With a growing population and limited freshwater resources, the hydrogeology of the Galapagos Islands remains to a great extent unknown. Rainfall is relatively weak and unevenly distributed in space and time. The economical center of the archipelago, Santa Cruz Island, has only small intermittent streams, while several permanent streams are present on San Cristóbal Island. In the frame of this study, an interdisciplinary approach is used to characterize the hydrogeology of the archipelago. A new method has been developed to enhance the interpretation of airborne electromagnetics surveys. With geostatistical interpolation techniques, this method allows the construction of a 3D grid of resistivity. SkyTEM surveys completed in Galapagos were processed with this technique, and confronted to surface analysis with remote sensing and field work. The first hydrogeological conceptual model is proposed for San Cristóbal Island. Climatic conditions have been investigated with the installation of a monitoring network along the windward side of Santa Cruz Island. The occurrence of fog during six months of the year presents an additional input in the water budget and increases groundwater recharge. This input has been quantified with a physically based canopy interception model. The basal aquifer of Santa Cruz Island has been investigated from the analysis of tidal signal propagation, hydraulic tests, as well as fault and fracture mapping. Results show that young basalts, densely fractured by cooling joints, are highly permeable. Because they are poorly connected, faults have a limited impact over regional groundwater flow. Contrasting hydrogeological configurations in the Galapagos Islands are explained by an evolution pattern. In relatively young islands, such as Santa Cruz, basalts are fractured and permeable. Seawater intrusion is strong and freshwater rapidely flows to the ocean. On the opposite, conditions are more favorable for groundwater storage in older volcanic islands, where the regional permeability is smaller and valley incision leads to the existence of springs.