The percolation flux through the unsaturated zone at the proposed Yucca Mountain repository for high-level nuclear waste can potentially affect (a) the occurrence and magnitude of water influx into the emplacement drifts, (b) the onset and rates of waste-package corrosion, (c) the mobilization of waste into aqueous states, and (d) the transport of radionuclides to the saturated zone. The magnitude and spatial and temporal variations of percolation flux depend on the infiltration rate but may be significantly influenced by (a) lateral diversion of flow at stratigraphic interfaces between nonwelded and welded tuffs above the repository horizon, (b) focusing of flow within or near steeply dipping fault zones, and (c) lateral diversion of flow within thermal-mechanical altered zones. Results from numerical modeling are presented to argue that (a) areas of the repository located close to and on the up-dip side of faults that intersect the Paintbrush nonwelded Tuff (PTn) would experience elevated percolation flux, irrespective of whether the faults act as flow barriers or conduits; (b) mechanical response of the rock mass to waste-generated heat will likely cause the development of laterally discontinuous zones characterized by dilation of horizontal fractures and net dilation or closure of vertical fractures; (c) areas of the repository located on the downstream side of the thermal-mechanical altered zones would experience elevated percolation flux; and (d) repository areas subjected to elevated percolation flux would experience faster rewetting of dryout zones and, thus, longer periods of wetness and elevated humidity. These results indicate that models used to predict the occurrence and magnitudes of water influx into emplacement drifts and the variations of relative humidity within the drifts need to consider the location of the drifts relative to faults that intersect the PTn and the development, geometry, and hydrological characteristics of thermal-mechanical altered zones.