Low-lying coral reef islands will be significantly impacted by future sea-level rise (SLR). It is generally expected that SLR will destabilise reef islands because increasing reef submergence allows larger waves, and therefore greater energy transmission, across reef flats. However, the potential impacts of SLR on reef flat sediment transport and sediment delivery to island shorelines are poorly understood. Here, we use the currents of removal approach (coupling two-dimensional wave modelling with settling velocity data from 186 benthic sediment samples) to model shifts in both reef hydrodynamics and benthic sediment transport under different scenarios of mean reef submergence (MRS = +0 m, +0.5 m, +1 m) at two atoll rim reef sites in the Maldives. Under contemporary conditions (MRS = +0 m), we found that benthic sediment transport is likely occurring, consistent with active reef-to-island sediment connectivity. Under conditions of increased MRS, shifts in wave velocities, and in turn sediment potential mobility, were both non-linear and non-uniform. Significant between-site differences were found in the magnitude of projected shifts in sediment mobility under scenarios of increased MRS, which implies that morphological responses to increased MRS are likely to be diverse, even over local scales. Under increased MRS, the largest increases in sediment mobility were projected on the inner reef flat, whereas lagoonal zones remained as sinks for sediment deposition. We thus hypothesize that while reef islands will persist as sedimentary landforms under projected rates of MRS, lagoonward reef island migration is likely to occur. Findings have implications for predicting the future adaptive capacity of atoll nations. Our results highlight the need for national-scale vulnerability assessments to incorporate (1) potential increases in island mobility; (2) the importance of allowing natural sediment transport processes to occur (unhindered by human constructions); and (3) intra-regional diversity in reef system geomorphic responses to sea-level rise.