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Geologic characterization of the Pajarito Plateau, in support of environmental investigations of potential groundwater contamination at Los Alamos National Laboratory, has provided the opportunity to examine the nature and extent of deep perched groundwater in this semiarid setting. Deep perched groundwater occurs at widely dispersed locations across the Pajarito Plateau. A total of 33 perched-zone occurrences were identified in 29 wells. The saturated thickness of perched zones is highly variable, ranging from about 1 to > 122 m (>400 ft). Observations are consistent with a conceptual model of low-permeability horizons on which infiltrating water sits. Deep perched ground-water is most often found beneath wet canyons, suggesting that in addition to perching horizons, locally high percolation rates are required to yield saturated conditions. Two conceptual models of perching systems are considered, one relatively stagnant and one more dynamic. To simulate deep perched groundwater in vadose zone flow a new method is developed that considers the interfaces between hydrogeologic units to be the horizons where the saturated permeability is lower than either of the units above or below the interface. A constant multiplier called the permeability reduction factor is applied at the interface between two hydrostratigraphic units to simulate the perching horizon. We demonstrate the method with two-dimensional numerical simulations performed for Los Alamos Canyon, replicating perched saturation as observed and showing how contaminant dispersal may be enhanced in certain perched systems compared with dispersion in the underlying zone of regional saturation.