and C. compressum, and they are presumed extinct. Twelve (63%) of the remaining species had declines in distribution. Sixteen (80%) of the 20 localities sampled had lost species. The greatest declines occurred in Lago de Cuitzeo proper and in the lower portion of the Río Grande de Morelia watershed. Species losses from the lake were attributable to drying and hypereutrophication of the lake because of substantial reductions in the amount and quality of tributary inputs, whereas losses from the Río Grande de Morelia watershed were the result of pollution from agricultural, municipal, and industrial sources, especially in the region around the city of Morelia. Three localities in the upper portion of the Río Grande de Morelia watershed—Cointzio reservoir, La Mintzita spring, and Insurgente Morelos stream—contained most of the remaining fish species diversity in the basin and deserve additional protection. Fish faunal changes indicated major declines in the health of aquatic ecosystems in the Morelia–Cuitzeo basin.