Sea-level rise (SLR) will affect the hydrodynamics and flooding characteristics of estuaries which are a function of the geomorphology of particular estuarine systems. This study presents a numerical modelling of coastal flooding due to drivers such as spring-tides, storm surges and river inflows and examines how these will change under sea-level increases of 0.4 m and 0.9 m for two estuaries that are at different geomorphological evolutionary stages of infill. Our results demonstrate that estuarine response to SLR varies between different types of estuaries, and detailed modelling is necessary to understand the nature and extent of inundation in response to SLR. Comparison of modelling results indicates that floodplain elevation is fundamental in order to identify the most vulnerable systems and estimate how inundation extents and depths may change in the future. Floodplains in mature estuarine systems may drown and experience a considerable increase in inundation depths once a certain threshold in elevation has been exceeded. By contrast, immature estuarine systems may be subject to increases in relative inundation extent and substantial changes in hydrodynamics such as tidal range and current velocity. The unique nature of estuaries does not allow for generalisations; however, classifications of estuarine geomorphology could indicate how certain types of estuary may respond to SLR.