Atoll reef islands primarily consist of unconsolidated sediment, and their ocean‐facing shorelines are maintained by sediment produced and transported across their reefs. Changes in incident waves can alter cross‐shore sediment exchange and, thus, affect the sediment budget and morphology of atoll reef islands. Here we investigate the influence of sea level rise and projected wave climate change on wave characteristics and cross‐shore sediment transport across an atoll reef at Kwajalein Island, Republic of the Marshall Islands. Using a phase‐resolving model, we quantify the influence on sediment transport of quantities not well captured by wave‐averaged models, namely, wave asymmetry and skewness and flow acceleration. Model results suggest that for current reef geometry, sea level, and wave climate, potential bedload transport is directed onshore, decreases from the fore reef to the beach, and is sensitive to the influence of flow acceleration. We find that a projected 12% decrease in annual wave energy by 2100 CE has negligible influence on reef flat hydrodynamics. However, 0.5–2.0 m of sea level rise increases wave heights, skewness, and shear stress on the reef flat and decreases wave skewness and shear stress on the fore reef. These hydrodynamic changes decrease potential sediment inputs onshore from the fore reef where coral production is greatest but increase potential cross‐reef sediment transport from the outer reef flat to the beach. Assuming sediment production on the fore reef remains constant or decreases due to increasing ocean temperatures and acidification, these processes have the potential to decrease net sediment delivery to atoll islands, causing erosion.