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.