The complex Krupaja karst system, located in Serbia, which consists of a strong karst spring, a thermal karst spring, and a borehole that captures sub-thermal waters, has been studied. A phenomenon which gives rise to the occurrence of karst waters of three different temperatures within a relatively short distance (about 200 m) led us to assume that these karst waters are formed within the same karst aquifer and circulate through different levels of karst channels that are zonally distributed within a vertical profile; this was confirmed by assessing the groundwater ages. Based on the development of karstification, as presented in this paper, as well as on previous investigations, explanations of four types of circulation within same karst system are provided. The results of measurements of stable isotopes (H, 18O, and 13C) and radioactive isotopes of tritium and T+He and 14C, as well as hydrochemical water analyses, speleogenetic spatial modeling, speleodiving research, etc., confirmed the assumption that these groundwaters belong to the same karst system. However, these karst waters have different residence times, i.e., from only a few days to over several decades and even up to approximately 4000 years, circulating through channels with various distributions along the depth of the karst aquifer.