Records of ecological recovery in anthropogenically-degraded ecosystems are important for assessing management efficacy. Interpreting recovery is often complicated as ecosystems can experience local forcings alongside regional influences such as climate warming. Paleolimnology, which uses the environmental information preserved in freshwater sediments, can provide the long-term records needed to assess recovery and unravel the confounding influence of multiple stressors. In the historically contaminated St. Lawrence River at Cornwall, ON, long-term data are needed to assess the efficacy of natural recovery in reducing the ecological risk associated with sedimentary contaminants. Despite decades of remedial action, metal(loids) including neurotoxic mercury remain in waterfront sediment in concentrations exceeding provincial severe effect levels. To assess benthic recovery, long-term records of subfossil chironomid (Order: Diptera) assemblages in dated sediment cores were compared among two impacted Cornwall sites and a downstream reference site. Chironomids were functionally absent from the Cornwall sediment records during times of high industrial loading of contaminants. As contaminant concentrations declined, chironomid abundance increased, and the relative abundance of metal-tolerant taxa decreased in favour of warm-water, macrophyte-associated taxa. This suggests that ecological recovery has occurred, and that habitat and temperature are the primary drivers structuring modern-day chironomid assemblages.