The influence of eutrophication on the biogeochemical cycles of persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) is largely unknown, In this paper, the application of a dynamic air-water-phytoplankton exchange model to Lake Ontario is used as a framework to study the influence of eutrophication an air-water exchange, vertical fluxes, and phytoplankton concentrations of POPs. The results of these simulations demonstrate that air-water exchange controls phytoplankton concentrations in remote aquatic environments with little influence from land-based sources of pollutants and supports levels in even historically contaminated systems. Furthermore, eutrophication or high biomass leads to a disequilibrium between the gas and dissolved phase, enhanced air-water exchange, and vertical sinking fluxes of PCBs. increasing biomass also depletes the water concentrations leading to lower than equilibrium PCB concentrations in phytoplankton. Implications to future trends in PCB pollution in Lake Ontario are also discussed.