Despite the fact that PCB contamination of the global environment has been extensively studied in the last decades, the fate of these compounds in freshwater ecosystems is not fully understood and an important knowledge gap remains regarding the understanding of PCB dynamics and fate in perialpine lakes. This study relied on both field sampling performed and modeling to accurately identify the main fluxes involved in the PCB dynamics into the French perialpine Lake Bourget from 2013 to 2017. Our results show that the main inputs responsible for the PCB loading of the water column are tributaries inflows (~90%) rather than atmospheric inputs which could be related to the high catchment area over lake surface area ratio (i.e., 13). The main mechanism responsible for the lake natural decontamination was sediment burial (76%) due to the effect of the biological pump coupled with a high sedimentation rate. Volatilization represented 19% of the loss of PCBs from the water column and was mainly controlled by the high PCB concentration in water. These mechanisms are susceptible to be affected by the impact of the global change (increase of temperature, modification of the primary production rate) in the near future.