High background levels of fluorine in groundwater and soil in arid and semi-arid loess regions pose a severe threat to socio-economic development and human health, necessitating the evaluation of fluorine migration in loess. In this study, static leaching and dynamic seepage tests as well as scanning electron microscopy, mercury intrusion porosimetry, and X-ray fluorescence analyses were conducted using loess as the porous medium. Additionally, simulations using PHREEQC software were performed. The results indicated that the studied loess had a high background level of fluorine. Geochemical processes closely related to fluorine include dissolution of gypsum and dolomite, precipitation/dissolution of calcite and fluorite, and ion exchange between CaX and NaX. Under seepage of water with high fluorine levels, soil particles flocculated and formed aggregates; furthermore, the contact area between soil particles reduced, resulting in point-to-point contact between particles. Consequently, pores changed from small (intra- and inter-particle pores) to large (intra- and inter-granular pores) scale pores. Permeability initially decreased rapidly, then remained relatively stable, and subsequently rapidly increased with the passage of time. This was attributed to the dissolution of calcium minerals in loess, yielding Ca2+, which induced the precipitation of fluorite and promoted the dissolution of carbonates. Cation exchange and dissolution of other components were also important factors influencing permeability. The findings of this study can elucidate the coupling between loess microstructure, seepage behavior, and geochemical actions under the influence of high‑fluorine water, and are of great significance for in-situ regional research in loess areas.