Hydrogeological perturbations in response to earthquakes are widely described worldwide. In carbonate aquifers, a post-seismic discharge increase is often attributed to an increase of bulk permeability due to co-seismic fracturing and the attention on the role of faults to explain the diversion of groundwater is increasing. We focus on the reaction of carbonate hydrogeological basins to extensional seismicity, taking as an example the effects of the Central Italy 2016–2017 seismic sequence, on the Basal aquifer of the Sibillini Mountains area. Geo-structural, seismological and ground deformation data were collected and merged with artificial tracer tests results and with a 4-years discharge and geochemical monitoring campaign. The main NNW-directed groundwater flow was diverted to the west and a discharge deficit was observed at the foot-wall of the activated fault system with a relevant discharge increase, accompanied by geochemical variations, at the fault system hanging-wall. The observed variations are consistent with the combined action of a permeability increase along the activated fault systems, which modified the predominant pre-seismic along-strike regional flow, and with hydraulic conductivity increase due to fracturing, determining a fast aquifers emptying. We show that the prevailing mechanism depends on the aquifer systems position with respect to the activated faults.