In this paper, a multiple unsaturated soil barrier system consisting of multiple layers of gravel, sand, decomposed granite soil, and bentonite mixture soil is considered as a hardly permeable covering to prevent rainwater from infiltrating into waste deposits. Water infiltration is prevented due to both the low permeability of the bentonite mixture soil layer and a capillary barrier with different water-retention capabilities. A series of numerical simulations was carried out to evaluate the performance of the barrier system using a saturated/unsaturated soil/water coupled FE computation technique. Impermeability of the barrier system is shown as a graphical chart with rainfall duration on the x-axis and rainfall intensity on the y-axis. The simulation results show that the capillary barrier is a key parameter in evaluating the long-term performance of the barrier system. Results also confirm that the barrier system can work well against the maximum intensity of the rainfall recorded in Nigyo-toge.