Groundwater is a crucial water supply resource for Beijing, the capital of China. However, high fluoride (F) concentrations in groundwater have been reported previously on the southern Beijing Plain. In this study, F distribution in groundwater and aquifers of the southern Beijing Plain is comprehensively elucidated and its controlling factors are analyzed by integrating multiple approaches, including hydrogeochemical and isotopic analysis of groundwater, and chemical, lithological, and mineralogical studies of borehole sediment. Groundwater F- concentrations ranged from 0.01 to 0.95 mg/L, and were below the permissible limit in drinking water recommended by the Chinese government (1.0 mg/L). Relatively high F- -concentrations in groundwater were primarily distributed in the alluvial plain rather than those in alluvial fan. The spatial pattern of total F contents in the aquifer sediments was similar to that of groundwater F. The results of mineralogy, microstructure, and lithology also indicated that clay and F-bearing minerals (such as apatite, biotite, muscovite, fluorite, clinochlorite, and illite) in sediments provided geogenic sources of groundwater F. Various hydrogeochemical and mineralogical analyses provided corroborating evidence that sediment weathering (particularly silicates), dissolution of F-bearing minerals, and desorption from clay and iron (oxy)hydroxides were important processes that mobilize water-soluble and absorbed F into groundwater. Enrichment of groundwater F in the alluvial plain was attributed to high pH, groundwater flow path, long residence time, and the corresponding enhanced cation exchange of Ca2+ and Na+, reprecipitation of Ca2+, and substitution of F- by OH- under these conditions. Our findings highlight the combined effects of hydrogeochemical and mineralogical processes on F behavior in groundwater and have important implications for guiding the scientific control of high F groundwater.