Site-specific numerical modeling of four sites in two arid alluvial basins within the Nevada Test Site employs a conceptual model of deep arid system hydrodynamics that includes vapor transport, the role of xeric vegetation, and long-term surface boundary transients. Surface boundary sequences, spanning 110 kyr, that best reproduce measured chloride concentration and matric potential profiles from four deep (230--460 m) boreholes concur with independent paleohydrologic and paleoecological records from the region. Simulations constrain a pluvial period associated with infiltration of 2--5 mm yr-1 at 14--13 ka and denote a shift linked to the establishment of desert vegetation at 13--9.5 ka. Retrodicted moisture flux histories inferred from modeling results differ significantly from those determined using the conventional chloride mass balance approach that assumes only downward advection. The modeling approach developed here represents a significant advance in the use of deep vadose zone profile data from arid regions to recover detailed paleohydrologic and current hydrologic information.