Fluoride (F⁻) pollution is a serious global problem. However, relatively few studies have evaluated the occurrence mechanisms of F⁻ from an entire lake system perspective and determined their major causes via quantitative analysis. This study analyzes the distribution and occurrence mechanisms of F⁻ in the lake water, sediment, groundwater, and soil of Shahu Lake, as well as assessing the influence of the factors on the F⁻ in the lake water via quantitative analysis. Our results show that the F⁻ concentrations in groundwater are higher in the eastern area of the lake, which is different from that in the surface soil layer. The F⁻ concentrations in the lake water vary from 0.95 to 1.40 mg/L, most of which exceed Chinese standards (1 mg/L). Groundwater F⁻ concentrations at 35% of the sampling sites exceed 1 mg/L. The total F⁻ in the soil is significantly higher than the global mean. Ca²⁺-deficiency (which is mainly accelerated by cation exchange between Ca²⁺ and Na⁺) together with alkaline water conditions and intense evaporation are the major contributors of F⁻ enrichment in groundwater. The groundwater hydrochemistry is suitable for the dissolution of F⁻-bearing minerals. The F⁻ in soil is not easily leached into groundwater. Approximately 6.96 t of F⁻ is deposited into Shahu Lake annually, where 79.17% of the F⁻ originates from water recharge. Evaporation is the main direct cause of high F⁻ concentrations in the lake, whereas water recharge and obstructed surface water exchange are indirect causes. To effectively decrease the F⁻ concentrations in the lake water, water exchange within the Shahu Lake system should be enhanced, or at least 4.42 million m³ of lake water should be pumped out of the system before anthropogenic water recharge, with identically increasing volumes.