This paper describes the development of the EU Water Framework Directive central water quality elements from 1970 to 2010 in the Gulf of Finland, a eutrophied sub-basin of the Baltic Sea. The likelihood of accomplishing the management objectives simultaneously is assessed using Bayesian networks. The objectives of good ecological status in winter-time total nitrogen and phosphorus, summer-time chlorophyll-a and summer-time Secchi depth have not been met yet. In addition, the results indicate that it is unlikely for them to be achieved in the near future, despite the decreasing trend in nutrient concentrations over the past few years. It was demonstrated that neither phosphorus nor nitrogen alone controls summertime plankton growth. Reaching good ecological status in nutrients does not necessarily lead to good ecological status of chlorophyll-a, even though a dependency between the parameters does exist. In addition, secchi-depth status is strongly related to chlorophyll-a status in three of the four study-areas.