Sea-level rise, together with human activities, may induce significant coastline modifications that need to be assessed and analysed, to evaluate the future risks of inundation in coastal areas, and the impacts on local infrastructure. In this work, we present an integrated, GIS-based approach to examining this problem that relies on state-of-the-art numerical projections of future sea level in the Mediterranean area, for specific emission scenarios, and on the extrapolation of present trends of vertical ground motion obtained from the Copernicus European Ground Motion Service (EGMS). The approach is applied to five coastal areas hosting important Italian harbours, namely Brindisi, Napoli, La Spezia, Taranto, and Cagliari. Main outcomes of this study are coastal flooding maps at different time horizons. In creating these maps, sea-level rise information from the numerical simulations has been transported to the coast using the “bathtub” approach, without considering the effects of the local morphology on the inundation process, which is something to be refined in future implementations. The main assets exposed to flooding risk are low elevation wetlands, and backshore areas, together with coastal infrastructures. The high degree of subsidence of infrastructures during the first years after construction may significantly contribute to the risk of flooding. In these cases, however, predictions based on present EGMS data, with a limited time-span, should be considered with caution. Further investigation of the geotechnical interactions involved, together with the constant update of the Copernicus database, will be of help in making the related projections more reliable.