Fluctuations in groundwater content may produce surface deformation and affect the elastic properties of the Earth’s crust. In this study we evaluate the temporal variations of the Earth’s crust elastic properties (in the form of relative seismic-velocity variations) in a tectonically active region in Northern Italy characterized by the presence of karst systems. In this area, GPS measurements already revealed hydrologically-induced deformation, modulated by changes in groundwater storage. We study the relation of our seismological observations with the geodetic and hydrological results and identify the effects of groundwater-content variations in the seismic-velocity perturbations. Our results show that hydrologically-induced changes in karstic media produce significant seismic-velocity perturbations, therefore its role in tectonic-stress adjustment studies must not be ignored. Depth sensitivity analysis of our results constrain the crustal perturbations to range between 1 and 4 km depth. Results from scattering imaging locate the crustal perturbations along the main karst systems.