A comprehensive investigation of the mixing between salt/fresh surficial water and groundwater in transitional environments is an issue of paramount importance considering the ecological, cultural, and socio-economic relevance of coastal zones. Acquiring information, which can improve the process understanding, is often logistically challenging, and generally expensive and slow in these areas. Here we investigate the capability of airborne electromagnetics (AEM) at the margin of the Venice Lagoon, Italy. The quasi-3D interpretation of the AEM outcome by the spatially constrained inversion (SCI) methodology allows us to accurately distinguish several hydrogeological features down to a depth of about 200 m. For example, the extent of the saltwater intrusion in coastal aquifers and the transition between the upper salt saturated and the underlying fresher sediments below the lagoon bottom are detected. The research highlights the AEM capability to improve the hydrogeological characterization of subsurface processes in worldwide lagoons, wetlands, deltas.