The plausibility of land disturbance as a cause of declining phosphorus (P) concentrations in oligotrophic lakes within south-central Ontario, Canada, is evaluated using the process-based model INCA-P. The model was calibrated upon three catchments in the Muskoka–Haliburton region (MHR): Harp (HP), Dickie (DE), and Plastic (PC), which have varying degrees of declining P export and different forms of historic disturbances (timber harvesting, tree death, and soil acidification, respectively). Hindcasts (1978–2007) were run with and without simulated disturbances. Model performance of both DE and HP was greatly improved when effects of wetland tree deaths (DE) and harvesting (HP) were included. In PC, with no record of timber harvesting and relatively minor declines in P, initial hindcasts successfully accounted for the majority of interannual P fluxes, and performance was only marginally improved through the simulation of soil acidification. Vegetation decay, harvesting, and catchment acidification accounted for 63%, 24%, and 0.6%, respectively, of P export over the past 30 years. Of all disturbances, wetland vegetation death had the highest impact on areal P exports, indicating that riparian stability is particularly important.