The Great Lakes Unit of the Ministry of Environment (GLU) assists the Ontario Government in meeting its commitment to monitor areas of environmental concern within the Great Lakes. Accordingly, GLU has launched environmental impact assessment programs with the purpose of evaluating the progress towards restoration of environmental conditions. In order to identify environmental impacts of the water quality in the Great Lakes, GLU decided to develop a hydrodynamic and water quality model. GLU selected MIKE 3 as the preferred modelling tool as it fulfils the requirements for a 3D simulation tool describing surface water movements, sediments and contaminants. The knowledge provided by the model makes it possible to get an improved understanding of the effects on the water quality and will ultimately assist in an optimization of the water management of the water near to shore which is used for water supply and recreational purposes.