Eolian landforms in Estancia basin, central New Mexico, record two episodes of extreme drought and low groundwater levels during the middle Holocene (7000–5400 14C yr B.P.), followed by a rise in the water table through the late Holocene. Blowouts and associated lunettes formed when water levels fell below the desiccated floor of pluvial Lake Estancia, allowing widespread deflation. Elevation of the water table in the basin is regulated by a balance between evaporation from playas that occupy the blowouts and recharge of aquifers in the adjacent Manzano Mountains. Isotopic analyses of modern precipitation and groundwater reveal that recharge originates primarily as winter moisture, which is amplified during El Niños and diminished during La Niñas. Thus, changes in the elevation of a reconstructed Holocene water table may reflect systematic changes in El Niño–Southern Oscillation (ENSO) circulation.