The dinoflagellate cyst records in sediments from New Bedford Harbor and Apponagansett Bay demonstrate sensitivity to environmental change caused by human activity in the watersheds over the last 500 years. Changes in the species richness, as well as absolute and relative abundance of dinoflagellate cyst taxa reflect recent periods of development around the estuaries. Cyst taxa sensitive to these changes include Dubridinium spp., Polykrikos schwartzii, Lingulodinium machaerophorum, Operculodinium israelianum and Selenopemphix quanta. The greatest changes in the dinoflagellate cyst record occur during the 20th century, when New Bedford Harbor was exposed to both toxic pollution and heavy nutrient loading from point and non-point sources. Apponagansett Bay was not subject to industrial pollution and nutrient enrichment has been lower (from non-point sources). In Apponagansett Bay there is an increase in the dinoflagellate cyst species richness while species richness first increased, then declined in New Bedford Harbor. During the same period, the total dinoflagellate cyst concentration in New Bedford Harbor fluctuated over a wide range. The decline of species richness and the large fluctuations in the total cyst abundances signal the intensified anthropogenic disturbance in the watershed, notably a high degree of eutrophication and toxic pollution.