High fluoride concentrations (median=4.4 mg/L) in deep bedrock groundwater of South Korea prevent the usage of it as a drinking water source. The hydrogeochemistry of deep thermal groundwaters (N=377) in diverse bedrocks has been studied in order to evaluate the geologic and geochemical controls on fluoride concentrations in groundwater. The groundwater samples were clustered geologically, and the average and median concentrations of fluoride were compared by the Mann-Whitney U test. The order of median fluoride concentration with respect to geology is as follows: metamorphic rocks> or =granitoids > or =complex rock>>volcanic rocks> or =sedimentary rocks. This result indicates that the geological source of fluoride in groundwater is related to the mineral composition of metamorphic rocks and granitoids. With respect to groundwater chemistry, the fluoride concentration was highest in Na-HCO3 type groundwater and lowest in Ca-HCO3 type groundwater. Ionic relationships also imply that the geochemical behavior of fluoride in groundwater is related to the geochemical process releasing Na and removing Ca ions. The thermodynamic relationship between the activities of Ca and F indicates that fluoride concentration is controlled by the equilibrium of fluorite (CaF2). In other words, the upper limits of fluoride concentration are determined by the Ca ion; i.e., Ca concentrations play a crucial role in fluoride behavior in deep thermal groundwater. The result of this study suggests that the high fluoride in groundwater originates from geological sources and fluoride can be removed by fluorite precipitation when high Ca concentration is maintained. This provides a basis for a proper management plan to develop the deep thermal groundwater and for treatment of high fluoride groundwater frequently found in South Korea.