The resistivity structure of the Tenerife geothermal system has been determined by the 3-D inversion of data from different magnetotelluric surveys. In this paper, the ocean and topography effects on the magnetotelluric data were investigated by constructing a 3-D conceptual geoelectrical model of the island. The study showed that these effects should be taken into account in order to obtain a reliable subsurface model of the island. Data from 148 sites were used during three-dimensional inversion. The most interesting feature in the final geoelectrical model of the geothermal system is a low resistivity structure (<10 Ωm) above the resistive core of the system. The low resistivity structure has been interpreted as a hydrothermal clay alteration cap typically generated in the conventional geothermal systems. The resistivity model has been correlated with a recent seismic velocity model, showing that a low resistivity structure surrounds an area with high P wave velocity and medium-high resistivity. This medium-high resistivity area can be associated with a slowly solidified magma and, therefore, with a hotter part of the geothermal system.