New research at Tell al-Hiba, ancient Lagash, has revealed evidence of significant flooding and widespread destruction in the Mesopotamian city during the Early Dynastic period. We identify and date a prominent water-formed feature that cut through its primary temple district. Geoarchaeological trenching and geophysical prospection indicate that an upstream river avulsion led to rapid fluvial sedimentation within the settlement. Further analysis of archaeological data, including newly reported radiocarbon dates, suggests that this environmental crisis occurred during or shortly after Lagash was attacked by Lugalzagesi, king of Uruk. This study therefore also contributes to an improved chronometry of 3rd-millennium BC Mesopotamia.