We present an overview of physical processes that drive water circulation within the extended system of coastal embayments in the Toronto Harbour. The different water circulation patterns occur at various spatial and temporal scales, and our article provides context for the various efforts to improve water quality by the Toronto and Region Remedial Action Plan. Velocity profiles and water level measurements showed that the harbour’s Helmholtz pumping mode drives a 1-h period oscillation, which can influence flushing of the shallow embayments. This process likely persists year-round and would lead to flushing time-scales of between 1–11 days for these shallow embayments. If this ubiquitous pumping is combined with solar heat fluxes, it partially explains the persistent temperature gradients amongst the shallow embayments. In the larger and deeper (∼10 m) Inner Harbour, the prevailing westerly winds drive most of the mean circulation, with a current entering through the Western Gap and leaving through the Eastern Gap. This wind driven circulation leads to a residence time of water in the Inner Harbour between 7–14 days. In addition, periodic strong and sustained westerly winds can induce frequent upwelling events in Lake Ontario (between 4 to 10 times during the stratified season) that mildly increase the exchange flow and help maintain good water quality by exchange nearshore waters with cleaner hypolimentic waters. The intrusion of cold water into the harbour can also lead to highly variable temperature regimes with sudden drops in temperature that could have negative effects on aquatic organisms.