Environment Canada recently developed a coupled lake–atmosphere–hydrological modelling system for the Laurentian Great Lakes. This modelling system consists of the Canadian Regional Deterministic Prediction System (RDPS), which is based on the Global Environmental Multiscale model (GEM), the MESH (Modélisation Environnementale Surface et Hydrologie) surface and river routing model, and a hydrodynamic model based on the three-dimensional global ocean model Nucleus for European Modelling of the Ocean (NEMO). This paper describes the performance of the NEMO model in the Great Lakes. The model was run from 2004 to 2009 with atmospheric forcing from GEM and river forcing from the MESH modelling system for the Great Lakes region and compared with available observations in selected lakes. The NEMO model is able to produce observed variations of lake levels, ice concentrations, lake surface temperatures, surface currents and vertical thermal structure reasonably well in most of the Great Lakes. However, the model produced a diffused thermocline in the central basin of Lake Erie. The model predicted evaporation is relatively strong in the upper lakes. Preliminary results of the modelling system indicate that the model needs further improvements in atmospheric–lake exchange bulk formulae and surface mixed layer physics.