We used hydrogeochemical techniques and environmental isotopes (δ¹⁸O and δ²H) to characterize karst aquifers without a well-known hydrogeological conceptual model. The selected study area corresponds to carbonate outcrops located in the Sierra Grazalema Natural Park (SGNP) in southern Spain. The combination of high rainfall, large areas of carbonate outcrops and the high permeability of the outcropping rocks means that the SGNP is a strategic water reserve in a region that periodically suffers from a scarcity of water. There are still many uncertainties regarding the hydrogeological functioning of these aquifers, such as the groundwater flow paths, the identification of recharge areas and a possible hydrogeological connection with adjacent systems. The objectives of this work were: (1) to gain an insight into the hydrogeochemistry of groundwater in the SGNP aquifers; (2) to identify the recharge areas of the main springs of the karst system; and (3) to contribute to our understanding and conceptualization of the SGNP aquifers. Our results show marked differences in the chemical composition of the groundwater, which can be classified into three main groups: CaHCO₃ waters (southern sector); Ca–MgHCO₃ waters (northern sector); and those with higher SO₄²⁻, Na⁺ and/or Cl⁻ concentrations. These hydrochemical differences are principally dependent on the mineral composition of the rocks the groundwater flows through and comes into contact with. These results also shed light on the recharge areas associated with the main springs and seem to corroborate a possible net groundwater flow from the eastern part of the SGNP (Sierra del Endrinal) towards carbonate outcrops situated several kilometres to the SE.