To gain a better insight of the hydrogeology and the location of the main tectonic faults of Stromboli volcano in Italy, we collected electrical resistivity measurements, soil CO2 concentrations, temperature and self-potential measurements along two profiles. These two profiles started at the village of Ginostra in the southwest part of the island. The first profile (4.8 km in length) ended up at the village of Scari in the north east part of the volcano and the second one (3.5 km in length) at Forgia Vecchia beach, in the eastern part of the island. These data were used to provide insights regarding the position of shallow aquifers and the extension of the hydrothermal system. This large-scale study is complemented by two high-resolution studies, one at the Pizzo area (near the active vents) and one at Rina Grande where flank collapse areas can be observed. The Pizzo corresponds to one of the main degassing structure of the hydrothermal system. The main degassing area is localized along a higher permeability area corresponding to the head of the gliding plane of the Rina Grande sector collapse. We found that the self-potential data reveal the position of an aquifer above the villages of Scari and San Vincenzo. We provide an estimate of the depth of this aquifer from these data. The lateral extension of the hydrothermal system (resistivity ~15-60 ohm m) is broader than anticipated extending in the direction of the villages of Scari and San Vincenzo (in agreement with temperature data recorded in shallow wells). The lateral extension of the hydrothermal system reaches the lower third of the Rina Grande sector collapse area in the eastern part of the island. The hydrothermal body in this area is blocked by an old collapse boundary. This position of the hydrothermal body is consistent with low values of the magnetization (<2.5 A m-1) from previously published work. The presence of the hydrothermal body below Rina Grande raises questions about the mechanical stability of this flank of the edifice. © 2011 The Authors Geophysical Journal International © 2011 RAS.