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Identifying Hg sources to aquatic ecosystems and processes controlling the levels of monomethylmercury (MMHg) is critical for developing efficient policies of Hg emissions reduction. Here we measured Hg concentrations and stable isotopes in sediment, seston, and fishes from the various basins of the Baltic Sea, a large brackish ecosystem presenting extensive gradients in salinity, redox conditions, dissolved organic matter (DOM) composition, and biological activities. We found that Hg mass dependent fractionation (Hg-MDF) values in sediments mostly reflect a mixing between light terrestrial Hg and heavier industrial sources, whereas odd Hg isotope mass independent fractionation (odd Hg-MIF) reveals atmospheric inputs. Seston presents intermediate Hg-MDF and odd Hg-MIF values falling between sediments and fish, but in northern basins, high even Hg-MIF values suggest the preferential accumulation of wet-deposited Hg. Odd Hg-MIF values in fish indicate an overall low extent of MMHg photodegradation due to limited sunlight exposure and penetration but also reveal large spatial differences. The photodegradation extent is lowest in the central basin with recurrent algal blooms due to their shading effect and is highest in the northern, least saline basin with high concentrations of terrestrial DOM. As increased loads of terrestrial DOM are expected in many coastal areas due to global changes, its impact on MMHg photodegradation needs to be better understood and accounted for when predicting future MMHg concentrations in aquatic ecosystems.