The presented multiproxy study sheds light on the intricate interplay between the biological and environmental factors which shaped the middle Miocene landscapes of the Paratethys region. Moreover, they highlight the diverse and dynamic nature of these ancient ecosystems. Here, we study the reasons for the predominance of nine miliolids in the Badenian and Sarmatian sediments, validate systematic and morphogroup approaches using geochemical methods, and finally reveal the bio stratigraphic potential of miliolid horizons during the Serravallian (late Badenian–Sarmatian). Trace elements (Mg/Ca, Ba/Ca, Mn/Ca) from the MZ 102 borehole and isotopic (δ¹⁸O, δ¹³C) analyses from ŠVM 1 and MZ 102 were measured. On the basis of the morphogroup division, an autecological comparison, and geochemical analyses, three main (MG 1, 2, 3) and two small (SG 1, 2) miliolid groups representing distinct microhabitats were characterised. Specific faunal communities (MG 1) document the environment of arborescent algae, such as Cutleria and Fucus in detritus-rich water substrates, which can lead to suboxia or anoxia in muddy-sandy sediment layers. Other associations (MG 2) correspond to shallow marine environments of hypo/hypersaline lagoons overgrown by short-stemmed arborescent algae, such as Padina, Halopteris, and Pseudolithophyllum, as well as notable salinity fluctuations. Host faunal communities (MG 3) inhabiting the inner shelf are characterized by motile epiphytic foraminifera on algae and Posidonia rhizomes. The observable changes to the paleoenvironment can be characterized by fluctuations in salinity and the occasional depletion of oxygen at the bottom.