Paleoecological interpretations based on stable isotope study of benthic (Uvigerina semiornata) and planktonic (Globigerina bulloides, Globigerinoides trilobus) foraminiferal shells from the Paratethys Vienna Basin (southwestern Slovakia) are presented. The study was performed on sediments of the Devinska Nova Ves-clay pit deposited during the Middle and Late Badenian (Middle Miocene). Our δ^13C data show an enhanced nutrient input to the water column and the organic matter accumulation at the bottom of the Vienna Basin. The remineralization of accumulated organic matter on the sea floor resulted in the formation of oxygen-depleted zones, where no oxic indicators but the oxygen-deficiency tolerant species were found. Positive benthic δ ¹⁸O signal can be attributed to the influence of the global cooling recognized in the world-ocean during the Middle Miocene. At the same time, variations observed in the water column are interpreted as reflecting the local temperature and salinity changes resulting from the fluvial and rain inflow. The differences between surface and bottom water temperature reflect the stratification of the water column. Such stratification might be related to the isolation process of Central Paratethys in the Badenian. This study confirms that δ ¹³C and δ ¹⁸O are not always in isotopic equilibrium with the ambient water but are also influenced by vital effects (respiration, symbiont photosynthesis ...). The vital effects led to the incorporation of isotopically light metabolic CO₂ into Globigerina bulloides resulting in high similarity between δ ¹³C values of Uvigerina and Globigerina. It has been shown that the extremely high δ ¹³C and very low δ ¹⁸O of Globigerinoides trilobus clearly imply the influence of algal photosymbionts.