Over the last decades, the intensification of anthropogenic activities and associated disturbances on lake watersheds have led to major changes in lakes trophic functioning through accelerated eutrophication. In many lakes, these changes are characterized by an unprecedented increase in organic carbon fluxes, potentially leading to a shift in biogeochemical cycles and in the balance between carbon sequestration and greenhouse gas emissions. Understanding the response of the carbon cycle to natural and anthropogenic environmental changes is becoming a crucial challenge in the context of increasing global pressures. In this study, we reconstructed the changes in the trophic functioning of the benthic and pelagic food web, in response to accelerated eutrophication in four lakes over the last millenium. Changes in carbon pathways in food webs were assessed using stable carbon isotope analysis of chitinous subfossil remains of Daphnia, Bosmina, and Chironomini archived in sedimentary records. Changes in the trophic state were inferred from sedimentary geochemical analysis, including carbon accumulation rates, Chl a accumulation rates and carbon-to-nitrogen ratios. Agro-pastoral activities were tracked by analysis of coprophilous ascospores. Results provided by this multi-proxy approach highlight recent disruptions in carbon sources and transfer pathways in lakes food webs. In particular, changes in the carbon isotopic signature of pelagic consumers suggest a recent increase in the use of 13 C-depleted carbon sources such as methanogenic or respiration-derived carbon linked to recent changes in trophic state under the intensification of anthropogenic pressures.