The sedimentary sequence of the Central-Carpathian Paleogene Basin provides proxy records of climatic changes related to cooling events at the Eocene/Oligocene boundary (TEE). In this basin, climatic deterioration is inferred from the demise of the carbonate platform and oligotrophic benthic biota in the SBZ19 and from the last species of warm-water planktonic foraminifers in the E14 Zone. Upper Eocene formations already indicate warm-temperate to cool-temperate productivity and nutrient-enriched conditions (Bryozoan Marls, Globigerina Marls). Rapid cooling during the earliest Oligocene (Oi-1 event) led to a temperature drop (~11 °C), humidity, fresh water influx and continental runoff, water mass stratification, bottom water anoxia, eutrofication, estuarine circulation and upwelling, carbonate depletion, sapropelitic and biosiliceous deposition, H₂S intoxication and mass faunal mortality, and also other characteristics of Black Sea-type basins. Tectonoeustatic events with the interference of TA 4.4 sea-level fall and the Pyrenean phase caused basin isolation at the beginning of the Paratethys. The Early Oligocene stage of Paratethyan isolation is indicated by a stagnant regime, low tide influence, endemic fauna development, widespread anoxia and precipitation of manganese deposits. The episodic rise in the sea-level, less humid conditions and renewed circulation is marked by calcareous productivity, nannoplankton blooms and the appearance of planktic pteropods and re-oxygenation. Paleogeographic differentiation of the Carpatho-Pannonian Paleogene basins resulted from plate-tectonic reorganization during the Alpine orogenesis.