Migration of nuclides in a water-saturated high-level radioactive waste repository is analyzed by a newly developed two-dimensional numerical model incorporating a multiple-canister configuration and a nonuniform horizontal flow field of the host rock. The nonuniform flow field is established numerically by obtaining space-dependent groundwater flow velocity vectors using the finite element method. Transport of nuclides is simulated for the instantaneous-pulse-input source condition using the random-walk method. The current study for advection-dominant host rock shows quantitatively that the migration of nuclides in a repository adopting the disposal-pit vertical-emplacement concept is influenced not only by the canister configuration but also by flow boundary conditions, where groundwater flow is considered to be horizontal to the repository plane. The effects of applied hydraulic gradient direction h on nuclide migration become more significant as the number of canisters increases, while the effects are negligible for the single-canister configuration. As the number of canisters increases, the results of nuclide migration with respect to h range more widely and are bounded by two extreme cases. The h orthogonal to the orientation of the disposal tunnel is observed as most advantageous in terms of the isolation of the radionuclide. The single-canister configuration yields conservative results compared with the multiple-canister configuration.