An accurate representation of physical and biological processes is crucial to resolve larval dispersal pathways and characterize connectivity of coral reef ecosystems. We investigate how hydrodynamic forcings drive larval retention rates during the bi-annual mass coral spawning of the coral genus Acropora within a coral reef atoll (Mermaid Reef), located off northwestern Australia. By analyzing hydrodynamic conditions during 41 yr of historical spring and autumn coral spawning events, we identify typical and extreme hydrodynamic forcing conditions. Particle tracking using the output from a fine-scale coupled wave-flow hydrodynamic model forced with typical hydrodynamic conditions during coral spawning, revealed a mean transport of larvae eastward across the atoll. Transport was mainly driven by a combination of wave and tidal currents, where the residual tidal flow and unidirectional wave flow increased the net export of particles, and the oscillatory tidal (non-residual) flow reduced the net export of particles from the reef. Importantly, however, numerical simulations forced with extreme hydrodynamic conditions generated by episodic tropical cyclones (11 out of 41 yr) showed large deviations from the typical eastward flow during autumn spawning, generating different connectivity pathways within the reef. Considering the substantial time larvae can be retained within reef systems, overlooking fine-scale hydrodynamic processes may greatly overestimate larval transport distances between adjacent coral reef atolls. As a result, we emphasize the need to consider fine-scale hydrodynamic processes within regional connectivity predictions, which is generally not considered yet critical to understand the capacity of reefs to recover following disturbances.