The inner continental shelf off the northern Outer Banks of North Carolina was mapped using sidescan sonar, interferometric swath bathymetry, and high-resolution chirp and boomer subbottom profiling systems. We use this information to describe the shallow stratigraphy, reinterpret formation mechanisms of some shoal features, evaluate local relative sea-levels during the Late Pleistocene, and provide new constraints, via recent bedform evolution, on regional sediment transport patterns. The study area is approximately 290 km long by 11 km wide, extending from False Cape, Virginia to Cape Lookout, North Carolina, in water depths ranging from 6 to 34 m. Late Pleistocene sedimentary units comprise the shallow geologic framework of this region and determine both the morphology of the inner shelf and the distribution of sediment sources and sinks. We identify Pleistocene sedimentary units beneath Diamond Shoals that may have provided a geologic template for the location of modern Cape Hatteras and earlier paleo-capes during the Late Pleistocene. These units indicate shallow marine deposition 15–25 m below present sea-level. The uppermost Pleistocene unit may have been deposited as recently as Marine Isotope Stage 3, although some apparent ages for this timing may be suspect. Paleofluvial valleys incised during the Last Glacial Maximum traverse the inner shelf throughout the study area and dissect the Late Pleistocene units. Sediments deposited in the valleys record the Holocene transgression and provide insight into the evolutionary history of the barrier-estuary system in this region. The relationship between these valleys and adjacent shoal complexes suggests that the paleo-Roanoke River did not form the Albemarle Shelf Valley complex as previously proposed; a major fluvial system is absent and thus makes the formation of this feature enigmatic. Major shoal features in the study area show mobility at decadal to centennial timescales, including nearly a kilometer of shoal migration over the past 134 yr. Sorted bedforms occupy ~ 1000 km2 of seafloor in Raleigh Bay, and indicate regional sediment transport patterns between Capes Hatteras and Lookout that help explain long-term sediment accumulation and morphologic development. Portions of the inner continental shelf with relatively high sediment abundance are characterized by shoals and shoreface-attached ridges, and where sediment is less abundant, the seafloor is dominated by sorted bedforms. These relationships are also observed in other passive margin settings, suggesting a continuum of shelf morphology that may have broad application for interpreting inner shelf sedimentation patterns.