The effects of contaminated bottom sediments on the species composition, growth cycles and diversity of epipelic algal communities were determined between April and November 1978 in a shallow, eutrophic lake (Thompson Lake) situated in the Canadian subarctic. The sediments had become contaminated by gold mining wastes, deposited in the lake between 1941 and 1949. Although the concentrations of total mercury, copper, lead and zinc were high near the mine, averaging 440 μg kg −1, and 85, 30 and 115 mg kg −1, respectively, they decreased rapidly beyond this distance and were near background levels 2.1–3.0 km from the mine. The algal communities in the zone of heaviest contamination consisted of 63 species, the most common of which were Anomoeoneis vitrea, Pinnularia brebissonii and Cymbella species. There were more taxa (111–132) at stations situated 1.1–3.0 km from the mine and the main species included several forms of Achnanthes, Fragilaria and Navicula. Although epipelic densities in the zone of heaviest contamination were only about 50% of those recorded at the other stations, the seasonal growth patterns of the flora were generally similar throughout the lake. Based on these data, it is concluded that: (1) Mine wastes may have a long-term impact on epipelic algae in northern environments; (2) The effects of heavy metal pollution on the epipelon in subarctic lakes are similar to those in temperate zone systems; and (3) No species or group of species could be designated as indicators of heavy metal contamination.