The late Badenian and Sarmatian (Serravallian) evolution of depositional environments in the Danube Basin (Želiezovce Depression) has never been fully explored. Here, we clarify the paleoenvironmental changes which took place in this area during the late Badenian and Sarmatian on the basis of sedimentological, petrographic, biostratigraphic and paleobotanical analyses performed at multiple sections. The combination of these methods with sequence stratigraphy allowed us to divide the sedimentary record into three main intervals: 1) the transgressive late Badenian rocky shore deposits (transgressive and/or highstand system tract), followed by a gap in the stratigraphic record (that can approximately coincide with the latest Badenian falling stage system tract). 2) Earliest Sarmatian terrestrial deposits connected with the beginning of the Sarmatian transgression (synchronous with the lowstand system tract). 3) The early Sarmatian deltaic environment influenced by tidal processes associated with the highstand system tract. The fossil leaf association indicates a climatic turnover from subtropical to temperate conditions between the earliest (lowstand system tract) and the early Sarmatian (highstand system tract). Sediments of the late Sarmatian (falling stage system tract) were not deposited or were later eroded. However, they may be present in the neighbouring depressions, which tectonically opened during the late Sarmatian. The Badenian–Sarmatian boundary in the Želiezovce Depression is developed in transgressive shallow marine to terrestrial volcano-sediments as is typical for this boundary in most other Paratethys depocentres.