The Pajarito Plateau in northern New Mexico, on which the Los Alamos National Laboratory is situated, is characterized by a thick vadose zone overlying the regional aquifer of the western Espanola Basin. In this study, conceptual models of vadose zone flow and transport processes are presented and then supported through the interpretation of field data, including synthesis with numerical models. The conceptual models differentiate the rate of percolation by their location and surface hydrologic setting, including wet and dry canyons, and wet, dry, and disturbed mesas. Net infiltration beneath wet canyons is the highest, with rates on the order of a meter per year (100–1000 mm yr−1). Transport to the regional aquifer beneath the wettest canyons is likely on the order of several years to several decades, depending on the thicknesses of the various hydrostratigraphic layers. Perched water is sometimes found beneath wetter canyons and is associated with near-surface alluvial systems and at intermediate depths along low-permeability interfaces such as buried soils or unfractured regions of basalt flows. Percolation through the volcanic tuffs is generally considered to be via matrix-dominated flow, whereas fracture flow may play a key role in contaminant transport through densely welded tuffs or basalt units beneath wet canyons. Infiltration beneath dry canyons and dry mesas is much slower (10 mm yr−1 or less), yielding transport times to the aquifer of hundreds to several thousands of years. However, long-term surface disturbances at mesa-top locations may alter infiltration rates such that at a local scale, the infiltration rates temporarily approach those of wetter canyons.