The data for the paleoenvironmental study was obtained on the basis of complex analysis of short sediment cores retrieved in the Arcona, Bornholm, and Gdansk Basins of the Baltic Sea. The cores were collected using a short gravity sediment corer (Niemistö type). The upper layers (0-5 cm) of sediment cores were stained with the 80% ethanol solution of rose Bengal following the protocol (Schönfeld et al., 2012, doi:10.1016/j.marmicro.2012.06.001) and were used only for the microfossil analysis. The rests of the cores (below the 5 cm) were continuously sampled with the 1 cm step and were used for the loss on ignition (LOI), microfossil, X-ray fluorescence (XRF), and grain-size analyzes.The XRF analysis was performed with the Olympus Vanta C Series XRF Analyzer on the wet sediments. The concentrations of chemical elements were recalculated for the dry weight of sediment samples following the method of Boyle et al. (2015, doi:doi:10.1007/978-94-017-9849-5_14). The ratios of elements were calculated using the concentrations for the wet weight.