Precious metal mining activities have left complex environmental legacies in lakes around the world, including some sites in climatically sensitive regions of the Canadian sub-Arctic. Here, we examined the long-term impacts of past regional gold mining activities on sub-Arctic lakes near Con Mine (Yellowknife, Northwest Territories) based on sediment core analysis (paleolimnology). In addition to receiving metal(loid)s from roaster stack emissions, the study lakes were also influenced by salt-rich mine drainage from Con Mine tailings. Water samples from these lakes had some of the highest concentrations for salinity-related variables (e.g. Ca, Cl, Na) and metal(loid)s (e.g. As, Cu, Ni, Sb) in the Yellowknife area. Furthermore, the presence of halophilic diatom (Bacillariophyceae) taxa (Achnanthes thermalis and Navicula incertata) in the recent sediments of Keg and Peg lakes suggest that the extreme saline conditions are strongly influencing the present biota, more than 10 years after the cessation of gold mining activities at Con Mine. The sedimentary metal(loid) profiles (e.g. As, Cu, Ni) of Kam Lake tracked the influence of regional gold mining activities, particularly those at Con Mine, while the algal assemblages recorded the biological responses to salinization and metal(loid) pollution (e.g. marked decreases in diatom species richness, Hill's N2 diversity, and chrysophyte cyst:diatom valve ratio). At Kam Lake, the algal assemblage changes in the post-mining era were indicative of climate-mediated changes to lake thermal properties (e.g. rise in planktonic diatoms), nutrient enrichment related to urbanization (e.g. increase in eutrophic Stephanodisucs taxa), and/or a combination of both stressors. The lack of biological recovery (i.e. return to pre-mining assemblages) is consistent with investigations of mine-impacted lakes in temperate regions where elevated contaminant levels and emerging stressors (e.g. climate warming, land-use changes) are influencing lake recovery.