A methodological approach using inverse modeling was used to characterize the functioning of the deep and shallow reservoirs of the Thau karst aquifer system. Three springs were monitored at the convergence of rising saline water diluted with shallow groundwater in karst conduits and unmixed shallow groundwater that behaves as confined groundwater. In such a method, impulse responses of flow and fluxes are combined in order to separate hydrographs. The model explains the salinity and hydraulic head variations of the submarine and inland springs. It confirms and improves the conceptual model of this groundwater system in which mixing of saline and subsurface waters occurs. The different forces driving the upward flowing mixed water into the drainage axis and faults were studied in order to elucidate the springs' functioning. A comparative study of spring functioning is proposed, which clearly shows the very high sensitivity of the groundwater system to changes in recharge and discharge conditions.