This study provides a comprehensive examination of algal bioherm structures, including reefs and carpets that contain nannoplankton and foraminifera, originating from the upper Badenian (Middle Miocene) strata of the Vienna Basin in the Central Paratethys. These lithofacies primarily consist of calcareous red seaweeds from the Lithothamnion genus. Through an integrated approach that combines calcareous nannoplankton, foraminifera, sedimentology, and palynology, the study explores the Serravallian (upper Badenian) sediments from the Paratethys Sea shelf. The biostratigraphic age, consistent with the NN6 and CPN9 zones, is further corroborated by 87Sr/86Sr dating. Our research highlights the importance of taphonomic processes and paleoecological proxies in small-scale characterization and detecting short-term shifts within paleoenvironmental conditions. These unique bioherm structures contribute to recognizing a novel limestone formation within the Vienna Basin (The Sandberg Formation), which seems pervasive across the Central Paratethys region. The findings uphold the hypothesis of a profound connection between the Mediterranean and Central Paratethys via the Trans Tethyan Trench Corridor, bolstered by upwelling conditions observed in the eastern perimeter of the Vienna Basin. We confirm two main inhibitory mechanisms for carbonate growth in the upper Badenian epoch within the Central Paratethys area: the first is a substantial siliciclastic influx from the Alps and Carpathians, supported by the ongoing rifting of the Vienna and Danube basins; the second is the propagation of evaporites in the Transcarpathian and Transylvanian basins leading to precipitation, which disrupts carbonate growth. This investigation underlines the intertwined relationship between regional geodynamics and carbonate sedimentation processes during the Miocene era.