The aim of this study was to characterize mercury (Hg) contamination in the coastal waters of the Southern Baltic Sea, and to investigate transformations of Hg in the initial links of the marine food chain. Concentrations of Hg in water, particulate roarer, plankton and macrophytes at various stations in the coastal zone (a bay with restricted water exchange, near an industrial city, river mouths, and the open sea) were measured in 2006-2008. Hg concentrations observed in the Southern Baltic varied greatly, showing the highest average values in all environmental compartments near the river mouths. In shallow, sheltered parts of the gulf, where water exchange is restricted, Hg concentrations in the water and in macrophytes were elevated relative to those in the coastal zone of the deeper part of the bay and in the open Baltic. Distance to the river mouth, terrestrial runoff, and quantity and quality of organic matter were more important than seasonal variations in controlling Hg and HgSPM concentrations in water samples. Mercury concentrations in the surface microlayer at the air/sea interface were over 10 times higher than those in the bulk surface water. Concentrations of Hg in macrophytes in the winter were significantly higher than those in the warm seasons (spring, summer, autumn). This was probably the combined effect of higher availability of Hg in porewaters and leaf growth inhibition.