While climatic triggers for collapse and population migrations of ancestral Pueblo communities have been proposed, little is known about the overall climatic backdrop for the entire pre-Hispanic Pueblo period (ca. 1300 to 460 B2K). Here, we report data from stalagmite HC-1, from Hidden Cave, Guadalupe Mountains, New Mexico, covering the past 3400 years, showing an interval of increased frequency of droughts from 1260 to 370 yr B2K that is coeval with the entire pre-Hispanic Pueblo period. Our record suggests that this puebloan Late Holocene climatic interval was the most arid and highly variable climatic period of the last 3400 years. Climatic conditions favoring the introduction of cultivation existed prior to the Pueblo period during more pluvial-like conditions from at least 3400 to 1260 yr B2K. Hence, the change from the Desert Archaic/Basketmaker to Pueblo cultures was associated with a quick transition to increasing aridity into and through the Pueblo period associated with greater urbanization and the establishment of pueblo population centers.