© 2015 CIWEM. Fresh groundwater lenses (FGLs) are of utmost importance for human survival on small and isolated atolls. This article examines saline damage to atoll FGLs from wave washover caused by storm surge and studies the particular influence of central topographic depressions (CTDs). We model storm surge over atoll islets of contrasting widths (400 and 800m), both with and without CTDs of various sizes. Three key findings emerge. First, under equilibrium undisturbed conditions, the CTD slightly reduces the size of the FGL compared to atoll islets without this feature. Second, during marine flooding, prior saturated conditions at the base of a CTD impede seawater infiltration into the substrate, thereby limiting saline damage in that location. Third and most crucial, however, the amount of salt accumulated within the CTD is significant, ranging from 2 to 10 times higher than the net subsurface infiltration during the period of the storm inundation.