Results of a fault test performed in the unsaturated zone of Yucca Mountain, Nevada, were analyzed using a three-dimensional numerical model. The fault was explicitly represented as a discrete feature and the surrounding rock was treated as a dual-continuum (fracture-matrix) system. Model calibration against seepage and water-travel-velocity data suggests that lithophysal cavities connected to fractures can considerably enhance the effective fracture porosity and therefore retard water flow in fractures. Comparisons between simulation results and tracer concentration data also indicate that matrix diffusion is an important mechanism for solute transport in unsaturated fractured rock. We found that an increased fault-matrix and fracture-matrix interface areas were needed to match the observed tracer data, which is consistent with previous studies. The study results suggest that the current site-scale model for the unsaturated zone of Yucca Mountain may underestimate radionuclide transport time within the unsaturated zone, because an increased fracture-matrix interface area and the increased effective fracture porosity arising from lithophysal cavities are not considered in the current site-scale model.