The forecast of climate change effects on the groundwater system in coastal areas is of key importance for policy makers. The Dutch water system has been deeply studied because of its complex system of low-lying areas, dunes, land won to the sea and dikes, but nowadays large efforts are still being done to find out the best techniques to describe complex fresh-brackish-saline groundwater dynamic systems. In this paper, we describe a methodology consisting of high-resolution airborne electromagnetic (EM) measurements used in a 3-D variable-density transient groundwater model for a coastal area in the Netherlands. We used the airborne EM measurements in combination with borehole-logging data, electrical conductivity cone penetration tests and groundwater samples to create a 3-D fresh-brackish-saline groundwater distribution of the study area. The EM measurements proved to be an improvement compared to older techniques and provided quality input for the model. With the help of the built 3-D variable-density groundwater model, we removed the remaining inaccuracies of the 3-D chloride field and predicted the effects of three climate scenarios on the groundwater and surface water system. Results showed significant changes in the groundwater system, and gave direction for future water policy. Future research should provide more insight in the improvement of data collection for fresh-brackish-saline groundwater systems as it is of high importance to further improve the quality of the model.