Erosional surfaces set the architecture of fluvio-deltaic stratigraphy, and they have classically been interpreted in terms of changes in boundary conditions such as climate, tectonics, and base level (allogenic forces). Intrinsic dynamics of sedimentary systems (autogenic dynamics) can also create a rich stratigraphic architecture, and a major knowledge gap exists in parsing the relative roles of autogenic versus allogenic processes. Emerging theoretical and experimental work suggests that backwater hydrodynamics play an important role in driving transient channel incision in river deltas, even those experiencing net aggradation. Here, we identify and quantify two autogenic mechanisms that produce broad erosional surfaces in fluvio-deltaic stratigraphy, namely, floods and avulsions. Using a simple mass-balance model for single-threaded delta channel systems, we show that flood-induced scours begin near the shoreline, and avulsion-induced scours begin at the avulsion site, and both propagate upstream over a distance that scales with the backwater length, bed slope, and bed grain size. We also develop scaling relationships for the maximum scour depths arising from these mechanisms, which are functions of characteristic flow depth and formative flood variability. We test our theoretical predictions using a flume experiment of river delta evolution governed by persistent backwater hydrodynamics under constant relative sea level. Results indicate that autogenic dynamics of backwater-mediated deltas under conditions of constant base level can result in stratigraphic surfaces and shoreline trajectories similar to those often interpreted to represent multiple sea-level cycles. Our work provides a quantitative framework to decouple autogenic and allogenic controls on erosional surfaces preserved in fluvio-deltaic stratigraphy.