The Sierra Gorda aquifer is one of the most extensive of southern Spain. The main groundwater discharge is produced at its northern boundary through several high-flow springs. In this study, stable isotopes of dissolved sulfate (δ34S and δ18O) and groundwater chemistry were used to determine the origin of the sulfate and to characterize the groundwater flow. We sampled the main springs, as well as other minor outlets related to perched water tables, in order to determine the different sources of SO42− (e.g., dissolution of evaporites and atmospheric deposition). The substantial difference in the amount of dissolved SO42− between the springs located in its northwestern part (≈25 mg/L) and those elsewhere in the northern part (≈60 mg/L) suggests zones with separate groundwater flow systems. A third group of springs, far from the northeastern boundary of the permeable outcrops, shows higher SO42− content than the rest (≈125 mg/L). The isotopic range of sulfate (−0.3‰ to 14.82‰ V-CTD) points to several sources, including dissolution of Triassic or Miocene evaporites, atmospheric deposition, and decomposition of organic material in the soil. Among these, the dissolution of Triassic gypsum—which overlies the saturated zone as a consequence of the folds and faults that deform the aquifer—is the main source of SO42− (range from 12.79‰ to 14.82‰ V-CTD). This range is typical for Triassic gypsum. The higher karstification in the western sector, together with important differences in the saturated thickness between the western and eastern sectors, would also be due to the tectonic structure and could explain the difference in SO42− contents in the water. This singular arrangement may cause a higher residence time of groundwater in the eastern sector; thus, a higher contact time with Triassic evaporitic rocks is inferred. Accordingly, the stable isotopes of SO42− are found to be a valuable tool for identifying areas with different flow systems in the saturated zone of karstic aquifers, as well as for evaluating aspects such as the degree of karstification.