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The cause of the middle Miocene Badenian salinity crisis in the Central Paratethys is addressed by examining the palaeotemperature evolution of Badenian waters before and after the deposition of evaporites. Selected foraminifer taxa (Globigerinoides spp., Globigerina bulloides, and Uvigerina) characterizing, respectively, the near-surface, intermediate, and bottom layers of the water column, were studied in two boreholes of SW Poland. The δ18O and δ13C values for these taxa show distinct differences which can be explained by the temperature difference between surface and bottom waters during deposition. These values also show temporal changes corresponding to the water temperature evolution in the Badenian basin. Different and quickly changing environmental conditions have been inferred from changes in foraminifer assemblages. They explain why biostratigraphic subdivisions based on well-recognized assemblages are the most accurate approach for determining the biostratigraphy of middle Miocene deposits in the Central Paratethys. The results of isotopic studies indicate that evaporites occur in a part of the Badenian section that was characterized by the lowest temperatures in the studied sections.