A 3D transport model is used to perform a comparative analysis of several potential drinking water intakes located along the northwest shore of Lake Ontario between Toronto and Oshawa. The model is specifically used to assess each intake under both long- and short-term transport of a potential pollutant release from the Pickering Nuclear Generating Station and potential and actual pollutant releases from local land sources respectively. A model based on a 500 m grid resolution is calibrated using data collected in the aftermath of the 1992 tritium spill at the Pickering Nuclear Generation Station and subsequently used to simulate long-term transport. A model based on a 100 m grid resolution is verified using drogue studies and used to simulate short-term transport events. Both models are used to assess pollutant levels at each of nine potential intake locations under different wind scenarios and pollutant releases. Field data for the study included water quality and flow measurements from local sewers and rivers, and estimates of pollutant levels from the local waste water treatment plants. This paper describes the model setup for both the long-term and short-term transport models, calibration using field data, long-term transport modeling, short-term transport modeling, and the comprehensive analysis approach used to evaluate the nine potential intake locations proposed. Results indicated that four intakes in particular outperformed other intake locations by maintaining bottom pollutant levels within governmental standards and warning times that exceeded 20 hours.