Palaeoenvironmental changes in the upper Middle Miocene Central Paratethys were reconstructed by using qualitative and quantitative palaeontological analyses of foraminifera and ostracods, coupled with trace elemental (Mg/Ca) and stable isotope (δ18O and δ13C) analyses of their carbonate skeletons and of gastropod shells. Mean annual air temperatures were estimated using the oxygen isotope composition of contemporaneous rodent teeth. The studied aquatic fossils come from two boreholes in the Zsámbék Basin (northern central Hungary), while the terrestrial ones are from localities in NE Hungary and E Romania. In the studied Sarmatian successions, three zones could be distinguished, based on palaeontological and geochemical results. At the Badenian/Sarmatian boundary, faunal diversity decreased markedly. In the lower zone a transgressive event culminated in a seawater incursion into the semi-open basin system of the Central Paratethys. Stable bottom-water temperature (~15 °C) and variable salinities (20–32 ‰) are estimated for the Early Sarmatian Sea. The faunal changes (notably a strong reduction in biodiversity) occurring at the boundary between the lower and the middle zone can be explained by a sea-level highstand with dysoxic conditions. A relative sea-level fall is documented at the end of this middle zone. After a short regressive event, a marine connection between the Paratethys and the Mediterranean was established at the beginning of the upper zone. This is indicated by an increased microfaunal diversity and the re-appearance of marine Badenian ostracods and foraminifera, which are completely absent from the older Sarmatian series. During the upper zone, the temperatures and salinities are estimated to have fluctuated from 15 °C to 21 °C and from 15 ‰ to 43 ‰, respectively.