Carbonate deposits from Zrin in the Mt. Zrinska Gora were deposited in the SW part of the Central Paratethys Sea during the Middle Badenian (Middle Miocene). The studied section contains a rich fossil community of non-geniculate coralline red algae (Subfamily Melobesioideae), bryozoans, benthic and planktonic foraminifera, echinoderms, ostracods, molluscs, and calcareous nannoplankton. Based on lithological variations and changes in the biogenic components, four facies associations (FA) are distinguished. Their distribution points to skeletal production and sedimentation on a middle to proximal outer carbonate ramp. The main lithological feature of the section is an alternation of two lithofacies: fully lithified grainstone–rudstone and packstone, and semi-lithified rudstone–floatstone with a carbonate sandy matrix. Depositional environments on the ramp were periodically influenced by minor high-frequency sea-level changes and/or changes of hydrodynamic conditions, which are suggested as the driving mechanisms causing the alternation of the two lithofacies. Vertically in the succession, the two lithofacies alternate to give three thinning- and fining-upward units. The lower part of each unit is formed of a rhodolith and coralline algal FA, which passes upwards into a bryozoan-coralline algal FA and/or FA of bioclastic packstone-grainstone. Based on the vertical upward change in FAs, each unit can be interpreted as a deepening-upward sequence. Patterns in the relative abundance of bryozoan colony growth form (vinculariiform, cellariiform, adeoniform, membraniporiform, celleporiform, and reteporiform), size and abundance of rhodoliths and coralline branches, and benthic foraminifera are interpreted by comparison with data from modern and fossil environments. Based on these data, a water depth range for each FA is interpreted, providing evidence of low-frequency relative sea-level changes. It is hypothesized that relative sea-level fluctuated in the water depth range from 30 to 80 m, and in the uppermost part of the section, rich in planktonic foraminifera and calcareous nannoplankton, possibly deeper. Causes of the low-frequency relative sea-level fluctuations and the general deepening trend observed within the succession cannot be interpreted based on one section; however, they may be related to the subsidence of the depositional basin. The benthic biotic communities are a vertical alternation of rhodalgal and bryorhodalgal associations, and this is attributed to relative sea-level fluctuations. These biotic associations gave rise to warm-temperate carbonates of the Middle Badenian N9 planktonic Zone (Orbulina suturalis, O. universa) and NN4–NN5 nannoplankton Zones (Sphenolithus heteromorphus).