Sequence stratigraphy relies on the identification of unconformity-bound sedimentary packages in order to understand variations in sediment supply, subsidence, and eustasy, which are themselves controlled by external (allogenic) drivers such as climate and tectonics. However, intrinsic (autogenic) river dynamics can also create a rich stratigraphic architecture in the absence of allogenic changes. Here, we outline scaling relationships for the expected depth and length scales of autogenic scour resulting from non-uniform flows in coastal rivers, and apply these relationships to the Upper Cretaceous Castlegate Sandstone—a classic fluvial sandstone unit in the Book Cliffs of Utah (USA). Theoretical and experimental work suggests that hydrodynamics within the backwater reach of coastal rivers—the zone of non-uniform flow that extends upstream of the river mouth—causes spatially extensive erosion during floods; this in turn creates erosional surfaces within fluvio-deltaic stratigraphy that may appear similar to sequence boundaries. Results demonstrate that scour patterns within the Castlegate Sandstone are consistent with the predictions of backwater-induced scours, and show how allogenic versus autogenic erosional surfaces can be parsed within fluvio-deltaic stratigraphy.