During the Middle Miocene, the northern Croatian Medvednica Mt. was an island within the Pannonian Basin System, situated on the SW margin of the Central Paratethys Sea. Miocene sedimentary rocks (the Late Badenian Bulimina–Bolivina Zone and Ammonia beccarii ecozone), from the SW slopes of Medvednica Mt. clearly reflect a transgressive-regressive cycle with emersion during the Badenian/Sarmatian boundary. After the initial phase of transgression, the pioneer Elphidium–Asterigerinata–Ammonia benthic foraminiferal assemblage is present in bioclastic limestones, such as those at the Borovnjak locality. This marginal marine assemblage from a highly energetic, normally saline environment is characterized by poor preservation of foraminiferal tests, low diversity and strong domination. Advanced transgression is followed by establishment of the Elphidium–Asterigerinata assemblage, which is found in biocalcsiltites from the laterally deeper and more sheltered environment at Gornje Vrapče. This diverse assemblage is typical for inner/middle shelf environment with sufficient oxygen content. A general shallowing upward trend can be recognized at both localities, followed by visible interchange of different sedimentological and biotic features. Successive and oscillatory regression in the marginal marine environment was followed by salinity fluctuations and final brackish conditions with Ammonia–Elphidium assemblage. The laterally deeper environment reacted to regressive trends on finer scale with almost regular changes of benthic foraminiferal assemblages in the laminae (Heterolepa–Bolivina assemblage/Bolivina–Cassidulina assemblage/Elphidium–Asterigerinata assemblage). It might reflect sea-level oscillations with periodically increased siliciclastic and nutrient input from land or influence of seasonality on benthic assemblages, which occurred in the advanced phase of the regression near the Badenian/Sarmatian boundary.

Several short sections from Istria (northern Adriatic Sea) were studied to determine the impact of short-term climate variability on pelagic assemblages from the northern mid-latitudes during a critical period of evolution in the mid-Eocene greenhouse climate. Two important warming events were documented in this interval—the Late Lutetian Thermal Maximum (LLTM) and the Middle Eocene Climate Optimum (MECO). The warmings were characterised by the highest calcareous nannofossil species richness and an eutrophic environment. Our records of calcareous nannofossil index species allowed the standard Zones NP16–NP17 (Mediterranean Subzones MNP16A–MNP17A) to be applied. Common occurrences of the planktonic foraminiferal genera Subbotina and Turborotalia indicate eutrophic-to- mesotrophic conditions between the mixed layer and the shallow thermocline waters in the basin. Episodes of eutrophication from periodic upwelling under an accelerated warming event (in MNP16A) are indicated by the subdominant Coccolithus pelagicus. According to the isotope data, the maximum negative δ¹³C occurred at 45° N in Alano, with a prominent second peak at 39.66 Ma, which is in agreement with our possible second peak, suggesting higher insolation in the North during the warming event. The warm water Reticulofenestra producta dominated in Subzone MNP17A, suggesting a relatively shallow mesotrophic environment with decreased species richness characteristic of the post-MECO phase.

Lake Pannon was a huge central European long-lived endorheic lake settled in the Pannonian Basin System and surrounded by the Alps, Carpathians and Dinarides mountain ranges during the late Neogene. The rise of brackish Lake Pannon enabled establishment of specific environmental conditions which triggered a spectacular adaptive radiation of a great number of autochthonous mollusk and ostracod species. The latter species represent excellent regional paleoecological proxies and biostratigraphic markers due to their good preservation-potential and taxonomic richness. Although dominantly endemic to Lake Pannon, some of its taxa managed to migrate into the Eastern Paratethys and have also been reported from the Mediterranean. These species are restricted to the Lago Mare interval, representing the ultimate stage of the Messinian Salinity Crisis, a significant environmental perturbation characterized by massive evaporite deposition. The Lago Mare interval was apparently forced by a drainage of the Eastern Paratethys brackish water into the Mediterranean. The Bozara section is situated in the southern Pannonian Basin at the southern slopes of Mt. Papuk and carries a well-preserved benthic fauna representative of Lake Pannon. The 27 -m-thick section consists of alternating pelitic sediments and sand packages divided into 4 facies: silty marl and calcareous silt (F1), sand (F2), intercalation of sand and sandy silt (F3) and clayey silt (F4). According to the regional stratigraphic division it belongs to the Nova Gradiška Formation. We detected therein 25 ostracod and 17 mollusk taxa allowing an integrated evaluation of the depositional setting, biostratigraphic position and paleogeographic distribution pattern. The paleoecology of Bozara fauna documents a general shallowing upward trend along the section from calm deep-water sublittoral to deltaic high-energy littoral conditions. Based on presence of several biostratigraphic markers, such as the bivalve Rhombocongeria rhomboidea and the ostracod Caspiocypris pontica the stratigraphic position of the Bozara section is constrained to the Portaferrian substage (8.0-4.5 Ma).From 16 ostracod taxa determined at species level, 10 can be found in the Eastern Paratethys deposits, whereas only 3 are shared with the Mediterranean Lago Mare. In contrast, among 12 corresponding mollusk taxa, only 4 are shared with the Eastern Paratethys, while being completely absent from the Lago Mare interval. Such a paleobiogeographic pattern suggests that the Lake Pannon outflow and faunal migration into the Eastern Paratethys, ceased distinctly before the Lago Mare phase and the corresponding migration of Paratethys biota into the Mediterranean basin.