Reliable predictions of future inundation extent within estuaries require a precise evaluation of future extreme sea levels and the application of accurate numerical models that account for the physical processes driving estuarine hydrodynamics. In this study, a methodology that integrates the estimation of local extreme sea levels with high-resolution numerical modeling was applied to assess the future inundation extent in five estuarine systems located on the Portuguese Coast. The main findings obtained were compared with available results from the popular bathtub approach, that disregards the physical processes driving estuarine hydrodynamics and therefore provide imprecise predictions of inundation extent and associated socio-economic impacts. The inundation extent is revealed to be highly dependent on the extreme sea levels and on the estuarine geomorphology, which controls the propagating long-wave. As the long-wave height is highly attenuated within estuaries that have adjacent low-lying areas, restricted inlets, or extensive tidal flats, the results of this study revealed that the extent of inundation is considerably smaller than that obtained by the bathtub approach. The uncertainties associated with mean sea level rise and the estuarine geomorphological evolution constitute the greatest difficulty in assessing the extent of flooding, posing major challenges to the efficient and sustainable management of estuaries.