Multi-model ensemble simulations for the marine biogeochemistry and food web of the Baltic Sea were performed for the period 1850–2098, and projected changes in the future climate were compared with the past climate environment. For the past period 1850–2006, atmospheric, hydrological and nutrient forcings were reconstructed, based on historical measurements. For the future period 1961–2098, scenario simulations were driven by regionalized global general circulation model (GCM) data and forced by various future greenhouse gas emission and air- and riverborne nutrient load scenarios (ranging from a pessimistic ‘business-as-usual’ to the most optimistic case). To estimate uncertainties, different models for the various parts of the Earth system were applied. Assuming the IPCC greenhouse gas emission scenarios A1B or A2, we found that water temperatures at the end of this century may be higher and salinities and oxygen concentrations may be lower than ever measured since 1850. There is also a tendency of increased eutrophication in the future, depending on the nutrient load scenario. Although cod biomass is mainly controlled by fishing mortality, climate change together with eutrophication may result in a biomass decline during the latter part of this century, even when combined with lower fishing pressure. Despite considerable shortcomings of state-of-the-art models, this study suggests that the future Baltic Sea ecosystem may unprecedentedly change compared to the past 150 yr. As stakeholders today pay only little attention to adaptation and mitigation strategies, more information is needed to raise public awareness of the possible impacts of climate change on marine ecosystems.