For many countries, karst aquifers are a significant source of potable water; thus, understanding their hydrogeological behavior is of great importance. However, in tectonically complex karst areas, knowledge of their hydrogeological behaviors has remained largely limited due to the high heterogeneity, often necessitating the use of costly and time-consuming techniques. In this study, spring discharge hydrographs, water balance estimates, hydrochemical and stable isotopic analyses, geomorphological surveys, and a consideration of the geological and structural setting of the study area were used to investigate the hydrogeological function of karst aquifers drained by two large permanent springs: the Bibitalkhone (Bt) and Sabzab (Sa) springs, located in a highly faulted catchment in the Zagros Mountains (southwest Iran). The results obtained from these different approaches suggested that fault-controlled, external waters from neighboring karst aquifers are responsible for more than two-thirds of the total discharge recorded at both springs. In this study, this predominantly conduit-type recharge is referred to as “regional (or external) autogenic recharge”. A smaller portion of the springs’ discharge (∼25% and ∼5% of the Bt and Sa springs’ discharge, respectively) originates from internal waters associated with the springs’ host aquifer, which is supplied by rainfall and infiltrates into the subsurface via joints and fractures. This type of recharge is largely diffuse and is referred to here as “local (or internal) autogenic recharge”. A relatively large portion of the Sa Spring’s discharge (∼35%) originates from a nearby dam reservoir, which can leak into the host spring aquifer through joints and fractures. This type of recharge is described as “local (or internal) allogenic recharge” and is primarily diffuse. The results of this study demonstrate that the karst aquifers in the downstream catchments can supply a stable and continuous source of potable groundwater that can meet the region’s annual consumption, agricultural, and industrial demands. This study will provide insights into the hydrogeological regimes of fault-influenced aquifers, contributing to the sustainable development and proper management of water resources in tectonically complex karst catchments.