[1] In order to study the peculiarities of the thermohaline structure of the Baltic Sea, we conducted a research based on the Copernicus Marine Environment Monitoring service (https://marine.copernicus.eu/) products and field data collected in 2004–2006. The study of the reanalysed Baltic Sea hydrography allows us to show that it adequately reproduces elements of the thermohaline structure of the cold intermediate layer obtained from the measurement data. Here we examine the hypothesis about the formation of a lower part of the cold intermediate layer in early spring under the influence of a mechanism related to the estuary salinity/density gradient along the main axis of the Baltic Sea. Several numerical experiments were carried out to analyse the back trajectories of Lagrangian particles in the southeastern Baltic Sea. The analysis showed that in the Gdask Basin, at the depth corresponding to the lower part of the cold intermediate layer, there are particles coming from the Bornholm Basin and the Slupsk Channel. This confirms the contribution of the estuary salinity gradient to the formation of the lower part of the cold intermediate layer.