The Curonian Lagoon (SE Baltic Sea) and the coastal wetland system play a vital role in maintaining the overall cultural, economic and ecological health of the region. However, its value is still largely underestimated and there is a lack of integrated ecosystem management based on multiple ecosystem services assessment. In this study, 34 ecosystem services (ES) were identified, assessed and mapped following the Common International Classification of Ecosystem Services (CICES). Using expert opinion, 35 land cover classes were scored for their ES potential, these being 15 CORINE land cover classes (CLC) and 20 Natura 2000 areas of conservation (habitat types, i.e., Sites of Community Importance). The total ES potential was calculated by averaging the opinions of experts, using self-confidence scoring as weights, and the ES relative importance index was derived from a questionnaire. As a result, three maps corresponding to each ES potential category (provisioning, regulation and maintenance and cultural) were calculated and further used for hot- and coldspot analyses. Regulation and maintenance and cultural ES were highly interrelated and had the highest potential in the studied area. Forested areas had the highest total ES potential and contributed significantly to the land cover of the ES hotspots.