To investigate the impact of fluoride pollution on bacterial communities in the water-soil system, this study collected 66 sets of surface water, sediment, and riparian soil samples from the Qingshui River basin in Ningxia in 2022. The samples were categorized into three groups based on the fluoride concentration in the surface water: low fluoride group (F? < 1.0 mg/L), high fluoride I group (1.0 ≤ F? < 1.5 mg/L), and high fluoride II group (F? ≥ 1.5 mg/L). Bacterial community responses were systematically analyzed through 16S rDNA high-throughput sequencing and polymorphic fluoride species analysis. The results revealed that fluoride pollution decreased bacterial α-diversity (low fluoride group > high fluoride I group > high fluoride II group), although the Chao1 index of sediments increased due to niche release by rare species. The phyla Campilobacterota and Desulfobacterota were identified as fluoride-tolerant bacterial phyla, with species of Desulfobacterota participating in sulfate reduction to alleviate fluoride toxicity at low abundances. Genera such as Sulfurovum were recognized as fluoride-tolerant bacterial genera in the water-soil system. Bacteria facilitated the conversion of residual fixed fluoride (Res-F) in sediments and soils by decomposing and transforming it into other forms, with soil environments proving more favorable for bacterial decomposition of Res-F. This study establishes the first framework linking bacterial communities to polymorphic fluoride in the Qingshui River basin, enhancing the understanding of the impact of fluoride on bacterial communities in river ecosystems. It provides a scientific basis for the development of effective ecological and environmental protection policies, contributing to mitigating or reducing the potential risks of fluoride pollution to the ecological environment.