<p>The Great Lakes form an important freshwater drinking source for many urban areas surrounding the Lakes but also provide a sink for pollutants and runoff. Consequently introducing new drinking water intakes into any of these water bodies requires investigation into local pollutant sources and their transport in order to determine the most appropriate location and depth of any new intake. Two methods involving the calibration of a 3D wind driven transport model, to spill data collected over a 4 week period, are described. The methods include the traditional trial and error approach and the application of a nonlinear inverse model to optimize parameter estimates. Results show that calibration using the inverse modeling approach was an improvement over the traditional trial and error approach by providing a clear quantitative analysis of parameter sensitivity and importance, and ultimately yielding a better fit between observed and simulated data. The calibrated three-dimensional model was ultimately applied to assess the impacts of a potential local pollutant source to several proposed new drinking water intakes located along the north shore of Lake Ontario.</p>