The dynamics of the sandy coast between Castellaneta and Taranto (Southern Italy) has been influenced by many natural and anthropogenic factors, resulting in significant changes in the coastal system over the last century. The interactions between vertical components of sea-level changes and horizontal components of the sedimentary budget, in combination with anthropogenic impact, have resulted in different erosion and accretion phases in the past years. Local isostatic, eustatic, and vertical tectonic movements, together with sedimentary budget changes, must be considered in order to predict the shoreline evolution and future marine submersion. In this study, all morpho-topographic data available for the Gulf of Taranto, in combination with Vertical Land Movements and sea-level rise trends, were considered by assessing the local evolution of the coastal trend as well as the future marine submersion. Based on the predicted spatial and temporal coastal changes, a new predictive model of submersion was developed to support coastal management in sea-level rise conditions over the next decades. After that, a multi-temporal mathematical model of coastal submersion was implemented in a Matlab environment. Finally, the effects of the relative sea-level rise on the coastal surface prone to submersion, according to the Intergovernmental Panel on Climate Change Assessment Reports (AR) 5 Representative Concentration Pathways (RCP) 2.6 and RCP 8.5 scenarios, were evaluated up to 2100.