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Abstract A three‐dimensional quantitative stratigraphic forward model is employed to investigate the controls leading to the Messinian events in the lacustrine Pannonian Basin of Central Paratethys, and the link between the Messinian salinity crisis in the Mediterranean and the late Miocene‐Pliocene stratigraphy of the Pannonian Basin. Subsurface geological data show that a prominent unconformity surface formed during Messinian time in the Pannonian Basin associated with a sudden forced regression, abrupt basinward shift of facies and a subsequent, prolonged lowstand normal regression. The lowstand prograding series filled up the shallow basin fast, while, at the same time, the marginal areas of the basin were subject to tectonic inversion. The Dionisos program used in this research is built on a nonlinear water‐driven sediment diffusion process, and it employs multiple sediment classes, basin flexure and compaction. Four different scenarios were built in the experiments to test possible basin histories with different rates and timing of tectonic inversion. Each scenario was modelled in two versions: including and not including a lake‐level fall in the Messinian. The results confirm that the Pannonian Basin in the study area has undergone a tectonic inversion since the Messinian, although the exact rates of uplift at different locations remain uncertain. The unconformity and the observed stratigraphic architecture and facies pattern could be modelled adequately only in the versions that applied a Messinian lake‐level fall. Our research concludes that the Messinian unconformity in the Pannonian Basin was caused by an absolute lake‐level drop, likely linked to the desiccation of the Mediterranean, followed by subsidence and normal regression in the basin centre and concomitant tectonic inversion and uplift along the basin margins.