Overlying vegetation plays a key role in the hydrodynamics of desert vadose zones. To investigate the roles of vegetation and climate on vadose zone dynamics, eleven 5–10 m boreholes were drilled under ponderosa pine, juniper, grassland, and creosote vegetation communities along a transect ranging in elevation from 1470 to 2380 m in central New Mexico and were analyzed for soil water content and potential and environmental tracers. The results indicate that there has been no downward liquid movement past the root zone under the creosote sites over the past ∼20 kyr. There have been periodic, downward fluxes past the root zone under the grass and juniper sites (<0.4 mm yr−1) as well as preferential flow, but under ponderosa pine, downward fluxes are appreciable (2.3 mm yr−1). Fluxes were similar within vegetation communities, even at sites separated by considerable distance and elevation (and thus climate), but differed markedly over short distances across ecotones, demonstrating that vegetation ecology strongly modulates the influence of climate and that characteristic vadose zone hydrological regimes are associated with the various vegetation communities.