Bacterial metabolisms influence the behavior of uranium (U) in deep geological repository (DGR) system because bacteria are ubiquitous in the natural environment. Nevertheless, most studies for the U(VI) bioreduction have focused on a few model bacterium, such as Shewanella putrefaciens, Desulfovibrio desulfuricans, and Geobacter sulfurreducens. In this study, the potential of aqueous U(VI) ((U(VI)aq) reduction by indigenous bacteria was examined under anaerobic conditions with addition of 20 mM sodium acetate for 24 weeks. Three different indigenous bacterial communities obtained from granitic groundwater at depths of 44–60 m (S1), 92–116 m (S2), and 234–244 m (S3) were applied for U(VI)aq reduction experiments. The S2 groundwater contained the highest U concentration of 885.4 μg/L among three groundwater samples, where U mainly existed in the form of Ca2UO2(CO3)3(aq). The S2 groundwater amended 20 mM of sodium acetate was used for the U(VI)aq bioreduction experiment. Variations in the U(VI)aq concentration and redox potential were monitored for 24 weeks to compare U(VI)aq removal efficiency in response to indigenous bacteria. The U(VI)aq removal efficiencies varied among three indigenous bacteria: 57.8% (S3), 43.1% (S2), and 37.7% (S1). The presence of the thermodynamically stable uranyl carbonate complex resulted in the incomplete U(VI)aq removal. Significant shifts in indigenous bacterial communities were observed through highthroughput 16S rRNA gene sequencing analysis. Two SRB species, Thermodesulfovibrio yellowstonii and Desulfatirhabdium butyrativorans, were dominant in the S3 sample after the anaerobic reaction, which enhanced the bioreduction of U(VI)aq. The precipitates produced by bacterial activity were determined to be U(IV)-silicate nanoparticles by a transmission electron microscope (TEM)-energy dispersive spectroscope (EDS) analysis. These results demonstrated that considerable U immobilization is possible by stimulating the activity of indigenous bacteria in the DGR environment.