Based on an earlier published ecosystem model, we have explored possible effects of different management scenarios for the Baltic Sea. The scenarios include an oligotrophication of the system, a drastic increase in the number of seals, and changes in the fishery management. From these simulations we conclude that fisheries, seals, and eutrophication all have strong and interacting impacts on the ecosystem. These interactions call for integrated management. The modeling highlights the potential for conflicts among management mandates such as flourishing fisheries, rebuilt seal populations, and substantially reduced eutrophication. The results also suggest that fisheries management reference points have to be adjusted in response to changes in the presence of natural predators or ecosystem productivity.