The timing and mode of the marine flooding of the southern margin of the Pannonian basin in SE Europe is still a matter of debate. In central Serbia, integrated bio-magnetostratigraphic data and quantified high-resolution records are completely missing. Here, we provide paleoenvironmental and paleoecological constraints from the Slanci section located near Belgrade that has an excellent preservation of micro-fauna and flora, i.e., planktonic and benthic foraminifera and calcareous nannoplankton. We integrate their quantified records with sedimentological, natural gamma radioactivity and magnetic susceptibility logs and include the non-quantified records of mollusks, corals, and ostracods to reconstruct the regional depositional history. The section shows upper bathyal to outer shelf depositional settings and alternating nutrient bottom conditions. The shallowing upwards trend marked by increasing terrestrial input, attributes it to the early Highstand Systems Tract of the first marine third order sequence in this part of the Pannonian Basin. We infer that the marine flooding in central Serbia took place at an age of ∼ 14 Ma, slightly predating the Langhian/Serravallian boundary (13.82 Ma) and the Badenian Salinity Crisis (∼ 13.8–13.4 Ma) in the Central Paratethys. Our results support an eastwards directed, tectonically forced, flooding of the southern Pannonian Basin. This major paleoenvironmental turnover was forced by syn-rift tectonics in the Pannonian Basin system, which started in the late early Miocene in the Styrian Basin (SE Austria) and ended more than 3 Myr later in the late middle Miocene in the Morava depression (E Serbia).