Thousands of lakes in a ~ 17,000 km2 area around Sudbury (Ontario) acidified (pH < 6) and became metal contaminated as a result of local smelting activities that have taken place since the 1880s. Middle Lake, an urban lake located in Sudbury, acidified to pH ~ 4.3, and was subsequently limed and fertilized in the 1970s and 1980s as part of experimental remediation efforts. Little is known about the long-term impacts of acidification, metal contamination, and subsequent remediation efforts on the benthic invertebrate communities in Middle Lake. Thus, we used paleolimnological methods to examine long-term trends in Chironomidae and Chaoboridae (Diptera) assemblages. Three important chironomid assemblage zones were identified, corresponding to pre-smelting/mining (i.e. reference) conditions, acidification/metal contamination, and subsequent remediation efforts. Acidification led to the increased abundance of acid-tolerant chironomid taxa such as Psectrocladius and Zalutschia, as well as the dominance of Chaoborus americanus indicating the loss of the fish community in the lake between ~ 1920 and ~ 1990. Liming, fertilization, and fish stocking abruptly shifted the chironomid assemblages from Chironomus- to Sergentia-dominated, likely through alterations to habitat quality, food availability, and predation pressure. Fish stocking efforts were clearly visible in the record by the loss of Chaoborus americanus. Following mitigation efforts, chironomid assemblages did not return to their pre-impact state; however, they remained relatively stable after ~ 1990. The recorded shifts in taxonomic composition provide insights into the impacts of smelting operations and remediation efforts on benthic invertebrates, which is important in future lake management and in the future inference of environmental conditions using chironomids in multiple-stressor systems.