Scaled chrysophytes preserved in modern and fossil sediment samples from lakes in south-central Ontario were examined to evaluate changes in water quality since preindustrial times. Redundancy analysis determined that chrysophyte distributions were related to a primary gradient of pH, alkalinity, and ion concentration (λ1 = 0.26). A 117-lake reconstruction model from Ontario, the Adirondacks, and northeastern U.S.A. was used to infer the lakewater pH of present-day and preindustrial samples. A comparison of predicted and measured pH values of modern samples, analog matching, and an examination of inferences from triplicate cores in four lakes suggested that the inferences were reliable. Reconstructions indicated that presently acidic lakes (pH < 6) had acidified, whereas lakes with measured pH > 7 had become more alkaline. In comparison to other acid-sensitive regions, however, the overall change was small. The relatively short pH gradient, higher preindustrial pH values, and amount of acid deposition are factors that may explain these trends. Finally, we introduce a novel, multi-indicator reconstruction model, which provides an average of environmental reconstructions from diatom, chrysophyte cyst, and scaled chrysophyte assemblages. This model performed as well or better than the individual inferences when used to predict the pH of modern samples.