We provide evidence of rapid, recent environmental change in two lakes in the highlands of central Mexico. Multiple sediment cores were obtained from Lago de Zirahuén (Michoacán) and Laguna de Juanacatlán (Jalisco). Analysis of diatom assemblages, magnetic susceptibility, and metal concentrations was carried out, with the chronology provided by ²¹⁰Pb dating, ¹⁴C dating, and tephrochronology. There is evidence of catchment disturbance during the colonial period in both basins, but the most striking feature at both sites is the rapid change in diatom assemblages during the last 20 y, indicating the onset of eutrophication. Limnological data from Lago de Zirahuén support this interpretation, although none are available from Laguna de Juanacatlán. Paleolimnology is a powerful tool in tracking recent change, particularly in the absence of regular limnological monitoring programs. These lakes appear to be highly sensitive to changes in catchment exploitation, which must be considered in future drainage basin management.