During the Badenian (Langhian–early Serravallian), a high diversity marine biocenosis inhabited the warm, normal-salinity environments spanning the epicontinental sea of the Alpine-Carpathian-Dinarides region known as Central Paratethys. The 95 m thick sedimentary succession of the Striježevica core, located in the southwestern part of the Pannonian Basin (North Croatian Basin), provides a unique insight into the palaeoenvironmental evolution from this part of the Paratethys, including changes in water depth, salinity, oxygen, and nutrient levels. An integrated analysis, including calcareous nannoplankton, dinoflagellate cysts, benthic and planktonic foraminifera, ostracods, and diversity proxies, revealed three phases of palaeoenvironmental evolution. The stratigraphic position of the studied succession in the NN4/5 Zone is indicated by the nannoplankton assemblage with Helicosphaera waltrans, along with the presence of the planktonic foraminifera Orbulina suturalis, and the dinoflagellate cyst Unipontidinium aquaeductus, correlated to the Middle Miocene Badenian stage. Micropalaeontological proxies indicated shelf to upper slope environments under the influence of shallow-water conditions. At the base of the Striježevica core, the composition of small benthic foraminiferal assemblages and their diversity indices indicated a eutrophic-mesotrophic environment with constant nutrient input. A “transitional environment” in the middle part of the Striježevica core was characterized by eutrophication related to the fertilization effect of enhanced volcanic activity in the surrounding area. A shallowing upward trend is suggested by an increase in oxygen content at the sea bed, a decrease in species richness, and a diversity drop in the benthic foraminiferal assemblage. The upper part of the section depicted a shallow, oligotrophic environment with seagrass meadows evidenced by the predominance of Biasterigerina planorbis and cibicidoids.