Unsaturated-zone profiles in alluvial sediments of the Amargosa Desert reveal distinct patterns of groundwater recharge corresponding to tectono-geomorphic setting and land-use history. Profiles of water potential, water content, and solute concentrations beneath irrigated fields, undisturbed native vegetation, and the normally dry channel of the Amargosa River reflect strongly contrasting recharge regimes. Profiles beneath irrigated fields and channel sites indicate quasi-steady percolation at depths sufficient to be isolated from seasonal variations in meteorologic forcing. Displaced chloride and nitrate peaks beneath a recently converted agricultural field and a weakly incised channel site capture newly initiated deep percolation moving previously accumulated salts from the upper profile to greater depths. Channel migration caused by an extreme flood initiated deep percolation at the latter site. Downward-advected nitrate peaks beneath an irrigated field mark resumption of cultivation following eight years of dormancy. Where available, travel time estimates of recharging fluxes support chemical mass balance estimates. Recharging fluxes range from ~6 to 22% of applied water for irrigated fields and from ~12 to 15% of infiltration for channel sites. Profiles of environmental tracers beneath undisturbed native vegetation in interfluvial areas are consistent with negligible recharge and sustained profile drying throughout the Holocene. Four to five times more chloride is accumulated on older, uplifted alluvium than on younger, non-uplifted alluvium, showing that tectonic controls on recharge become important when timescales extend to many millennia. Groundwater recharge in desert basins is limited to features that occupy a small fraction of the land surface and are not necessarily stationary.