A critical hydrologic process in arid and semiarid regions is the interaction between ephemeral channels and groundwater aquifers. Generally, it has been found that ephemeral channels contribute to groundwater recharge when streamflow infiltrates into the sandy bottoms of channels. This process has traditionally been studied in channels that drain large areas (tens to hundreds of square kilometers). Since the water table in arid and semiarid regions is typically far from the surface, measured streamflow losses or percolation into the deep vadose zone is equated to groundwater recharge. In this study, we use a water balance approach to estimate deep percolation in a first‐order, instrumented watershed (4.7 ha) on a piedmont slope of the Jornada Experimental Range (JER) in the Chihuahuan Desert. Results indicate that runoff generated within the piedmont slope contributes significantly to deep percolation. During the short‐term 6‐yr study period, we estimated 385 mm of total percolation, 62 mm/yr, or a ratio of percolation to rainfall of 0.26. Based on the instrument network, we identified that percolation occurs inside channel areas when these receive overland sheetflow from hillslopes. We observed less streamflow leaving the watershed as compared to percolation during the study period, leading to an outlet streamflow to rainfall ratio of 0.02. Using long‐term data sets available from the JER, we estimate that over the last 100 yr, 48 mm/yr of percolation occurs at the study site, a ratio of percolation to rainfall of 0.19. We then scale this up to determine the contribution of similarly sized watersheds on the piedmont slopes of the JER. These observations highlight the importance of arid piedmont slopes for generating groundwater recharge, in particular during above‐average rainfall periods.