The mineralization and mobilization of uranium (U) are strongly associated with subsurface redox processes, which can affect the U inventory of deep geological repositories of nuclear waste and are to be considered in safety assessments. The Korea Atomic Energy Research Institute (KAERI) underground research tunnel (KURT) is located in an active groundwater recharge area in granitic bedrock, where oxidizing meteoric water infiltrates the subsurface through permeable zones of highly weathered granite, forming multiple redox fronts. Fracture-filling materials (FFMs) are U-enriched, with concentrations of up to ∼50 mg/kg. We examined long-lived radioactive isotopes of 230Th, 232Th, 234U, 235U, and 238U and other redox-sensitive elements and isotopes, e.g., Fe, δ56Fe, and Ce/Ce*, in the FFMs to understand fluctuations in redox conditions in the granitic fracture system. The primary focus was on U migration processes and to decipher the depths of meteoric water infiltration over geological timescales. Enrichment of uranium and other redox-sensitive elements occurred in FFMs at relatively shallow depths (∼180 m below ground level, bgl), implying that the U distribution was associated with redox interactions of the intruding groundwater that precipitated the secondary minerals. Interaction of FFMs with groundwater caused activity ratios (AR) of the FFMs to deviate moderately from secular equilibrium (AR = 1); 234U/238U AR of 0.87–1.25, and 230Th/238U AR of 0.76–1.22. A dynamic redox transition zone, witnessed by uranium series disequilibrium, shows both deposition and complex redistribution in the 120–205 Ka time frame, is confined to the upper ∼180 m bgl of the fractured rock. The results provide new insights into the long-term paleo-redox processes in the complex granitic fracture systems, which are analogs of potential deep-seated geological repositories for high-level radioactive waste.