Humans have exerted large‐scale changes on the terrestrial biosphere, primarily through agriculture; however, the impacts of such changes on the hydrologic cycle are poorly understood. The purpose of this study was to test the hypothesis that the conversion of natural rangeland ecosystems to agricultural ecosystems impacts the subsurface portion of the hydrologic cycle by changing groundwater recharge and flushing salts to underlying aquifers. The hypothesis was examined through point and areal studies investigating the effects of land use/land cover (LU/LC) changes on groundwater recharge and solute transport in the Amargosa Desert (AD) in Nevada and in the High Plains (HP) in Texas, US. Studies use the fact that matric (pore‐water‐pressure) potential and environmental‐tracer profiles in thick unsaturated zones archive past changes in recharging fluxes. Results show that recharge is related to LU/LC as follows: discharge through evapotranspiration (i.e., no recharge; upward fluxes <0.1 mm yr⁻¹) in natural rangeland ecosystems (low matric potentials; high chloride and nitrate concentrations); moderate‐to‐high recharge in irrigated agricultural ecosystems (high matric potentials; low‐to‐moderate chloride and nitrate concentrations) (AD recharge: ∼130–640 mm yr⁻¹); and moderate recharge in nonirrigated (dryland) agricultural ecosystems (high matric potentials; low chloride and nitrate concentrations, and increasing groundwater levels) (HP recharge: ∼9–32 mm yr⁻¹). Replacement of rangeland with agriculture changed flow directions from upward (discharge) to downward (recharge). Recent replacement of rangeland with irrigated ecosystems was documented through downward displacement of chloride and nitrate fronts. Thick unsaturated zones contain a reservoir of salts that are readily mobilized under increased recharge related to LU/LC changes, potentially degrading groundwater quality. Sustainable land use requires quantitative knowledge of the linkages between ecosystem change, recharge, and groundwater quality.