A geological repository for vitrified high-level radioactive waste (HLW) has a range of different types of tunnels with different geometries depending on function: transport and emplacement of engineered barrier materials and waste packages, or access to underground facilities etc. At points where tunnels intersect, a complex arrangement of closure components will be placed to ensure long-term isolation performance of a disposal system. It is a key issue to identify requirements for the design of the materials and layout of these components, including clay-based backfill and plug. In this study, three-dimensional simulations of groundwater flow are conducted to investigate the sealing performance of clay-based backfill and plug at the tunnel intersection for given hydraulic conditions around the tunnels. In the analytical results, it is found that the direction of hydraulic gradient, hydraulic conductivities of concrete and backfilling materials and the position of clay plug had impact on flow condition around the engineered barrier system (EBS).