Fluoride (F−) enrichment in groundwater poses significant risks to drinking water safety; however, reports of high F− concentrations in groundwater in a vast desert and its hydrogeological indications are limited. In this study, we collected 275 groundwater samples from various depths in the Badain Jaran Desert (BJD) to investigate the distribution characteristics and enrichment mechanisms of F− in desert groundwater, utilizing hydrochemistry, environmental isotopes, and statistical methods. The results indicate that (1) the groundwater F− concentrations in the mountainous areas, desert areas, and downstream wetland areas are 0.10–9.45 mg/L (average of 3.05), 0.19–58.00 mg/L (average of 4.32), and 0.62–9.91 mg/L (average of 1.99), respectively, with corresponding exceedance rates (>1 mg/L) of 83%, 71%, and 80%. (2) In mountainous areas, F− enrichment mechanisms are attributed to ion exchange, evaporative concentration, and the dissolution of fluoride minerals. In desert areas, F− enrichment mechanisms involves multiple hydrogeochemical processes, with the dissolution of fluoride minerals being the most significant, followed by evaporative concentration and desorption. And evaporative concentration is particularly pronounced in shallow groundwater (depth <4 m). In wetland areas, F− enrichment mechanisms are mainly ion exchange and desorption. (3) The F− concentration characteristics (<2 mg/L) and the significant correlation between F− and HCO3− (R = 0.55, P < 0.01) in the deep groundwater of the desert suggest that groundwater does not originate from deep geothermal sources. (4) Based on the significant differences in groundwater F− concentrations, there is a weak hydrodynamic connection between the groundwater in the Quaternary aquifer and that in the underlying Cretaceous bedrock in desert areas. These findings not only facilitate the safe use of groundwater in desert environments but also provide new insights into the formation, circulation, and evolution of desert groundwater.