Aftermath of catastrophic flooding of a desiccated ocean basin

5.33 Million years ago, a mile-high marine cascade terminated the Messinian Salinity Crisis due to partial collapse of the Gibraltar arc/sill that isolated a largely desiccated Mediterranean from the Atlantic Ocean. Atlantic waters may have refilled the basin within 2 years. Prevailing hypotheses suggest that normal marine conditions were established across the Mediterranean immediately after the catastrophic flooding. Here we use new proxy data and modelling to show that normal conditions were likely for the western Mediterranean (wMed), but that flooding caused massive wMed salt transfer to the eastern Mediterranean (eMed), which became a hyper-salinity-stratified basin. Hyper-stratification inhibited deep-water ventilation, causing anomalously long-lasting organic-rich (sapropel) sediment deposition. Model:data agreement indicates that hyper-stratification breakdown required 26,000 years. Testing an alternative hypothesis—reconnection of a largely refilled Mediterranean—reveals hyper-stratification in both the wMed and eMed, which would have left sapropels in both basins, in disagreement with observations. Our findings offer novel insight into the processes involved in re-establishing normal marine conditions following abrupt refilling of a previously desiccated ocean basin.