In the spring (April), summer (July), and autumn (October) of 2019 and 2021, samples were collected six times from 99 points in the Ningxia section of the Yellow River Basin. These 99 points were categorized into eight hydrological networks: the main stream of the Yellow River (S1), Qingshui River (S2), Kushui River (S3), drainage ditch on the north bank of the Yellow River in the Weining section (S4), drainage ditch on the south bank of the Yellow River in the Weining section (S5), drainage ditch on the west bank of the Yellow River in the Qingshi section (S6), drainage ditch on the east bank of the Yellow River in the Qingshi section (S7), and urban landscape rivers and lakes (S8). The spatial and temporal distribution characteristics of fluorine in sediments were analyzed, the ecological risk of sedimentary fluorine was evaluated, and its impact on fluorine pollution in surface water was discussed. The results showed that the average contents of water-soluble fluorine (Ws-F), exchangeable fluorine (Ex-F), total fluorine (T-F) in sediments from the Ningxia section of the Yellow River Basin were 9.42 mg/kg, 3.23 mg/kg, and 517 mg/kg, respectively. The evaluation results of ER_bc and ER_bf can better reflect the actual ecological risk. The contents of Ws-F, Ex-F, and T-F in the sediments of S3, S2 and S7 and the ecological risk of fluorine were all high, while those of S1 were low. Ws-F was an important factor that directly affected the F^- content in surface water. T-F indirectly affected the F^- content of surface water by transforming into Ws-F. The strong release capacity of fluoride in sediments of S3, S2 and S7 promoted the increase of fluoride content in surface water, which should be taken as the key control area. The dilution effect of S1 and the weak release ability of fluoride in sediments of S6 reduced the fluoride content in surface water.