Geological studies offshore of Wrightsville Beach, North Carolina reveal subtle large-scale regions of coarse sand with gravel and shell hash (widths between 100 and 200 m and negative relief of ∼1 m) that trend obliquely to the coast. It was previously suggested that these regions serve as conduits for sand exchange between the shoreface and inner shelf during storm-associated downwelling. Consequently they were classified as rippled scour depressions. More recently, the role of alongshore flows and self-organization as a result of inhibited settling of fine sand has been discussed. In this study, 45 days of near-bed current measurements were analyzed using benthic boundary layer and sediment transport models to examine the role of along- and cross-shore flows in driving sediment transport at this site. The wind climate was found to be a dominant influence on near-bed flows. Six distinct sediment transport events were recognized. During these events, sediment transport models show that bedload transport is directed mainly in the cross-shore direction, while suspended sediments are directed alongshore to the southwest. Current observations during these sediment transport events provide no evidence of cross-shore sediment transport caused by steady downwelling currents. Instead, benthic boundary layer model results are used to show that differences in bed roughness between the coarse areas of the seabed within the “rippled scour depressions” and the finer areas of the inner shelf are more pronounced during increasingly energetic wave and current conditions. The enhanced difference in roughness results in increased turbulence intensities over coarse regions inhibiting the deposition of the fine sand that is resuspended over the shelf during these events relative to finer areas over the shelf. Findings from this study contribute to explaining the observed long-term persistence of these features.