Compacted bentonite buffer blocks placed in the engineered barrier system for high-level nuclear waste disposal can undergo swelling, intrusion into rock fractures, and erosion with saturation. Bentonite erosion and intrusion can lead to bentonite mass loss via groundwater flow and can ultimately compromise the overall integrity of the disposal system. To ensure the long-term safety of deep geological disposal, it is essential to assess the hydro-mechanical interactions between the bentonite buffer and surrounding rock. In this study, the impact of bentonite erosion and intrusion on the mechanical properties of the jointed rock mass were assessed via elastic wave propagation measurements using the quasi-static resonant column test. Granite rock discs obtained from the Korea Underground Research Tunnel and Gyeongju bentonite were used to simulate jointed rock specimens with different bentonite intrusion conditions. Different degrees of bentonite intrusion were simulated by mixing bentonite and water to create bentonite paste and gel. The longitudinal and shear wave velocities under different normal stress levels were used to quantify the effects of bentonite intrusion on the mechanical characteristics of the rock joint. Complementary numerical analysis using the three-dimensional distinct element code (3DEC) was conducted to provide improved understanding of wave propagation within bentonite gouge-filled rock mass.