Understanding the groundwater flow in carbonate aquifers represents a challenging aspect in hydrogeology, especially when they have been struck by strong seismic events. It has been proved that large earthquakes change springs hydrodynamic behaviour showing transitory or long-lasting variations and making their management much more difficult. This is the case of Sibillini Massif (central Italy), which has been hit by the well-known 2016–2017 seismic period. This work aims to improve the knowledge of carbonate aquifers groundwater circulation and their possible changes in the hydrodynamic behaviour, during and after a series of strong seismic events. The goal has been achieved by comparing long-time tracer tests and transient time-series analysis, based on a sliding-window approach. This approach allowed investigating transient variations in the carbonate aquifers recharge system, highlighting the changes of relationships between the inflow contributions to the spring discharge in the area. As a result, the seismically triggered pore pressure distribution, and the hydraulic conductivity variations, because of the ground shaking and the fault systems activation, account for all the mid-and long-term modifications in the recharge system of Sibillini aquifers, respectively. These outcomes provide valuable insights to the knowledge of aquifer response under similar hydrogeological conditions, that are vital for water management.