Ecosystem goods and services define and measure the importance of environmental resources for the well-being and prosperity of societies, considering complex social-ecological interactions and relationships. The management of coastal ecosystem services seeks to analyse the various service characteristics and potentials in relation to human activities in coastal zones which are major contributors to Blue Economies. Shellfish reefs provide many of these ecosystem services, but their efficient use and conservation depend on MSP strategies. Therefore, a conceptual framework was adapted and applied to allow an evidence-based decision making that protects and ensures a sustainable use of shellfish reefs. The Dutch Wadden Sea was selected as a case study that could benefit from the implementation of this theoretical framework. This application included an ecological modelling approach that enabled the exploration of future climate scenarios. Four shellfish-based management strategies were developed: Do nothing, Hold the line, Advance the line and Recolonization. These strategies were applied to the modelled climate scenarios and evaluated by their potential effects to the net flow of Ecosystem Services from shellfish reefs. A multi-criteria analysis identified the benefits that could be derived from actively preserving and maintaining shellfish reefs. Results indicate that the performance of different management choices varies under different scenarios, thus the selection of one or another must be well informed. Knowing the effects of different management strategies on the provision of ecosystem services creates awareness among stakeholders and can help policy makers in their decisions to efficiently manage the Dutch Wadden Sea from a conservation perspective.