The hydrological regime of Baltic Sea bottom water is strongly influenced by irregular inflows of high-saline, oxygen-rich North Sea water through the narrow Danish Straits. The aim of this work was to study the interrelation between the distribution of benthic foraminifera in the South-Eastern Baltic Sea and hydrology of the bottom water. Benthic foraminiferal distribution was analyzed in the 26 surface sediment samples, collected in the Baltic Sea during spring and winter 2016. Micropaleontological data were compared to the changes in dissolved oxygen content and the salinity of the bottom water. The species diversity of the benthic foraminifera in the studied region was very low. Agglutinated species, mostly single-chambered, were the most abundant in the assemblages. The distribution of the foraminiferal concentrations in the sediments had similar spatial patterns in both seasons. High shell concentrations as well as increase in faunal diversity were identified at the deeper parts of the study region where saline oxygen-enriched North Sea water is accumulated. Maximum foraminiferal concentration was found in the sediments of the Gdansk-Gotland Sill where halocline reaches the bottom which favors nutrient accumulation. However, the sharp dominance of very small individuals of Pseudothurammina shows that only some species can survive in the variable conditions associated with the halocline.