Since the discovery of calcareous nannofossils, dinoflagellate cysts and planktonic foraminifers in deposits from the Dacic Basin, intensive research has been performed in order to evidence which gateway this microplankton used to connect Paratethys and the Mediterranean prior and after the Messinian Salinity Crisis (MSC). Such a gateway is also to be regarded at the origin of successive influxes of Paratethyan organisms (molluscs, ostracods, dinoflagellates) into the Mediterranean Basin (“Lago Mare” events). Observing that the İstanbul area, usually proposed for this purpose, was inefficient, we examine the succession of marine well-dated pre-MSC and post-MSC deltaic deposits through the Balkans, from northern Greece to southern Romania, that constitutes a reliable candidate for such a marine corridor, the origin of which was caused by the regional tectonic extension. The reconstructed palaeogeography for high sea level episodes that encompassed the MSC clarifies the context of the so-called North Aegean Lake. This marine gateway probably evolved as a powerful river during the peak of the MSC, contributing to the deposition of clastics in the hydrocarbon Prinos Field. A tectonically controlled subsidence to the north and south of the Skopje region caused the closure of such a gateway. •A marine gateway crossed the Balkans from 8 to 4Ma at high sea level episodes.•It was at the origin of organism exchanges between the Mediterranean and Paratethys.•During the Messinian Salinity Crisis, it was probably changed into a powerful river.