This dissertation explores the impact of backwater hydrodynamics on the development of fluvial-deltaic strata across a range of spatiotemporal scales by linking numerical modeling, field observations of channel bathymetry from the modern Mississippi River, and stratigraphic patterns from the ancient Tullig Sandstone of the Western Irish Namurican Basin (Co. Clare, Ireland). The research topics include: (1) assessing the response of channel hydrodynamics to external environmental forcings and associated feedback on stratigraphic development, (2) evaluating bedform dynamics as a function of systematically varying sediment transport conditions within a river backwater reach and determining the impact on cross strata, and (3) inverting stratigraphy to improve accuracy of paleohydraulic reconstructions of ancient fluvial-deltaic systems. The numerical model developed in this study incorporates channel morphodynamics and a grain size-specific sediment transport relation, and allows the tuning of input boundary conditions so to account for geological forcings (e.g., base level change, basin geometry). It is thus capable of simulating not only short-term (seconds to hours) and reach-scale hydrodynamics of fluvial-deltaic system, but also long-term (millennia) and basin-scale patterns of stratigraphy. Simulation results using this newly developed modeling framework reveal that the influence of variable channel hydrodynamics extends beyond the typical backwater length scale of modern fluvial-deltaic systems due to in-channel sedimentation that migrates upstream. Coupled with shoreline movement, the degree of channel deepening enhances downstream, independent of long-term base-level fluctuations. However, channel deepening is not indefinite, because a state of dynamic equilibrium is reached during periods of base-level rise, which generates an autoretreat of the river system and unique (recognizable) basin-scale patterns of stratigraphy. At the bedform scale, dune dynamics and morphology are shown to be impacted by backwater hydrodynamics. An analytical model predicts that the dune-scale cross-set thickness (an important paleohydraulic indicator) increases, and then decreases, progressing downstream towards the river outlet. This trend is opposite to what traditional paleohydraulic reconstruction methods predict, but yet is observed for a modern river (the lowermost Mississippi River), and an ancient fluvial-deltaic system (Tullig Sandstone). These results support the hypothesis that sedimentary strata may preserve distinct signatures of backwater hydrodynamics. This hypothesis is further tested in the Tullig Sandstone, by parameterizing the numerical model from this study to assess predicted patterns and observed patterns of stratigraphy found in rock outcrops. A distinct trend in cross-set thickness is identified and used to improve paleohydraulic reconstruction methods. The physics-based model frameworks presented in this dissertation can be adopted for other settings, and used to constrain planetary surface evolution by assessing the response of fluvial-deltaic systems to internal and external changes in boundary conditions.