Monitoring biogeochemical properties of groundwater in rock aquifers near radionuclide-generating facilities is essential for effective water management and protection. Geochemical and microbiological properties vary with depth, influencing subsurface redox and trophic conditions. However, many studies lack depth-discrete sampling and an understanding of depth-dependent biogeochemical properties. In this study, we conducted a depth-discrete sampling assessment of major and trace elements, along with microbial community composition, in deep granitic groundwater from boreholes to evaluate the geochemical and microbiological characteristics of groundwater within and near an underground research tunnel (URT). Boreholes DB1 and DB3 are located inside the URT, while the JH well is outside. A total of 25 groundwater samples were collected from these boreholes at depths of 0-500 m (DB1), 0-350 m (DB3), and 0-150 m (JH), using packer systems. The results showed that groundwater types changed with depth, ranging from Ca-HCO3 to Na-HCO3. Redox profiles did not consistently correlate with increasing depth, suggesting preferential groundwater flow through altered zones and faults. Compared to the DB wells, the JH well showed higher dissolved oxygen levels and a broader range of geochemical parameters, including pH, Cl-, and NO3-. Consistent with these observations, 16S rRNA gene amplicon sequencing revealed higher microbial diversity in JH. The community composition also differed among the three wells, shaped by water-rock interactions (more intense in DB), redox conditions (reducing in DB vs. oxic in JH), and possible surface-induced contamination (in JH). Further analysis of JH groundwater samples collected with and without a packer system revealed clear depth-dependent variations in dissolved ions, radionuclide concentrations, and microbial community structures. Fluoride (F-) and uranium (U) concentrations exceeded drinking water guidelines at specific depths but fell below these limits without depth-discrete sampling. These findings highlight the importance of depth-resolved assessment of groundwater chemistry and microbiology for effective groundwater quality management and for evaluating the suitability of deep geological repositories.