Resting cysts attributed to the freshwater dinoflagellate genus Peridinium were found in surface sediments from Severn Sound, southeastern Georgian Bay (Lake Huron, Laurentian Great Lakes of North America). Two distinct cyst morphotypes were present and they were assigned to Peridinium wisconsinense Eddy, 1930 and Peridinium willei Huitfeldt-Kaas, 1900 by establishing cyst–theca relationships through germinations and single-cell LSU rDNA analysis on an excysted cell of Peridinium willei. Sediments recovered from deep, sheltered portions of Severn Sound and restricted basins like Honey Harbour contained between ~ 750 and 8500 cysts/cm3. However, winnowing by bottom currents and high concentrations of dissolved oxygen adversely impact the dinoflagellate cyst record on the lakebed, and cyst concentrations in easily remobilized muds on bathymetric highs were < 100 cysts/cm3. Down-core changes in the relative abundances of these two cyst morphotypes were attributed primarily to cultural eutrophication related to land-use changes around Severn Sound over the last six centuries. Cysts of Peridinium willei, a cosmopolitan dinoflagellate species that occurs in a broad range of temperature, pH and nutrient conditions, comprise 60–74% of the cysts identified in Ambrosia (ragweed)-rich sediments in the upper 20 cm of a gravity core taken from Honey Harbour. Euro-Canadian settlement and land-clearing that began in the Midland-Penetanguishene region around A.D. 1840 are evident in the increase in Ambrosia (ragweed), Gramineae (grasses) and other herbs (non-arboreal pollen) that mark the base of the Ambrosia zone (pollen zone 4) as well as an overall increase in terrigenous flux. In addition to siltation, this terrigenous flux increased the availability of limiting nutrients to the previously oligotrophic waters of Severn Sound, leading to increased cyst flux in Honey Harbour peaking at nearly 3000 cysts/cm2/y in A.D. 1966, an order of magnitude higher than cyst fluxes prior to the Euro-Canadian Ambrosia zone. Peridinium wisconsinense was the more common dinoflagellate cyst species in Honey Harbour prior to Euro-Canadian settlement, when cyst flux was an order of magnitude lower. This is consistent with the restriction of this species to relatively warm, oligotrophic to mesotrophic lakes in North America. An earlier increase in P. willei at the expense of P. wisconsinense in the core from Honey Harbour within pollen zone 3 d (~ 700 to ~ 150 yBP) is attributed to earlier land-clearing by the Wendat (“Huron”), who practiced agriculture in the Penetanguishene peninsula between ~ A.D. 1450–1650. The cysts of these freshwater dinoflagellates thus appear to be sensitive to cultural eutrophication.