Assessments of the environmental status of marine ecosystems are increasingly needed to inform management decisions, regulate human pressures and meet policy objectives. Ecosystem assessments however have a number of methodological challenges including the selection of appropriate indicators and definition of reference conditions corresponding to “good” or “bad” status of the ecosystem. Furthermore, the combination of individual indicators to an overall ecosystem status involves a number of methodological choices. Currently ecosystem assessments usually focus on the outcome of the evaluation and corresponding management actions, with less attention paid to the evaluation procedure itself. However, the methodological choices made during the evaluation process can, in some cases, be highly influential to the overall result of the evaluation. Here the case study of the Baltic Sea is used to address some of these methodological challenges in order to improve the transparency of the assessment procedure and help to set priorities for future work.