Paleowater depth observations suggest that a large sea level drop occurred in the Black Sea coeval with the Messinian salinity crisis in the Mediterranean Sea. This sea level drop would have induced vertical motions of the solid earth, which influenced strait dynamics with major implications for the hydrological regime of the region. Using three-dimensional flexure models we find that a sea level drop between 1730 and 2230 m is required to reproduce the observed paleowater depths. The models predict that uplift reduced the seaway connectivity between the Black Sea and the Mediterranean Sea (Aegean region) and between the Black Sea and the Caspian Sea (Stavropol Highlands). The Miocene Paratethys Sea consequently became fragmented, and the remaining subseas likely became more sensitive to climate change. This agrees with the discovery of erosional surfaces in the Caspian Sea and in the Pannonian Basin. To explain the synchronicity of the sea level lowering in the Black Sea and the Mediterranean, we speculate that a regional shift toward a drier climate occurred in response to the Messinian salinity crisis in the Mediterranean, which led to a fall in sea level within the Black Sea.