Significant variations in interannual and decadal recharge rates are likely in alluvial basins of the semiarid southwestern United States on the basis of decadal variations in climate and precipitation and correlation of El Niño with high rates of winter precipitation and streamflow. A better understanding of the magnitude of recharge variations in semiarid and arid regions would reduce water budget uncertainty. Variability of ephemeral channel recharge with climate in southeastern Arizona was investigated through analysis of hydrologic monitoring near three ephemeral streams in southeastern Arizona during the middle to late 1990s and by relating the results to long‐term hydrologic and climatic trends. The analysis used precipitation, streamflow, water levels in wells, estimates of groundwater storage change from repeat gravity surveys, and two climatic indicators of El Niño–Southern Oscillation (ENSO), Southern Oscillation index, and Pacific Decadal Oscillation (PDO). Results indicate that variations in winter recharge are related to ENSO. El Niño conditions correspond with a greater probability of high rates of winter precipitation, streamflow, and recharge. La Niña conditions are almost exclusively associated with below‐average recharge. Rates of recharge along Rillito Creek near Tucson during 1977–1998, a period of frequent El Niño conditions and positive PDO values, were 3 times recharge rates during 1941–1957, a period dominated by La Niña conditions and low PDO values. Quantification of recharge variability with decadal climate cycles should improve estimates of rates of aquifer drainage and replenishment in the region. Similar methods are applicable to other regions where thick unsaturated zones can accept significant periodic recharge.