Regional lake sediment records, including late Pleistocene Lake Estancia, New Mexico, show that the southwestern USA was wetter than present over the last glacial maximum and drier during the Holocene. Chronology of speleothems that mark groundwater levels in Cavenee Caverns near Lake Estancia, indicates water-level lowering through the cave during the early to middle Holocene (8500 yr BP) consistent with the timing of desiccation of Lake Estancia and deflation of the basin floor. The speleothem record also shows the same wetter to drier climatic shift during the penultimate glacial and interglacial transition at 134 kyr BP (subaqueous crusts formed when cave submerged) to 121 kyr BP (cave rafts formed during water table drop). Our data support wet glacials and dry interglacials as being a general feature of Pleistocene climate in the southwestern USA. The timing suggests that the process is orbitally controlled.