Several lakes near Wawa (Ontario, Canada) present a rare opportunity for studying rapid chemical and biological recovery from acidification and metal contamination. Surface water pH levels in some of these lakes have increased from 3 to 7 following local sulphur emission reductions and closure of an iron ore sintering plant. We used paleolimnological techniques to track diatom community responses to historical water quality changes in five lakes. Pre-industrial diatom assemblages recorded in lake sediments were dominated by species typical of circumneutral pH levels and were characterized by minimal species compositional change. Following the onset of sintering in 1939, there was a striking shift towards acid- and metal-tolerant Eunotia-dominated species assemblages, sometimes consisting of high quantities of teratological Eunotia valves. Recent dramatic water quality improvements, following first reductions in and then cessation of emissions, were accompanied by decreases in the relative abundance of benthic acid- and metal-tolerant species in the sediment record. However, diatom recovery trajectories did not entirely progress towards predisturbance communities, as the contemporaneous increase in relative abundance of other species was restricted to a few groups. Moreover, diatom responses were not synchronous among cores, with recovery rates influenced by local bedrock and the hydrological regime of each lake.