Various types of algae (dominantly desmids, chlorophytes and dinoflagellate cysts) and protozoans (thecamoebians/ testate amoebae and cilates) are common in palynological preparations from Cook’s Bay. The downcore distribution of these non-pollen palynomorphs shows a clear correlation with chemical proxies of water quality and heavy metal concentrations, illustrating their potential in paleoenvironmental studies.  Pollen stratigraphy allowed the microfossil and chemical data to be compared with the well-documented historical record, and three significant anthropogenic events in the watershed are evident upcore: 1) initial European colonisation in the late 18^th century, marked by initial low abundances of Ambrosia and a steady increase in nutrients (TP, NO₂); 2) the inception of intensive agriculture during the 1920’s and 1930’s when Euro-Canadian settlers drained the East and West Holland Marsh to create polders (marked by the influx of abundant Gramineae and phytoliths to Cook’s Bay, and a shift from high nitrate to high nitrite concentrations in response to the sudden increase in BOD); and 3) a population boom and urbanisation in the Cook’s Bay watershed following the Second World War (marked by an initial peak in phytoliths and a sharp rise in Ambrosia and other NAP and in concentrations of heavy metals like zinc, chromium, lead, copper, arsenic and cadmium). Desmids (particularly Cosmarium spp.) decreased sharply in abundance in response to initial European colonisation, while other algae like Peridinium spp. appear to have responded positively to the nutrient influx, as did thecamoebians, particularly difflugiid species. A sudden influx of unknown NPP (presumably wetland taxa) dominates the phytolith-rich sediments attributed to the creation of polders during the early 20^th century and the base of the sharp Ambrosia rise attributed to rapid urbanisation in the Cook’s Bay watershed (notably the cities of Newmarket and Aurora). Depleted dissolved oxygen (DO) associated with biochemical oxygen demand (BOD) is associated with a transition from high nitrite to high nitrate concentrations in these phytolith and grass-pollen rich sediments, but heavy metal concentrations remain low below the sharp ruse in Ambrosia. Abundant Pediastrum spp. and Codonella cratera in Ambrosia-rich sediments deposited since the Second World War are consistent with the documented eutrophication, BOD and low DO, that have stressed the cold-water sport fishery that is important to the local economy.