Long-range atmospheric transport is a major pathway for delivering persistent organic pollutants to the oceans. Atmospheric deposition and volatilization of chlorinated pesticides and algae-produced bromoanisoles (BAs) were estimated for Bothnian Bay, northern Baltic Sea, based on air and water concentrations measured in 2011–2012. Pesticide fluxes were estimated using monthly air and water temperatures and assuming 4 months ice cover when no exchange occurs. Fluxes were predicted to increase by about 50 % under a 2069–2099 prediction scenario of higher temperatures and no ice. Total atmospheric loadings to Bothnian Bay and its catchment were derived from air–sea gas exchange and “bulk” (precipitation + dry particle) deposition, resulting in net gains of 53 and 46 kg year−1 for endosulfans and hexachlorocyclohexanes, respectively, and net loss of 10 kg year−1 for chlordanes. Volatilization of BAs releases bromine to the atmosphere and may limit their residence time in Bothnian Bay. This initial study provides baseline information for future investigations of climate change on biogeochemical cycles in the northern Baltic Sea and its catchment.