A linked hydrodynamic–hydrophobic organic chemical mass balance and food chain bioaccumulation model, LOTOX2, was developed to support the Lake Ontario Lakewide Management Plan (LaMP) for establishing contaminant load reduction strategies. This paper describes the development of LOTOX2, including the linkage with a relatively finer-scale hydrodynamic model (the Princeton Ocean Model, POM). An important component of this development was the reconstruction of PCB loading history (1930–2005), which was used to understand historic trends and to conduct model calibration/confirmation for total PCBs (tPCBs) in the lake water, sediments, and adult lake trout using data for the last 25years. A separate mass balance was conducted for the radioisotope cesium-137 (137Cs) in order to develop a sorbent mass balance model for the system. Following calibration and confirmation, a diagnostic application of the model showed that the lake is not yet at steady-state with current loads. It will take more than 50years for tPCB concentration in lake trout to decrease to a steady-state value of about 0.4ppm if year 2005 loads remain constant. If all external loads were instantaneously eliminated in 2005, it would take approximately 40years for the adult lake trout tPCB concentration to reach 0.05ppm (the uniform Great Lakes protocol value for unrestricted consumption) from its current level of 0.74ppm.