Worldwide, aquifers in low-lying coastal areas are threatened by saltwater occurrence, as a result of small head gradients, high groundwater abstraction rates, and drain management of the landscape, which is likely to intensify with climate change. Numerical models can serve as tools to identify the sources of the salt and thus to increase understanding of the driving mechanisms and important parameters controlling the extent of saltwater intrusions. This way, areas vulnerable to sea level rise can be identified and managed. Challenges include unknown initial salt concentrations, heterogeneous geology, and anthropogenic alterations. In this study, hydrogeological, geophysical, and geochemical data are used to develop a numerical density-dependent groundwater flow and transport model with the objective to understand the history of a saltwater-affected groundwater system and its likely response to historic and future changes. The extent of the simulated saltwater intrusion compares well with Airborne Electromagnetic data that show salt water up to 20 km inland. The results reveal that the salt water originates from a combination of laterally intruding seawater and vertically infiltrating transgression water. Main features controlling the progression of the modern seawater into the coastal aquifers are high permeable, deep Miocene sand aquifers, buried valleys that provide preferential flow paths in combination with extensive Miocene clay layers that delay saltwater intrusion. Anthropogenic activity enhances the saltwater inflow from the ocean and induces transient conditions. Future scenarios show that saltwater progression due to nonstationarity leads to enhanced contamination of the deeper aquifers. Climate change affects primarily the shallow aquifer systems.