A composite hydrogeothermal survey of the magmatic-metamorphic post-NeoTethyan late Paleogene - Neogene crustal core-complex of the Kopaonik Mt., southwestern Serbian highlands, provides new constraints on the subsurface hydraulic across- and along-fault flow fluid regimes and geothermal anomalies associated with the two shallow reservoirs. The study is involving synergistic approach by combining structural geology, exploratory drilling, temperature logging, hydrochemical and hydrodynamic constraints further illustrating a complex conduit–barrier fault-controlled spatial compartmentalization of the two thermal water reservoir(s). The thermal waters of the Kopaonik Mt. geothermal field are channeled by the major regional faults and associated fracture zones that are crosscutting the volcanics and the adjoining metamorphites. The results show that the subsurface compartmentalization of the active reservoirs, which are supplying the spa town of Jošanička banja, are controlled by a seismically active regional faults (including the fault that is crosscutting the Slanište locality, having N-S trending). Owing to the linear channeling of the fault-controlled reservoirs, in which the main quantitative water circulation takes place, it was possible to identify the thermal fluid flow paths and associated recharge zones (catchments). The Jošanička banja thermal waters reservoir is accommodated at ca. 400–500 m depth, whereas the Slanište aquifer maintains a shallower position. The new surface - subsurface constraints allowed the estimation of the subsurface reservoir elevations, pinpointing the origin of shallow crustal geothermal processes. Of particular importance is better understanding of the subsurface spatial distribution and the ultimate depth of the developing Kopaonik Mt. geothermal field. The new interpretation shows a qualitative agreement with the core-complex-related heat sourcing, as well as the fault-controlled reservoir compartments, impacting the efficient extraction of the thermal waters, in terms of quantity, quality and water temperature.