Lake-level variations preserved as beach ridges in the Laguna El Fresnal and Laguna Santa María subbasins, northern Mexico, record millennially spaced episodes of increased precipitation during the Holocene epoch. We find that the early, middle, and late Holocene were punctuated by periods wet enough to establish large pluvial lakes in currently dry basins in the Chihuahuan Desert; the largest dated pluvial lake covered ∼5650 km2 during the early Holocene. Constructional beach ridges in these subbasins are 221 ± 33 14C yr B.P. (Little Ice Age equivalent), 3815 ± 52 to 4251 ± 59 14C yr B.P. (early Neoglacial), 6110 ± 80 to 6721 ± 68 14C yr B.P. (mid-Holocene), and 8269 ± 64 to 8456 ± 97 14C yr B.P. (early Holocene), dates that correlate with other millennially spaced wet or cold events in the Northern Hemisphere. We attribute these wet episodes to increased precipitation, cooler temperatures, and reduced evaporation following southward shifts in winter storm tracks, which are related to long-term El Niño–Southern Oscillation variability during the Holocene.