A program is developed that includes two hydrodynamic models, a 2D depth-averaged (2DH) and a Quasi-3D (Q3D), and a pollutant transport model that uses a 1st order upwinding and a 3rd order QUICKEST numerical schemes. Several tests were performed in two test basins in order to examine the performance of the above models. The Q3D model is successfully applied to Lake Ontario, using a 4-km-square grid, to simulate the wind-induced circulation. Simulations of pollutant transport show that the 1st order upwinding scheme can be used for estimating pollutant concentrations near the pollutant source in the case of continuous point source. However, numerical diffusion affects the estimates further downstream the pollutant source. Therefore, higher order schemes such as the third order QUICKEST scheme are required for estimating pollutant concentration at these locations.