The restoration of Hamilton Harbour, from an environmental standpoint, is a current concern for the agencies involved with remediation efforts in the harbour. Estimates of circulation and mixing are needed to assess the fate and transport of water quality constituents in the harbour. A three-dimensional hydrodynamic modeling system (ELCOM) is used to study the circulation and thermal structure in the harbour. The model results were compared with profiles of temperature at several moorings and currents and water levels in the harbour. The model showed considerable skill in reproducing the thermal structure, surface currents and water levels. Mean summer circulation in the harbour showed two counter-rotating gyres occupying the harbour. The model produced harbour-lake exchange characteristics are in agreement with previous studies. Simulations using passive tracers qualitatively agreed with chemical tracer studies conducted near a sewage treatment plant outfall. The accuracy of these simulations suggests that the model is capable of describing flow and transport of material required for detailed water quality simulations.