The Long Valley Caldera, located at the eastern edge of the Sierra Nevada range in California, has been in a state of unrest since the late 1970s. Seismic, gravity and geodetic data strongly suggest that the source of unrest is an intrusion beneath the caldera resurgent dome. However, it is not clear yet if the main contribution to the deformation comes from pulses of ascending high-pressure hydrothermal fluids or low viscosity magmatic melts. To characterize the nature of the intrusion, we developed a 3D finite element model which includes topography and crust heterogeneities. We first performed joint numerical inversions of uplift and Electronic Distance Measurement baseline length change data, collected during the period 1985–1999, to infer the deformation-source size, position, and overpressure. Successively, we used this information to refine the source overpressure estimation, compute the gravity potential and infer the intrusion density from the inversion of deformation and gravity data collected in 1982–1998. The deformation source is located beneath the resurgent dome, at a depth of 7.5 ± 0.5 km and a volume change of 0.21 ± 0.04 km3. We assumed a rhyolite compressibility of 0.026 ± 0.0011 GPa−1 (volume fraction of water between 0% and 30%) and estimated a reservoir compressibility of 0.147 ± 0.037 GPa−1. We obtained a density of 1856 ± 72 kg/m3. This density is consistent with a rhyolite melt, with 20% to 30% of dissolved hydrothermal fluids.