Estuaries are dynamic coastal features that support industry, food production, and recreation, and provide habitat for numerous animal species. Their typically low surface gradients make estuaries vulnerable to sea level rise, storms, and high river water discharge. This vulnerability combined with the large number of people who often live near estuaries has led to increasing efforts over recent decades to improve our understanding of how to minimize flooding and protect people and property. Despite these efforts, however, we still lack the tools to quantify the relationship between changes in estuarine morphology and flood risks. In particular, the interplay between bathymetric changes and water levels during storm conditions remains poorly quantified. To address this knowledge gap, we present a general enthalpy framework for modeling the evolution of estuaries that couples a low gradient subaerial topset and a subaqueous offshore region or foreset. Sediment transport in both the subaerial and subaqueous domains includes a non-linear term that relates sediment flux, local slope, and a threshold of motion. With this approach, we describe the evolution of the bathymetric profile and sediment partitioning between topset and foreset under a range of sea-level variations scenarios. We find that in some cases upstream sections of the topset can undergo erosion during periods of sea-level rise and deposition during sea-level fall, contradicting traditional stratigraphic models. These counterintuitive bathymetric changes could potentially lead to shifts in the location of maximum water levels along the estuary not accounted for by models of storm inundation.