The ecosystem approach has been used extensively as a guiding principle in water policies of the Baltic Sea Region since the 1970s. In addition to its operationalization as a management framework in this region, it also has expansive theoretical underpinnings. However, despite extensive literature on this approach, there has not yet been any systematic assessment of the internal and external factors that influence its implementation. This kind of assessment could form the basis for improved thinking around the concept and better implementation actions. As such, this article presents a Strengths, Weaknesses, Opportunities and Threats (SWOT) analysis of the ecosystem approach in the Baltic Sea Region by using content analysis on Baltic Sea documents. This study found that key strengths of the principle are its interdisciplinary focus and its acceptance as a framework for conservation, whilst resource intensiveness and its operational complexity are key weaknesses. The SWOT analysis revealed that a key opportunity in the external environment is the ease of alignment with other policies whilst the key external threat is the difficulty integrating disciplines. This study showed that with a streamlined allocation of resources, more stakeholder engagement through capacity building and political leadership, the ecosystem approach could facilitate interdisciplinary knowledge pooling to achieve a good ecological status of the Baltic Sea.