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The semi-isolated epicontinental Paratethys Sea in the Eurasian continental interior was highly sensitive to changes in basin connectivity and hydrological budget. The Caspian Sea, the easternmost basin experienced a five-fold increase in surface area during the Plio-Pleistocene climate transition, but a basic process-based understanding is severely hampered by a lack of high-resolution age constraints. Here, we present a magnetostratigraphic age model supported by Ar-40/Ar-39 dating of volcanic ash layers for the 1600 m thick Jeirankechmez section in Azerbaijan that comprises a sedimentary rock succession covering this so-called Akchagylian flooding. We establish the age of this major change in Caspian paleohydrology at around 2.7 Ma. The presence of cold water foraminifera, rising strontium isotope ratios and the possible arrival of the enigmatic Caspian seal in the basin hints at an Arctic marine source for the Akchagylian waters. The new age model indicates a direct link to the intensification of northern hemisphere glaciations at the end of the Pliocene and to concurrent hydrological shifts across Eurasia, such as the onset of cyclic Chinese Loess deposits. The transformation of the Paratethys region around 2.7 Ma from a series of small Pliocene endorheic lake basins to a large Early Pleistocene epicontinental water mass coincides with a more positive hydrological budget for the Eurasian continental interior. The drainage of additional high latitude, low salinity water to the Mediterranean, may have contributed towards variability in global paleoceanography, and could potentially provide a positive feedback towards Pleistocene climate cooling.