The rise in sea-level and the increase in frequency and intensity of extreme weather events (i.e., storms and associated surges) are expected to strongly impact coastal areas. The gradual impacts of sea-level rise may allow species to display adaptive responses to overcome environmental changes. In contrast, the abruptness of marine submersions during extreme weather events can induce changes that may exceed the ability of species to respond to brutally changing environments. Yet, site-specific topographical features may buffer the expected detrimental effects of marine submersions on wildlife. In order to test such topographical effects, we examined the long-term consequences of a major marine submersion (storm Xynthia) on the amphibian communities of two French Atlantic coastal wetlands that slightly differ in their topography and, thus, their susceptibility to marine submersion. Amphibians were monitored on 64 ponds for up to 13 years, using acoustic and visual methods, in conjunction with environmental parameters (e.g., pond topology, vegetation, salinity). We found that the amphibian communities at the two neighboring sites displayed different responses to the marine submersion linked to storm Xynthia. As predicted, slight differences in local topography induced strong differences in local magnitude of the landward marine surge, influencing salinization dynamics and associated consequences on wildlife (amphibians). The different species responses show that amphibian richness can recover to that of pre-storm conditions, but with significant changes in the composition of the community. Our results suggest that amphibian presence post-submersion in coastal wetlands results from an interaction between species traits (e.g., tolerance to elevated salinity), site-specific topography, and environmental parameters. Finally, our study emphasizes that relatively modest landscaping management may be critical to allow wildlife to successfully recover after a marine submersion.