A remarkable example of point-source lake acidification and metal pollution, and subsequent recovery in water quality, has occurred in lakes near the former iron sintering plant at Wawa (Ontario, Canada). Surface water pH levels in some of these lakes have increased from three to seven following local sulphur emission reductions and eventual closure of the sintering plant. Previous paleolimnological work documented striking successional changes in diatom species assemblages within dated sediment cores that could be related to past industrial activities. To gain additional insights into the chemical and biological recovery trajectories of the Wawa lakes, we used paleolimnological techniques to track euplanktonic scaled-chrysophyte (classes Chrysophyceae and Synurophyceae) species assemblage responses to historical water quality changes in five lakes. Coincident with the period of iron sintering from 1939 to 1998, striking successional changes were noted in the sedimentary profiles, with marked increases in the relative abundances of the acid- and metal-tolerant taxon synura echinulata. The scaled chrysophyte changes pre-dated diatom responses, confirming the former's status as reliable early warning indicators of lake acidification. Following closure of the sintering plant, species-specific chrysophyte responses to decreased emissions varied amongst the study lakes, perhaps reflecting differences in local bedrock geology and hydrological regime. Although some water chemistry variables may have recovered to near pre-industrial levels, similar to the diatom study, our data show that chrysophyte assemblages in the most recent sediments are now significantly different from pre-industrial assemblages.