The Beishan area of Gansu, China, is the primary candidate site for the geological disposal of China’s high-level radioactive waste (HLW). To assess the long-term safety of this repository, the evolutionary patterns of groundwater and the primary migration vector of radionuclides must be understood. Through experiments and hydrogeochemical simulations of snowmelt samples from the Qilian Mountains and deep rock samples from Beishan, we reveal different hydrochemical compositions and types of the snowmelt and deep groundwater. The results show that the hydrochemical type of Qilian Mountain snowmelt is SO4–Na·Ca, whereas that of the deep groundwater in the Beishan is Cl·SO4–Na, indicating substantial differences in the hydrochemical characteristics of the two samples. The water–rock interactions between snowmelt and granite are dominated by the dissolution of silicate minerals and the precipitation of carbonate minerals, accompanied by cation exchange and adsorption. After the interaction, the hydrochemical type of the snowmelt becomes SO4–Na, with total dissolved solids (TDS) consistently maintained at ~500 mg/L, which is distinct from the TDS range of 1540–2045 mg/L observed for the deep groundwater in the Beishan. Under the experimental and simulation conditions set in this study, the water–rock interactions between Qilian Mountain snowmelt and Beishan granite cannot reproduce the hydrochemical characteristics of the deep groundwater in the Beishan. This study provides theoretical support for the hydrogeological safety assessment of HLW geological repositories.