The morphod ynamic adaptation of estuaries to sea level fluctuations has been subject of geological studies based on sediment core analysis and qualitative modeling efforts. Limited attention has been paid to understanding bathymetric evolution based on a detailed process level. The current study aims to explore governing morphodynamic processes and timescales by application of a 2D, process-based modeling approach. The starting point of the analysis is an 80 km long and 2.5 km wide basin. Starting from a sandy flat bed, stable channel-shoal patterns emerge within a century under semidiurnal tidal forcing. We impose a gradual rise in sea level (up to 0.67 m per century) and compare the results with a run excluding sea level rise (SLR). Model results show that SLR drowns the basin so that intertidal area disappears. This process generates tidal asymmetry reflected by an emerging M4 tidal constituent. The basin shifts from exporting to importing sediment reflected by shoal patterns migrating in the landward direction. The landward sediment transport remains too limited to compensate for the loss in intertidal area and to restore equilibrium within a millennial time scale. Further sensitivity tests on initial bathymetry, tidal amplitude forcing, and rate of SLR show that shallow basins with limited tidal forcing are most vulnerable to SLR.