Understanding mechanisms of groundwater recharge in karst aquifers that are used as a source of drinking water is vital for sustainable water management. In this study, 18O, 2H and 3H isotopes were used to understand the physical processes which affect water flow in a karstic region and for determining the locations of groundwater recharge areas and residence time in the Namazgah Dam Basin in Turkey. Overlay analysis was carried out with a geographic information system platform using residence time, recharge altitude and type and the hydraulic conductivity of geologic formations to identify protection zones of springs used for water supply. This assessment was supported by dye-tracer tests and the use of geophysical techniques. The methodologies used in this study could be used to develop water resource protection zones in other karstic regions where limited data are available.