Identifying probable causes of spatial variation in benthic community structure is important for linking ecological disturbance with anthropogenic stressors. Information on taxon-specific sensitivities may be useful in identifying these stressors.  Profundal benthic communities from 10 lakes ranging in degree of metal contamination from a smelter in Abitibi, Québec, were assessed for variability in taxon densities. Variability among sites was analyzed in relation to concentrations of metals in sediment and overlying water, multi-species responses to lake sediment in laboratory toxicity tests, and generic-level metal sensitivity data from published studies.   Benthic communities in the two most contaminated lakes were distinctly impoverished compared to lesser contaminated lakes. Comparatively metal-tolerant Chironomus dominated in the contaminated lakes, whereas the more metal-sensitive amphipods, mayflies and sphaeriids were reduced or absent. Although Tubifex is also tolerant to metals and here showed low toxicity to sediment from the contaminated lakes, other tubificid genera native to the study area were notably absent from the contaminated lakes. Many taxa had “limiting factor”-type relationships to concentrations of Cd, Cu, Pb and Zn in sediment among sites. These results show how taxon-specific ecotoxicological information can help identify impacts of human activities on benthic communities.