Some of the possible water transport mechanisms through fractured rock in the unsaturated zone at Yucca Mountain are studied to analyze the performance of a high-level nuclear repository at the potential Yucca Mountain site. Analysis shows that water can flow in fractures as opposed to flow through the rock matrix if the incoming flux and the fracture aperture size exceed critical values. The rock matrix does not have to be nearly saturated for fracture flow to occur because the fractures and matrix can be in capillary disequilibrium during transient episodic infiltration events. As an example, the type of flow, fracture or matrix, is calculated for vertical fractures in the hydrogeologic units at Yucca Mountain. The results affect such issues as natural and total system performance, site characterization activities, and site suitability determination. Also, the important differences between an unsaturated and a saturated site are pointed out. The traditional concepts of near-field, far-field, and disturbed zone become blurred when talking about the unsaturated zone. The heat of decay may have beneficial aspects for an unsaturated site. Current regulations containing such concepts such as “groundwater travel time” are not consistent with some of the physical processes inherent in an unsaturated system.