Many countries define legislative targets for the ecological status of aquatic ecosystems. Fulfilling these legally binding targets requires often large scale and expensive management actions. The expected benefits from alternative actions are commonly compared with deterministic ecosystem models. However, from a practical management point of view the uncertainty in model predictions and the probability to achieve the targets are as essential as the point estimates provided by the deterministic models. For this reason, we extend a deterministic ecosystem model into a probabilistic form. We use the model for predicting the probability to achieve the targets set by EU's Water Framework Directive (WFD) in Finnish coastal waters in the Gulf of Finland, one of the most eutrophicated areas of the Baltic Sea, under alternative management scenarios. Our results show that the probability to reach the WFD objectives for total phosphorus is generally less than or equal to 0.51 in all areas. However, for total nitrogen the probability varies substantially as it is practically zero in the western areas but almost 0.80 or higher in the eastern areas. It seems that especially with phosphorus, international co-operation is needed in order for Finland to fulfill the objectives of the WFD.