Groundwater flow and transport are crucial for performance and safety assessment in the radioactive waste geological disposal. This study presents the groundwater flow and advective transport simulations for assessing the performance of a reference repository placed in fractured rocks. The study involves the concept of radionuclides migrating into the mobile water in fractures surrounding the deposition hole and calculates two specific quantitative indicators in the field of radioactive waste geological disposal. The indicators equivalent flow rate (Qeq) and flow-related transport resistance (F) are used to express the groundwater flow and transport resistance in the host rock. Based on the hydrogeological conceptual model, the study employs DarcyTools to model the groundwater flow and advective transport of a base case. This study then conducts sensitivity analyses by varying the hydraulic conductivity of the key hydrogeological unit and the excavation damage zone. The uncertainty analysis employs multiple discrete fracture network (DFN) realizations to quantify the influences of DFNs on the flow and advective transport. Results show that the hydraulic conductivity of host rock dominates the flow and advective transport in the model domain, and the highest Qeq is 1.91 × 10−4 m3/year, and the lowest F is 7.77 × 105 year/m. Results also indicate that simulations of the hydraulic conductivity variations of hydrogeological units are more critical than those obtained from the variations of DFN realizations (i.e., the uncertainty analysis). The solutions could be useful for site investigations to modify the hydrogeological conceptual model in the study.