We present here results of our investigation of the isotopic chemical composition of groundwater and carbonates in the Surdulica geothermal aquifer, Serbia. We considered the effects of carbonate dissolution and measured 13C, 14C, D, 18O, 3H, field pH, temperature, Na+, Ca2+, Mg2+, HCO−
3; and other aqueous species from 30 springs and boreholes. Geothermal waters are supersaturated with calcite. Carbon isotope compositions vary with carbonate mineral dissolution. The δD and δ18O of groundwater samples fit the meteoric water line, and indicate that groundwater is recharged mainly from higher altitudes and the cold season. Different groundwater residence times point out two mechanisms for their formation: fissure flow for young waters and standard diffusion processes for old ones.