Concentrations of Al, V, Mn, Fe, Co, Cu, Ni, Zn, Sr, Mo, Cd, Sb, Pb, Th, U, REE, Na, K, Mg, Ca, Si, P, S, Ti, Cr and Ba were determined in the <63 microm fraction of bottom sediments of the Szczecin Lagoon and the Gdansk Basin, Baltic Sea, by ICP-MS, ICP-AES and XRF methods. Sediment samples from the Szczecin Lagoon displayed somewhat higher concentrations of P, Mn, Cr, Cu and possibly Cd, Pb and Zn in those collected in October 1997 after the exceptional flooding of the Oder River than in those collected in December 2000. The data suggest that the flood resulted in the enhanced transport of redox-sensitive and anthropogenic elements in the Oder River and their subsequent redeposition mainly in the western part of Szczecin Lagoon. The sediments of the Szczecin Lagoon also appear to be the most polluted with heavy metals within the Polish Exclusive Economic Zone (EEZ) of the Baltic Sea. Cd, Pb, Zn and Cu are anthropogenically enriched in top layers of sediment cores from the Gdansk Basin, but the decrease of these elements with depth in the core is not systematic. The rare earth element (REE) patterns in sediments from both these areas do not appear to have been greatly modified during transport from their source into the southern Baltic. Factor analysis (FA) of the compositional data shows that sediments from Szczecin Lagoon can be divided into three main groups depending on their composition. It is concluded that clay minerals and organic matter build aggregates and flocs, which effectively concentrate trace metals and sink down to form a 'fluffy layer'.