We report the development of a methodology for assessing confidence in ecological status classifications. The method presented here can be considered as a secondary assessment, supporting the primary assessment of eutrophication or ecological status. The confidence assessment is based on scoring the quality of the indicators on which the primary assessment is made. This represents a first step towards linking status classification with information regarding their accuracy and precision. Applied to an existing data set used for assessment of eutrophication status of the Baltic Sea (including the Kattegat and Danish Straits) we demonstrate that confidence in the assessment is Good or High in 149 out of 189 areas assessed (79%). Contrary to our expectations, assessments of the open parts of the Baltic Sea have a higher confidence than assessments of coastal waters. We also find that in open waters of the Baltic Sea, some biological indicators have a higher confidence than indicators representing physical-chemical conditions. In coastal waters, phytoplankton, submerged aquatic vegetation and indicators of physical-chemical conditions have a higher confidence than indicators of the quality of benthic invertebrate communities. Our analyses also show that the perceived weaknesses of eutrophication assessments are due more to Low confidence in reference conditions and acceptable deviations, rather than in the monitoring data.