We simulated the sediment-water system of Lake Shahu. The raw fluoride (F^-) concentration of the Lake Shahu water was set to 1-fold concentration (0.69 mg/L). Five concentration-gradient groups (0.5-fold, 1-fold, 1-fold sterilization, 2-fold and 4-fold) were tested to investigate the migration of F^- in Lake Shahu sediments under different F^- concentrations of the overlying water. Results showed that the release of F^- from the sediments decreased with the gradient of F^- concentrations, and the sediments adsorbed F^- in the 2-fold and 4-fold groups. Alkaline waters were favorable for the release of F^- from the sediments. As the pH level increased, the release of F^- also increased. Results from analysis of the beta diversity hierarchical clustering of the microorganisms showed that F^- inhibited the relative abundances of Paenisporosarcina and Thiobacillus, but promoted the vital activities of Fusibacter. According to the redundancy analysis of the dominant genera and environmental factors, Acinetobacter and Thiobacillus were negatively correlated with the pH level. Fusibacter had a significant positive correlation with F^- concentrations, while Thiobacillus showed a weak negative correlation with F^-. Analysis of the significant ions in each group indicated that the migration of F^- in the 0.5-fold and 4-fold groups was strongly influenced by Ca²⁺, HCO₃^-, and SO₄^2- concentration. Correlation analysis showed that Ca²⁺ and HCO₃^- concentrations had a highly significant positive correlation with F^- concentration in the 0.5-fold concentration group, and a negative correlation was found between F^- and Ca²⁺ or HCO₃^- concentrations in the 4-fold group. Correlation between SO₄^2- and F^- concentrations in the 0.5-fold group showed a negative correlation, and the 4-fold group showed a highly significant positive correlation. This study comprehensively investigated the mechanisms of the release and migration of F^- in the sediments of Lake Shahu under different F^- concentrations of the overlying water. Thus, a theoretical support is provided for the control of F^- pollution in Lake Shahu and other fluorinated surface waters.