Intensification of anthropogenic activities in many lake catchments during the twentieth century led to increased autochthonous organic matter sedimentation and degradation of hypolimnetic oxygen conditions due to the intensification of heterotrophic processes. These processes can be amplified by the effect of climate warming on thermal stratification in lakes. This study aimed to assess how metabolic disruptions affect carbon sources and pathways in lake pelagic food webs, focusing on methanogenic carbon. The studied lakes showed strong seasonal variations of carbon source availability and transfers to pelagic food webs, characterized by increased methanogenic carbon transfers to Daphnia populations in winter. The magnitude of these winter transfers seems to largely depend on the amount of methane stored in the hypolimnion during the stratification period, and thus on the amount of methane released with autumnal turnover. Methane production, storage and transfer mechanisms partly depend on thermal stratification intensity, but also on external factors such as land use. This study provides new insights into the impacts of global changes on the sources and pathways of carbon in pelagic food webs through their influence on lake metabolism and thermal regimes. These functional changes may lead to greater production and release of greenhouse gases into the atmosphere.