The circulation driven by wave breaking, tides and winds within a fringing coral reef system (Ningaloo Reef) in Western Australia was investigated using the ocean circulation model ROMS two-way coupled to the wave model SWAN. Currents within the system were dominantly forced by wave breaking, with flow driven over the shallow reefs and towards the lagoon, which returned to the ocean through channels in the reef. Hindcast model simulations were compared against an extensive field dataset, revealing that the coupled wave–circulation model could accurately predict the waves and currents throughout this morphologically complex reef–lagoon system. A detailed momentum budget analysis showed that, over the reef, a dominant cross-shore balance was established between radiation stress gradients and a pressure (mean water level) gradient (similar to a beach). Within the lagoon, alongshore currents were primarily balanced by alongshore gradients in wave setup, which drove flow towards (and ultimately out) the channels. The importance of these wave-driven currents to Ningaloo Reef was quantified over a full seasonal cycle, during periods when wave and wind conditions significantly differed. These results showed that wave breaking still overwhelmingly dominated the circulation and flushing of Ningaloo Reef throughout the year, with winds playing an insignificant role.