Summary The distribution of metals (Pb, Cu, Cd, Ni, Cr, Zn) in surface sediments and the potential pollution sources in the south-eastern part (SE) of the Baltic Sea (Lithuanian zone) were investigated in relation to the environmental characteristics (amount of fine-grained particles, TOC content in sediments, origin of sedimentary organic matter, salinity, water depth) in 2011–2014. The higher metal concentrations were measured in sediments of the Curonian Lagoon and in the open waters. An approach using various environmental indices (enrichment factor EF, geoaccumulation index Igeo and contamination factor CF) was used to quantitatively assess a contamination degree. The principal component analysis (PCA) was applied in order to further scrutinize pollution from metal sources. The values of the contamination indices showed no/very low sediment contamination with Ni and Cr, minor–moderate contamination with Cu, Zn and Pb and moderate–considerable pollution with Cd. The strong relationships among metals suggested their similar distribution pattern and a combination of natural and anthropogenic sources. The higher metal concentrations coincided with an increasing amount of fine-grained fraction and organic carbon. In the territorial waters, the distribution of elements was related to the water depth. In addition, the binding of metals with insoluble iron sulphides might explain their high concentrations at the most remote and deepest stations.