Extensive data sets of water quality and sediment chemistry as well as detailed historical records were used to analyze environmental factors controlling dinoflagellate cyst distribution in shallow estuaries (lagoons and embayments) of southern New England. Cyst abundance, species richness, the proportion of cysts produced by heterotrophic and autotrophic dinoflagellates, and the composition of cyst assemblages reflect spatial and temporal variation in environmental conditions. The cyst record in sediment cores from two embayments, New Bedford Harbor and Apponagansett Bay, Massachusetts demonstrates cyst sensitivity to environmental change caused by anthropogenic activity in the watersheds. Intensive industrialization and urbanization occurred during the 20th century in New Bedford Harbor resulted in extreme eutrophication and toxic pollution (heavy metals and PCBs). These conditions are reflected in declining cyst diversity and wide fluctuation in total cyst production. At the same time, the proportion of certain heterotrophic taxa increases. As impacts of extreme eutrophication and toxic pollution cannot be separated, the cyst response must be interpreted as a cumulative «pollution signal». The spatial distribution of modern dinoflagellate cysts in the area supports this signal. Cysts vary along gradients of nutrient enrichment, corresponding to distance from sewage outfalls. Dinoflagellate cysts in surface sediments from New England lagoons also were studied. A comparison of assemblages to water quality parameters, that are affected greatly by the degree of water exchange between lagoon and ocean, indicates that temperature and salinity are the main abiotic factors controlling cyst distribution in these estuaries. A new species of dinoflagellate cyst, Islandinium brevispinosum, has been identified and described. This species was found within a narrow range of water temperature and salinity, and at elevated nutrient levels. Dinoflagellate cysts reflect environmental conditions at the small spatial scales necessary to characterize variability within estuaries. However, the relative importance of abiotic factors controlling the spatial and temporal distribution of dinoflagellate cysts is likely to vary with the hydrological differences between lagoons and embayments. Therefore, dinoflagellate cysts can be useful indicators of environmental conditions in and human impacts on shallow estuaries.

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