During the middle Miocene (15–12 Ma), the paleoenvironmental conditions in the Paratethys Sea of Central Europe changed from normal marine to hypersaline and from normal marine to brackish-marine conditions. These paleoenvironmental changes do not consistently correlate to global sea-level curves, indicating other driving mechanisms. Water circulation in the Paratethys strongly depended on two shallow and narrow gateways that were located in tectonically active regions. Here we combine the conservation of water and salt mass with strait-exchange theory to quantitatively link freshwater surface forcing and gateway dimensions to the observed environments. Our model confirms that the proposed sea-level drop of 50–70 m at 13.8 Ma could have restricted the western gateway to the Mediterranean to such an extent that halite formed in the Central Paratethys. Subsequently, the progressive opening of the eastern gateway to the Black Sea led to a decrease in lake level, exposure of the shallow margins, and a reduced surface area in the Eastern Paratethys. This entailed a reduction in water loss to the atmosphere, which, combined with constant river influx, resulted in a positive freshwater budget for the Paratethys proper, and reduced the salinity in the Central Paratethys. This provides a novel physics-based explanation for the change from evaporitic to marine to brackish-marine water conditions in a marginal basin.