Changes to coastlines and bathymetry alter tidal dynamics and associated sediment transport processes, impacting upon a number of threats facing coastal regions, including flood risk and erosion. Especially vulnerable are coral atolls such as those that make up the Maldives archipelago, which has undergone significant land reclamation in recent years and decades and is also particularly exposed to sea level rise. Here we develop a tidal model of Malé Atoll, Maldives, the first atoll-scale and multi-atoll-scale high-resolution numerical model of the atolls of the Maldives and use it to assess potential changes to sediment grain size distributions in the deeper atoll basin, under sea level rise and coastline alteration scenarios. The results indicate that the impact of coastline modification over the last two decades at the island scale is not limited to the immediate vicinity of the modified island but can also significantly impact the sediment grain size distribution across the wider atoll basin. Additionally, the degree of change in sediment distribution which can be associated with sea level rise that is projected to occur over relatively long time periods is predicted to occur over far shorter time periods with coastline changes, highlighting the need to better understand, predict and mitigate the impact of land reclamation and other coastal modifications before conducting such activities.