The European Union (EU) Water Framework Directive (WFD) and Marine Strategic Framework Directive (MSFD) call for member states to achieve the good environmental status of coastal waters and marine areas and to create ecosystem-based management plans that cover individual sectors. The Baltic Marine Environment Protection Commission (HELCOM) has listed the Archipelago Sea as an environmental hotspot in the Baltic Sea due to its vulnerability to the impacts of eutrophication. Agricultural runoff is the main source of excess nutrient loading, although aquaculture, tourism, wastewater treatment and internal loading also contribute. In this paper, we focus on the horizontal and vertical policy coherence in the Archipelago Sea region. The research data consist of policy documents and 11 thematic interviews. This paper aims to reveal how European water and marine policies are implemented in the Archipelago Sea and to identify the synergies and coherence challenges exist between policy sectors of agriculture, aquaculture and offshore wind. Evidence from the Archipelago Sea case study shows that a lack of coherence between sectoral policies can create challenges for ecosystem-based management. Moreover, the coherence and synergies in implementing regional and EU marine policy frameworks at the national and local levels can guide sectoral decisions towards strengthening of marine resilience and biodiversity.