A mass budget of polychlorinated biphenyls (PCBs) was constructed for two altitude lakes located in the French Alps to (i) quantify inward and outward PCB flux over the entire year of 2012, (ii) hierarchize the dominant pathways of PCB transfers, and (iii) evaluate towhat extent these pathways vary between both lakes. The annual PCB inputs were similar, and the glacial runoff and sediment-to-water exchange were negligible sources of PCBs to the water column relative to atmospheric deposition. The annual inputs were primarily introduced by snow deposition and transferred into the lakes during the few weeks of spring thaw. While the dominant deposition pathways were similar, the main processes by which the water column lost pollutants differed between the two lakes. Despite these differences, the mass budget revealed that PCB inputs exceeded outputs for both studied lakes and that the lakes acted as atmospheric PCB sinks for the surrounding mountain environment. The differences in the PCB distribution between the key compartments (sediment and water column) are most likely due to differences in the lacustrine internal processes.