Hydrogeological research in coastal areas has gained considerable attention over the last decades due to increasing stresses on fresh groundwater resources. Fundamental groundwater flow and solute transport analyses remain essential for a concise understanding of the governing processes that lead to salinisation of fresh groundwater resources. However, the challenge of modern research is the application and quantification of these processes in real world cases. In this context, deltaic areas are amongst the most difficult study areas as they often have a complex groundwater salinity distribution. The Wadden Sea area in the northern part of the Netherlands is an example of such an area. We quantified salt water intrusion and salinisation of groundwater flow systems in two representative case studies in the Wadden Sea area, using the density dependent groundwater flow and transport code MOCDENS3D. The results indicate that sea-level rise and autonomous processes will cause severe salinisation in the future, especially in the low polder areas close to the sea. In addition, we show that enhanced land subsidence due to salt exploitation accelerates this process. Salinisation can be mitigated to some extent by raising surface water levels in polders and by creating saline groundwater collection areas that maintain a low controlled water level.