments revealed the potential applicability of dinoflagellate cysts as biological indicators of environmental conditions in estuarine systems. Sites with the highest levels of toxic pollution and hypertrophic conditions are characterized by the lowest dinoflagellate cyst species-richness and concentrations. Among the abiotic factors influencing the distribution of dinoflagellate cysts, nutrients and toxic pollution are the major controls, as in these embayments salinity and temperature variability is low. Principal component analysis, based on the proportions of cyst taxa, indicated that cyst assemblages gradually change when moving away from the sources of nutrient pollution, sewage outfalls in particular.