Any perturbation of aquatic ecosystems that affects the quantity and quality of the phytoplankton, and thus the food resource available for primary consumers, might drive subsequent changes in carbon cycling within the food webs. For instance, shifts in lake nutrient regimes (eutrophication and subsequent re-oligotrophication) have caused long-term responses of the abundance and taxonomic composition of lake primary producers. Such changes at the first level of the food chain are expected to result in modified contributions of the autochtonous- versus terrestrial-derived organic matter in sustaining the lake secondary production, although such an hypothesis cannot be straighforwardly investigated with current tools in stable isotope analyses over long time scales. Through a paleolimnological approch combining stable isotope analyses on sub-fossil zooplankton remains and specific lipids, this study attempts to document multi-decennial changes in the origins of C fuelling the pelagic food web of two french sub-alpine lakes that have undergone eutrophication and partial re-oligotrophication over the last 100 years.