The conductivity structure of the top 2 km of the crust is examined using data from collocated magnetotelluric (MT) and time-domain electromagnetic (TDEM) soundings across the Vesuvius volcano. The MT data were corrected for static shift using dual-configuration TDEM data. The TEM and MT data were jointly inverted to yield 1D models while the TE and TM mode MT data were jointly inverted using a 2D inversion approach. The resulting models reveal the presence of a resistive cover layer underlain by an anomalous conductive layer (c. 250–500 m below the ground surface) that is shallowest underneath the caldera. We suggest that the conductive body below the caldera is related to enhanced hydrothermal circulation; outside the caldera, the conductor is consistent with the hydrological system and is interpreted as mapping a suggested aquifer system and underlying clayey deposits. Our results show that the aquifer hosted in the Vesuvius edifice is not homogeneous, but appears particularly conductive in the western and southern sectors of the volcano. It was found from 3D numerical modelling study that the presence of the shallow and thick conductors and the Tyrrhenian sea changes the penetration depth of MT data and must be taken into account during interpretation. Recommendations are made for any future MT field studies aimed at resolving the deep resistivity structure of Mt Somma-Vesuvius.