For over a century, the copper and nickel mining centre of Sudbury in northeastern Ontario (Canada) was a major source of sulphur dioxide and other pollutants, degrading terrestrial and aquatic ecosystems in the surrounding region. In the 1970s, emissions were drastically reduced due to concerns over widespread environmental damage. Killarney Provincial Park (KPP), located ~ 60 km southwest of Sudbury, was also impacted by Sudbury emissions, but little is known about how present-day conditions relate to pre-industrial conditions, or how recovery trajectories may be influenced by recent climate change. Here, we use a multi-proxy paleolimnological approach to examine ecological change in five lakes over the past ~ 200 years in Sudbury (Baby, Tillie, and Crooked lakes) and KPP (Ruth-Roy and Johnnie lakes). The study objectives were to: (1) infer past ecological conditions from diatom assemblages, whole-lake chlorophyll-a (VRS-Chl a) and lake-water dissolved organic carbon (DOC) concentrations; (2) explore patterns of potential ecological recovery from acidification over the past several decades; and (3) compare any changes to recent monitoring and meteorological data. Distance from smelting operations and differences in underlying bedrock geology likely contributed to differences in the magnitude of change observed in the paleolimnological indicators. In general, the acidification period was characterized by declines in circumneutral diatom taxa (i.e., Discostella spp., Achnanthidium spp., and Aulacoseira spp.), and inferred Chl a and inferred DOC, concurrent with increased relative abundances of acidophilic diatoms (i.e., Fragilariforma acidobiontica, Eunotia spp., Tabellaria flocculosa and Asterionella ralfsii). After ~ 1970, only limited recovery in diatom assemblages was recorded, although inferred DOC and Chl a levels increased, indicating biological recovery is lagging chemical recovery and/or the ecological trajectory has been influenced by other large-scale environmental stressors. However, given the impacted nature of the study lakes, a clear climate signal in recent diatom assemblages was not as evident as often noted in pristine Boreal Shield lakes. This highlights the need for case-by-case consideration of recovery patterns in lakes, and confirms the importance of conducting long-term, multi-proxy studies to assess ecosystem recovery and ecological trajectories.