Paleoclimate records across the Intermountain West region of North America show significant regional variation in timing and magnitude of wet conditions that accompanied the last glacial-interglacial transition. To understand the climate controls on paleohydrologic change, well-dated records are needed across the region. The Plains of San Agustin (New Mexico, USA) is a closed-basin watershed of the American Southwest influenced by both winter westerly and summer North American Monsoon precipitation. The flat valley floors of the Plains contain lake and groundwater discharge deposits that record multiple periods of past wet climate. We present a record of hydroclimate for the past 26,000 years based on radiocarbon, U–Th series, and OSL dating of these deposits and stratigraphic correlation across the three sub-basins of the lake system. We find that two major lake oscillations occurred, coincident with the global Last Glacial Maximum (∼23–18 ka) and with Heinrich Stadial 1 (∼17–14 ka). The LGM lake cycle created a deep lake in the lowermost sub-basin, fed by marsh/lake overflow in the upper sub-basins. The Heinrich Stadial 1 wet interval attained the highest recorded lake level between ∼17.0 and 15.3 ka, merging the lower two sub-basins into one lake. Both lake cycles agree well in timing and magnitude with other lake-based records from the southwestern U.S., supporting previous interpretations that a south-shifted cool season storm track brought a dipole-like pattern of enhanced moisture to the southwest at the expense of drier conditions in the northwest during the LGM and deglaciation. A transition from lake to groundwater discharge conditions followed during the Bølling-Allerød (14.7–12.9 ka) across the study area. Wet meadows prevailed in the lower sub-basin during the Younger Dryas (12.9–11.7 ka), with marsh and open lake conditions in the upper and middle sub-basins, respectively. During the early Holocene, discrete wet intervals are recorded by ages for wet meadow deposits in all sub-basins with centennial-millennial frequency at 9.9, 8.8, 8.2 ka. These events agree well with other Intermountain West records showing wetter-than-present conditions prior to 8 ka. Two additional wet periods, centered at 6.8 and 5.4 ka, occurred during the driest known interval of the middle Holocene, and likely were partly supported in the Plains of San Agustin by summer moisture associated with the peak strength of the North American Monsoon. Our record highlights that both winter and summer moisture support water resources in New Mexico watersheds.