Sustainable environmental management needs to consider multiple ecological and societal objectives simultaneously while accounting for the many uncertainties arising from natural variability, insufficient knowledge about the system's behaviour leading to diverging model projections, and changing ecosystem. In this paper we demonstrate how a Bayesian network-based decision support model can be used to summarize a large body of research and model projections about potential management alternatives and climate scenarios for the Baltic Sea. We demonstrate how this type of a model can act as an emulator and ensemble, integrating disciplines such as climatology, biogeochemistry, marine and fisheries ecology as well as economics. Further, Bayesian network models include and present the uncertainty related to the predictions, allowing evaluation of the uncertainties, precautionary management, and the explicit consideration of acceptable risk levels. The Baltic Sea example also shows that the two biogeochemical models frequently used in future projections give considerably different predictions. Further, inclusion of parameter uncertainty of the food web model increased uncertainty in the outcomes and reduced the predicted manageability of the system. The model allows simultaneous evaluation of environmental and economic goals, while illustrating the uncertainty of predictions, providing a more holistic view of the management problem.