Airborne Electromagnetics (AEM) is nowadays widely used worldwide to characterize the seawater-groundwater interface by inverting the AEM data in terms of electrical conductivity. Despite the effectiveness of this approach, the inversion in terms of electrical properties does not take into account the hydrogeological mechanism that determines the interface position. Furthermore, the standard approach in inverting AEM data is to use a 1D approximation in the data modelling, with the risk of creating severe artifacts in the interface mapping. In this study we use hydrological modelling for constraining the geophysical inversion, modelling the freshwater-saltwater interface of costal aquifers in terms of hydrogeological properties and the AEM data with a full 3D solution of the AEM partial differential equation. In particular, the interface flow below a strip island is modelled analytically as a function of: i) the island dimension; ii) the freshwater and groundwater densities; iii) the areal recharge; iv) the hydraulic conductivity. The corresponding AEM response is computed in 3D assigning the freshwater and groundwater electrical conductivities, and the AEM data are then inverted in 3D using as inversion parameters only the hydraulic conductivity and the freshwater/groundwater electrical conductivities. We believe that constraining the AEM geophysical inversion by hydrogeological modelling opens the way for a direct characterization of hydraulic parameters, as well as for a quantitative study of seawater/groundwater interactions in costal aquifers, both for characterizing seawater intrusion and submarine groundwater discharge.