Ocean circulation influences nearly all aspects of the marine ecosystem. This study describes the water circulation patterns on time scales from hours to years across Torres Strait and adjacent gulfs and seas, including the north of the Great Barrier Reef. The tridimensional circulation model incorporated realistic atmospheric and oceanographic forcing, including winds, waves, tides, and large-scale regional circulation taken from global model outputs. Simulations covered a hindcast period of 8 years (i.e. 01/03/1997–31/12/2004), allowing the tidal, seasonal, and interannual flow characteristics to be investigated. Results indicated that the most energetic current patterns in Torres Strait were strongly dominated by the barotropic tide and its spring-neap cycle. However, longer-term flow through the strait was mainly controlled by prevailing winds. A dominant westward drift developed in summer over the southeasterly trade winds season, which then weakened and reversed in winter over the northwesterly monsoon winds season. The seasonal flow through Torres Strait was strongly connected to the circulation in the north of the Great Barrier Reef, but showed little connectivity with the coastal circulation in the Gulf of Papua. Interannual variability in Torres Strait was highest during the monsoon period, reflecting variability in wind forcing including the timing of the monsoon. The characteristics of the circulation were also discussed in relation to fine sediment transport. Turbidity level in Torres Strait is expected to peak at the end of the monsoon, while it is likely to be at a low at the end of the trade season, eventually leading to a critically low bottom light level which constitutes a severe risk of seagrass dieback.