Natural formations of rock and coral can support geologically controlled beaches, where the beach dynamics are significantly influenced by these structures. However, little is known about how alongshore variations in geological controls influence beach morphodynamics. Therefore, in this study we focus on the storm response of a beach (Yanchep in south Western Australia) that has strong alongshore variation in the level of geological control because of the heterogeneous calcarenite limestone reef. We used a modified version of XBeach to simulate the beach morphodynamics during a significant winter storm event. We find that the longshore variation in topography of the reef resulted in: (1) strong spatial difference in current distribution, including areas with strong currents jets; and (2) significant alongshore differences in sand flux, with larger fluxes in areas strongly geologically controlled by reefs. In particular, this resulted in enhanced beach erosion at the boundary of the reef where strong currents jet-exited the nearshore.