Abstract A three-dimensional hydrodynamic/pollutant transport quality simulation model was developed to simulate the currents and pollutant transport in Lake Ontario and its nearshore areas. The computational efficiency of the model was improved by using an implicit scheme to compute barotropic pressures. The model was applied to Lake Ontario using a 4-km-square grid to simulate wind-induced circulation under isothermal and stratified conditions. A nested model approach was used to study the currents and pollutant transport in the nearshore area along the Metropolitan Toronto waterfront and the mouth of Mimico Creek. In this approach, three models were nested using the following spatial discretization: a 2-km grid for Lake Ontario, a 500-meter grid for the Metropolitan Toronto waterfront, and a 100-meter grid near the mouth of Mimico Creek. An interpolation scheme applied at the open boundaries minimized truncation errors generated by using different grid sizes. Two cases which consisted of lake stratified and isothermal conditions were selected for model calibration. Predictions of lake circulation patterns and conductivity were in good agreement with field measured time series data.