Coastal ecosystems are important ecosystem services (ES) suppliers. The degradation of these ecosystems jeopardizes the quality of ES provision. The Biodiversity 2020 Strategy aims at maintaining and restoring ES, although clear guidelines are missing on how to define the state to which ES should be restored. In this respect, synergies between ES assessments and the Water Framework Directive (WFD) exist, but methodological approaches to connect both are lacking. The Marine Ecosystem Services Assessment Tool (MESAT) can overcome this problem. In this study, the tool is applied to semi-open and open coastal water bodies in the Southern Baltic Sea, the Greifswald Bay and Pomeranian Bay. The resulting changes in ES provision confirm the ability of MESAT to be applied in all WFD water body types and a multitude of environmental and anthropogenic gradients. Nevertheless, problems such as data scarcity, spatial extent and historical background of the case studies require adaptations in the assessment process. The spatial extent of all case studies allowed to cover a connected system with a strong environmental (salinity) gradient. Analyzing changes in ES provision in connected systems can help to better understand linkages between ES provision and environmental and anthropogenic stressors as well as trade-offs between ES across water bodies. This information can be further used to support the design of management plans. From the analysis of all MESAT case studies, major factors were identified for the tool to be transfered into a European context, as well as potential problems and solutions. Following the WFD is a strong advantage, which ensures the tool’s transferability to other areas.
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