Diatom and chrysophyte assemblages from sediment cores were analyzed to assess the long-term trends of lake water quality in French Pond (New Hampshire), Joes Pond (Vermont), and Kenoza Lake (Massachusetts) as part of the US EPA's EMAP-SW (Environmental Monitoring and Assessment Program-Surface Waters) program in the northeastern USA. Sediment characteristics and geochemical data were also examined to interpret past limnological and watershed changes. Geochemical data indicate that exports of ions from the watersheds have increased and the lakes have received higher trace metal inputs over the post-industrial period. Stratigraphic changes in common diatom and chrysophyte taxa indicate that, over the last century, distinct water quality changes have occurred. Using the diatom- and chrysophyte-based weighted averaging inference models developed for lakes in the northeast, past changes in assemblages were used to infer trends in lakewater total phosphorus (TP), pH, and CI. In French Pond, inferred TP, pH, and CI changes were small, whereas Joes Pond and Kenoza Lake have experienced major changes. The latter two lakes have become more eutrophic, and lakewater pH and CI have also increased from their background values. Inferred water quality changes are closely related to watershed disturbances and resulting eutrophication. Our study illustrates that the inference models developed in EMAP-SW can be successfully applied in establishing long-term water quality trends in lakes throughout the northeastern USA. These models and subsequent sediment core data will help lake managers to develop effective management plans and to establish suitable targets for the restoration of other lakes of concern.