During the so-called Messinian Salinity Crisis (MSC: 5.97-5.33 Myr ago), reduced exchange with the Atlantic Ocean caused the Mediterranean to develop into a “saline giant” wherein ∼1 million km3 of evaporites (gypsum and halite) were deposited. Despite decades of research it is still poorly understood exactly how and where in the water column these evaporites formed. Gypsum formation commonly requires enhanced dry conditions (evaporation exceeding precipitation), but recent studies also suggested major freshwater inputs into the Mediterranean during MSC-gypsum formation. Here we use strontium isotope ratios of ostracods to show that low-saline water from the Paratethys Seas actually contributed to the precipitation of Mediterranean evaporites. This apparent paradox urges for an alternative mechanism underlying gypsum precipitation. We propose that Paratethys inflow would enhance stratification in the Mediterranean and result in a low-salinity surface-water layer with high Ca/Cl and SO4/Cl ratios. We show that evaporation of this surface water can become saturated in gypsum at a salinity of ∼40, in line with salinities reported from fluid inclusions in MSC evaporites.