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Organic contaminants constitute one of many stressors that deteriorate the ecological status of the Baltic Sea. When managing environmental problems in this marine environment, it may be necessary to consider the interactions between various stressors to ensure that averting one problem does not exacerbate another. A novel modeling tool, BALTSEM-POP, is presented here that simulates interactions between climate forcing, hydrodynamic conditions, and water exchange, biogeochemical cycling, and organic contaminant transport and fate in the Baltic Sea. We discuss opportunities to use the model to support different aspects of chemicals management. We exemplify these opportunities with a case study where two emission-reduction strategies for a chemical used in personal care products (decamethylcyclopentasiloxane) are evaluated, and where the confounding influence of future climate change and eutrophication on the impact of the emission-reduction strategies are assessed.