The Polish initially avoided involvement in the Thirty Years War, despite their hostility to Sweden. In 1648, the Cossack Hetman Bohdan Chmielnicki, led a major rebellion and sought Russian and Turkish help (the Cossacks were a people of mixed origin. but mainly Ruthenian and Pole). From 1655, in a period that became known as "the Deluge" (Potop), Poland  was invaded by Swedes, Turks and Muscovites. By 1657, the Swedes had been expelled, but at great cost. There was considerable loss of life and economic disruption.  In 1658, at Hadziacz, a temporary agreement was reached, but Russia (eyeing the Ukraine) instigated another Cossack rebellion in 1659. The Polish lost control of the Eastern Ukraine, and by the end of the century  Russian influence over Ukrainians and Cossacks was steadily increasing.

The ineffectual Michael Korybut Wisniowiecki suffered humiliating defeat at the hands of the Turks, and was forced in 1672 Treaty of Buczacz to cede Podolia to the Ottomans. John Sobieski defeated the Turks at Chocim (1673), but was initially unable to follow up his victory. The Ottomans invaded Austria and Hungary and laid siege to Vienna in 1683. Sobieski joined forces with the Hapsburgs, attacked the Turks and drove them back to the Balkans.

The Polish economy - especially the urban economy - suffered severely from war and depopulation. Poland had been known for religious toleration during the sixteenth century, but in the face of Protestant (Swedish), Orthodox (Muscovite) and Muslim (Turkish) onslaughts, Poles increasingly saw Catholicism as a part of their national identity.