The final stage of the Messinian salinity crisis (MSC) was characterized by brackish-water “Lago-mare” conditions in the intermediate and marginal basins of the Mediterranean Sea. The presence of Paratethyan (former Black Sea) fauna in these deposits has fueled long-lasting controversies over the connectivity between the Mediterranean and Paratethys and contemporary sea-level drops in both basins. Here, we use the results of sub-precessional climate simulations to calculate the freshwater budget of the Mediterranean and Paratethys in the Messinian. We show that, during the MSC, the freshwater budget of Paratethys was positive, while the Mediterranean was negative. Using these numerical constraints, we propose a Mediterranean outflow pump as an alternative scenario for the two most dramatic hydrological changes in the MSC: (1) the Halite–Lago-mare transition and (2) the Pliocene reestablishment of marine conditions. Following the maximum MSC lowstand during halite formation, progressive Mediterranean sea-level rise resulting from African river runoff and overspill from both the Atlantic and Paratethys eventually reached the level of the Paratethys sill. A density contrast at this gateway caused dense Mediterranean waters to flow into the Paratethys, driving a compensatory return flow. This “pump” mechanism significantly enhanced Paratethyan inflow to the Mediterranean, creating suitable conditions for the Lago-mare fauna to migrate and thrive. When the Mediterranean sea level finally reached the height of the Gibraltar sill, Mediterranean outflow restarted there and enhanced exchange with the Atlantic Ocean. During this reorganization of the circulation, brackish and hypersaline waters were pumped out of the Mediterranean, and open-marine conditions were reestablished without major flooding of the basin at the Miocene-Pliocene boundary.