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Tidal-inlet systems are dynamic features that respond to short-term (e.g., storms) and longer-term processes (e.g., sea-level rise, changes in tidal prism). The Chincoteague Inlet system, located along the northern Eastern Shore of Virginia (USA), is a dynamic coastal complex that experiences rapid change associated with sediment redistribution and a shifting inlet throat due to the southern elongation of adjacent Assateague Island. In this study, a numerical model based on Delft3D with coupled flow–waves, multiclass sediment transport, and morphologic feedback was developed to quantify the hydrodynamic and geomorphic controls within this rapidly evolving inlet–spit system and to develop a more comprehensive understanding of regional to local controls on sediment-transport pathways. Model results show that most of the sand transport along southern Assateague Island is sequestered nearshore and proximally in deeper sinks within Fishing Point, and, of that, only finer sand sizes are transported around the spit, confirming previous analysis and hypothesis. The model also showed that sand transport toward the south increases along Wallops Island and quantified spatially explicit transport trends for selected sediment classes, revealing that coarser sediment bypassing is a punctuated process that is proportional to storms.