The isotopic investigations of groundwaters stored in the Rogaška Slatina fractured aquifer system were performed in the periods 1978–1985 and 2007–2011 aiming at answering open questions on the groundwater recharge and dynamics, on connections between different types of aquifers and on solute transport. Environmental isotopes 2H, 18O, 3H, 13C of dissolved inorganic carbon and 14C were analysed in mineral, thermo-mineral and spring waters. Results indicated the source and mechanism of groundwater recharge, its renewability, a transit time distribution, hydraulic interrelationships, the groundwater origin and its evolution due to effects of water-rock interaction. They proved the hypothesis that the Boča massif should be a catchment area of the Rogaška mineral waters. The estimates of the mean residence time of mineral waters in the aquifer system are between 7200 and 3400 years, depending on the location and depth. Thermo-mineral water is the oldest water in the study area with the mean residence time of 14000 years.