Three southeastern Ontario lakes have responded differently to human disturbances in their catchments over the past 150 years. Catchments of Round and Long lakes were once subjected to deforestation and apatite mining but currently have no local watershed disturbances. Meanwhile, Hambly Lake has been surrounded by residences since the 1950s. Subfossil chironomid head capsules and diatom valves were identified and enumerated in sediment cores from Hambly and Round lakes, and diatom remains were analyzed from Long Lake sediments. Quantitative reconstructions for chironomid-inferred average hypolimnetic dissolved oxygen (CIDO) and diatom inferred total phosphorus (DITP) were performed. Paleolimnological data indicated that Round Lake was subject to considerable human impacts in the late-1800s, with a dramatic shift from oligotrophic to mesotrophic and eutrophic diatom taxa and the onset of hypolimnetic anoxia. In the past 60 years (ca. 1945-present), Round Lake reverted to pre-anthropogenic settlement conditions in response to the cessation of human activities in the catchment. Long Lake microfossils revealed similar trends to those recorded in Round Lake, probably due to a similar disturbance history and its close geographic proximity. In contrast to the other two study sites, Hambly Lake was naturally mesotrophic prior to human settlement, and despite the development of numerous cottages and residences in the catchment, only minor shifts to slightly more eutrophic chironomid and diatom assemblages occurred. Higher nutrients and hypolimnetic anoxia appear to be natural conditions, and consequently little additional change occurred after the arrival of European settlers. This study illustrates the importance of obtaining long-term data for identifying background limnological conditions when assessing impacts and developing management plans.