The distribution of non-pollen palynomorphs (NPP) in a core from Cook’s Bay, Lake Simcoe, Ontario, Canada shows a response to changes in water quality accompanying agriculture, urbanization, and industrialization. Low concentrations of nutrients in sediments with little non-arboreal pollen (NAP) record low disturbance prior to European settlement around the 1850s. These sediments are rich in desmids such as Cosmarium spp., Euastrum spp., and Staurastrum spp., an assemblage indicative of oligotrophic conditions. A decline in desmids, together with an increase in dinoflagellate cysts and thecamoebians up-core is consistent with increased nutrients. Abundant phytoliths in sediments that are relatively rich in Poaceae and other NAP records the draining of the Holland Marshes. A sharp increase in nutrient levels, together with a transition from high nitrite (NO2) to high nitrate (NO3) concentrations, records a sudden increase in biological oxygen demand leading to depletion of dissolved oxygen associated with the creation of polders in the 1920s and 1930s. A second influx of phytoliths immediately preceded the sharp rise in Ambrosia, recording rapid land clearing accompanying the five-fold post-World War II population boom in the Cook’s Bay watershed. These Ambrosia-rich sediments are rich in metals and have high total phosphorus and NO3, with abundant Pediastrum spp. and Peridinium spp., notably Peridinium willei and Peridinium volzii, recording eutrophication. The abundance of the ciliate Codonella cratera and the difflugiid thecamoebians Cucurbitella tricuspis and Difflugia protaeiformis in palynological preparations, as well as in washed thecamoebian samples from the upper part of the core, records low dissolved oxygen associated with continued eutrophication of Cook’s Bay.