The Baix Empordà-Selva-Gavarres aquifer system is related to the fault set that created the tectonic basins of Empordà and Selva areas (NE Spain) during the Neogene. In this work, we describe groundwater hydrogeological, hydrochemical and isotopical (3H, δD, δ18O, and the 87Sr/86Sr ratio) characteristics of this system in order to illustrate the relevance of fault zones in groundwater flow-paths and the recharge. In that way, we identify two flow systems, with distinct hydrochemistry and isotopes. A local flow system originates at the Gavarres Range, and it flows towards the basins of the Baix Empordà and Selva, with an approximate residence time of 20 years. Additionally, a regional flow system has only been identified in the Selva basin. This one is related to the main fault zones, as preferential flow paths. Its recharge is located in mountain ranges with higher altitudes, namely the Transversal and Guilleries Ranges, with residence times larger than 50 years. Isotopical data has also shown mixing processes between both flow systems and rainfall recharge while multivariate statistical analysis of principal components has shown the main processes that control hydrochemistry of each flow systems