Lakes Annecy, Bourget, and Geneva are large, deep carbonated peri-alpine lakes in eastern France. They are located in the same ecoregion but have been subject to differing degrees of anthropogenic pressure over the past decades. A comparative analysis of these ecosystems can therefore provide valuable information on how the lakes have responded to changes in phosphorus runoff, fish management practices, and global warming. Each of these lakes has undergone a restoration process, and changes in water quality and trophic state, as measured using parameters like transparency, chlorophyll a, nutrient concentrations, and phytoplankton biomass and structure, can be used to evaluate efforts made to preserve these ecosystems. Our results reveal that (1) peri-alpine lakes are exemplary cases of restoration in the world where freshwater eutrophication is on the increase, and (2) efforts must be maintained because of the new context of climate change, the effects of which on the quality and the ecological functioning of lakes are still poorly understood.