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) 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. For the LOI analysis the 1 g of dried sediments was burned at 550 °C for ~ 4 hours. The organic matter content was determined as resulting weight difference in % (Binczewska et al., 2018).