Biological recovery of aquatic ecosystems from acidification damage is a slow process. In lakes near the massive Cu and Ni smelters in Sudbury, Canada, the delays might be caused by residual metals, habitat damage, altered predator–prey interactions, or other persistent ecological stressors. Assessments of benthic invertebrate communities in 24 Sudbury lakes were conducted to evaluate the relative importance of these delaying factors. At the time of sampling, all lakes had chemically recovered to a pH >6.0, but they varied widely in the duration of time above this threshold and in current metal concentrations, watershed contributions of organic matter, littoral habitat composition, and fish community composition. A model developed with redundancy analyses (RDA) of 4 groups of environmental variables (i.e., water chemistry, fish communities, physical lake descriptors, and littoral habitat) accounted for 74.9% of the variance in benthic invertebrate community metrics across these environmental gradients. Fish species richness, duration of pH recovery, and % boulder habitat were the most significant variables and explained 22%, 9%, and 8% of the variance in benthic invertebrate community metrics, respectively. Damaged systems clearly need sufficient time to recover from severe disturbances. However, our study suggests that remediation techniques, such as manipulation of predator–prey interactions through fish introductions, might speed the recovery of benthic invertebrate communities.