Ruth-Roy Lake (Killarney Provincial Park, Ontario, Canada) is an ultra-oligotrophic, naturally acidic waterbody. Lakes in Killarney Provincial Park were impacted by long-range transportation of contaminants from copper-nickel smelting operations in nearby Sudbury, but recent lake monitoring indicates that Ruth-Roy Lake has been less acidic than inferred pre-industrial pH conditions. We assessed the effects of pH change, reduced sulphur emissions, and drivers of reduced acidity using biological and geochemical paleolimnological techniques. Ruth-Roy Lake experienced notable biological and chemical change over the past ~150 years. All examined proxies supported that Ruth-Roy Lake was naturally acidic but further acidified as early as ca. 1920s, with the strongest acidification signal apparent in ca. 1940s. Biological recovery in diatom and cladoceran assemblages, however, is modest. We highlight the importance of understanding reference conditions to assess ecosystem recovery and climate-mediated change in clear acidic lakes located in industrial landscapes.