Wave runup is a relevant parameter to determine the storm impact on barrier islands. Here, the role of the beach morphology on wave runup and storm impact was investigated at four coastal communities located on the northern Yucatan coast. Current wave conditions based on regional wind simulations, topo-bathymetric transects measured at each location, and a nonlinear wave transformation model were employed to reconstruct multi-year runup time series. Dune morphology features and extreme water levels (excluding storm surge contributions) were further employed to determine the storm impact at each site for different return periods. Despite the similar offshore conditions along the coast, extreme water levels (i.e., runup and setup) showed intersite differences that were mainly ascribed to subaerial and submerged morphological features. Numerical results showed that the average surf zone beach slope, sandbars, berm, and dune elevation played an important role in controlling extreme water levels and storm impact at the study sites under the present climate. Moreover, in order to assess the potential effect of climate change on coastal flooding, we analyzed wave runup and storm impact in the best-preserved site by considering wave conditions and sea level rise (SLR) projections under the RCP 8.5 scenario. Modelling results suggest no significant increase in the storm impact regime between the present and future conditions in the study area unless SLR is considered. It was found that to accurately estimate SLR contribution, it should be incorporated into mean sea level prior to performing numerical wave runup simulations, rather than simply adding it to the resulting wave-induced water levels.