The distribution of Ca, Mg, K, Na, Si, P, S, Al, V, Mn, Fe, Co, Cu, Ni, Zn, Sr, Mo, Cd, Sb, As, Bi, Pb, Tl, Th, U, Ti, Cr, Ba and REE (determined by ICP-MS, ICP-AES, XRF and AAS methods) in bottom sediments of the southern Baltic as well as the Vistula and Szczecin Lagoons were discussed. Based on enrichment factors (EFs) the accumulation of the chemical elements in surficial sediment with respect to their concentration in Earth’s crust showed that Cd, Pb, Cu, Zn and Ag in coastal regions seem to be generally anthropogenic in origin. It is shown that the sediments of the Szczecin Lagoon are the most polluted by heavy metals, especially Cd, Zn and Pb, and that the degree of heavy-metal pollution decreases substantially on passing from the Szczecin Lagoon to the Pomeranian Bay and then on passing to the Bornholm Deep and Słupsk Furrow. Fluffy material from the Oder estuary appears to be the main source of heavy metals in the muddy sediments of the Bornholm Deep. The distribution of the rare earth elements (REE) in sediments of the Polish EEZ is more complex than previously thought and may be controlled by the input of Fe-organic colloids from rivers and the presence of detrital material in the sediments. The rare earth element (REE) patterns in sediments from the study region do not appear to have been greatly modified during transport from their source into the southern Baltic. In each of the study areas, there is a slight enrichment in the LREE relative to the HREE in the sediments compared to the NASC. The lack of significant anomalies for the redox-sensitive elements such as Ce and Eu implies that redox processes have marginal significance in modifying the distribution of the REE in the sediments studied. Chemometric techniques (FA, EMA) appeared to be useful for interpreting the spatial differences of chemical element concentrations in the study area.