Three high-resolution climatic reconstructions, based on diatom analyses from lake sediment cores from the Canadian prairies, show that shifts in drought conditions have prevailed on centennial to millennial time scales for at least the past six millennia. These shifts in mean aridity exhibit broad regional synchrony, with particularly pronounced shifts at all sites between ∼1700–2000 cal. yr bp and ∼3600–3900 cal. yr bp, as well as at ∼5400–5500 cal. yr bp for the two sites which extend back to at least 6000 cal. yr bp. The two Saskatchewan lakes exhibited significant coherence in both the timing and direction of these shifts, whereas inferred changes at the westernmost site in Alberta were significantly correlated to the Saskatchewan sites, but opposite in sign, and exhibited more high-frequency variation on the scale of centuries. The mechanisms behind these abrupt shifts in aridity are poorly understood, but may be linked to changes in oceanic–atmospheric interactions that influence the mean position of the jetstream and the associated storm tracks. Natural shifts in mean climatic conditions may accelerate with increasing carbon dioxide levels intensifying the likelihood of extreme droughts in North American prairies.