Identification of geochemical factors controlling the formation of fluoride and quantifying exposure risks associated with fluoride in groundwater is important for drinking water resource protection and public health. In the present study, 129 groundwater samples [89 from a shallow aquifer (SG) and 40 from a deep aquifer (DG)] were collected from a drinking water resource in the North Anhui Plain in eastern China. Hydrogeochemical methods, mineral saturation indices, and a human health risk assessment model were used to determine the formation mechanism and noncarcinogenic risks of fluoride in groundwater. The results indicate that fluoride concentrations in 10.1% and 2.5% of the SG and DG samples, respectively, exceeded the Chinese groundwater quality standard. Concentrations of fluoride were higher in Na-HCO3 and Mg-HCO3 type water than in Ca-HCO3 type water. Ca2+/Na+ versus HCO3-/Na+ and Mg2+/Na+ diagrams suggest that weathering of silicate minerals is a key factor controlling groundwater chemistry and fluoride concentrations. Relationships between F- and F-/Cl-, pH and Ca2+ indicate that geologic sources are an important source of groundwater fluoride and that direct cation exchange and competitive adsorption in alkaline environments favor F- enrichment. A saturation index analysis demonstrated that calcite and dolomite were saturated, while fluorite and gypsum could be further dissolved. Noncarcinogenic risks to adults associated with fluoride in groundwater were low. However, 21.3% and 35% of the SG and DG samples, respectively, presented unacceptable noncarcinogenic risks for children. High-risk areas were identified in the central, northern and southern portions of the study area. Our findings suggest that groundwater quality management and control measures should be implemented to protect the health of the local population, particularly children, in high-risk areas.