Dune-scale cross-beds are a fundamental building block of fluvial-deltaic stratigraphy and have been recognized on Earth and other terrestrial planets. The architecture of these stratal elements reflects bed-form dynamics that are dependent on river hydrodynamic conditions, and previous work has documented a multitude of scaling relationships to describe the morphodynamic interactions between dunes and fluid flow. However, these relationships are predicated on normal flow conditions for river systems and thus may be unsuitable for application in fluvial-deltaic settings that are impacted by nonuniform flow. The ways in which dune dimensions vary systematically due to the influence of reach-averaged, nonuniform flow, and how such changes may be encoded in dune cross-strata, have not been investigated. Herein, we explored the influence of backwater flow on dune geometry in a large modern fluvial channel and its implications for interpretation of systematic variability in dune cross-strata in outcrop-scale stratigraphy. This was accomplished by analyzing high-resolution channel-bed topography data for the lowermost 410 km of the Mississippi River, which revealed that dune size increases to a maximum before decreasing toward the river outlet. This spatial variability coincides with enhanced channel-bed aggradation and decreasing dune celerity, which arise due to backwater hydrodynamics. An analytical model of bed-form stratification, identifying spatial variability of cross-set thickness, indicates a prominent downstream decrease over the backwater region. These findings can be used to inform studies of ancient fluvial-deltaic settings, by bolstering assessments of proximity to the marine terminus and associated spatially varying paleohydraulics.