Lack of long-term studies on drought in the boreal region of northwest Ontario limits our ability to assess the vulnerability of this region to climate change. We investigated changes in diatoms, scaled chrysophytes, and sedimentary pigments in two near-shore cores from Gall Lake to infer limnological and water-level changes over the last two millennia. The two coring locations, at modern water depths of 7.5 and 11.5 m, were selected to contrast inferences for past lake level based on distance from the modern water-depth boundary between predominantly benthic and planktonic diatom assemblages in surface sediments (6.0 m). Diatom-inferred depth inferences were more variable in the core from 7.5-m water depth, consistent with the hypothesis that the greatest changes occurred at water depths closest to the benthic:planktonic boundary. Both sites revealed a pronounced drought from ~AD 950 to 1300, synchronous with the medieval climate anomaly (MCA). This finding suggests a northeast expansion of the arid MCA into northwest Ontario, extending the known spatial extent of this megadrought. Scaled chrysophytes and sedimentary pigments suggest a recent increase in thermal stratification. Our findings indicate this region is more susceptible to changes in moisture than was previously suspected based on the instrumental record for the past century.