The most efficient way of mercury (Hg) transport to the Gulf of Gdańsk was river runoff. Therefore, hydrological conditions were the most important factors controlling the inflow of Hg to the sea. The second most important Hg source in the Gulf was atmospheric deposition, which transported seven times smaller load than rivers. The Hg wet deposition dominated in the warm season, while during the heating season the predominant was dry deposition of mercury. The Hg source, which should not be neglected during the creation of the mass balance of Hg in aquatic ecosystems, was the coastal erosion. In the Gulf of Gdańsk, it accounts for 6% of the Hg load reaching the sea. The main sink of Hg was bottom sediments. Other important processes that reduced the Hg load in the Gulf water were reemission of Hg to the atmosphere and export of this metal to the Baltic Proper. The mass balance of mercury in the Gulf of Gdańsk indicated that a larger load of this metal flowed into the Gulf than left it. Consequently, the Gulf of Gdańsk should be treated as a cleansing zone for the Baltic Proper.