Understanding the hydrogeological processes is critical for a sound management of groundwater resources in costal areas. Here lie majority of human settlements, industrial production, and fish farming. Human pressure on the coastland environment is constantly increasing, and many studies predict a rising of seawater level in the next 50 years raging from few cm up to several tens of cm, with expected threatening consequences (e.g., Carbognin et al., 2009). If these are common characteristics of most costal areas, wetlands, lagoons and estuaries also have often unique flora and fauna depending on the groundwater-surface water processes. The hydrologic setting of the transitional environments is complicated by their Late Quaternary subsoil architecture. The deposits represents the transition through the fluvial in tide-dominated depositional systems triggered by the sea level changes. In particular, in the Venice area numerous geomorphological features representing i.e. fluvial paleoriver beds, ancient tidal channels, and paleobeach ridges occur (Tosi et al., 2009). These features are generally filled by sandy deposits and can be considered preferential path for the groundwater flow, both in the horizontal and vertical directions. In order to have a better understanding of the hydrogeological setting of these areas, and also to produce more useful models, it is crucial to acquire information both inland and within the lagoon or wetland, covering both its permanent wet and tidal areas. Acquiring information that can be used to model the groundwater processes of these areas is often logistically challenging and therefore expensive and slow. This applies both to punctual, invasive and direct measurements such as depth to groundwater table and salinity from boreholes, to non invasive, area covering, indirect data such as resistivity or seismic investigations. Apart from the logistics, in many cases the quality of the data reflects the spatial and or temporal alternation of dry land and ponds-marshes-surface water in general. Airborne electromagnetics (AEM) can greatly improve the data quality and coverage in such areas, while cutting significantly the acquisition costs. Its direct output is geoelectrical cross sections or maps that are then used as input for hydrogeological models. The application of AEM for groundwater monitoring and modeling has been steadily rising in the past decade, due to parallel developments of better AEM systems and processing, e.g. inversion methodologies. However, so far there have been extremely limited attempts of applying AEM to areas such as lagoons, wetlands, rivers or bays. This manuscript shows that AEM can produce quantitative results useful for groundwater modeling also in these areas, presenting the results of a survey carried out in the central and southern sectors of the Venice Lagoon, Italy, by the SkyTEM system. We present some of the inversion outcome as horizontal average resistivity maps at different depth intervals and cross sections obtained by SkyTEM application in the two areas where different hydrogeological processes are under investigation.