Marine, coastal and freshwater ecosystems are complex and characterized by different outcomes and by the potential of rapid change, they present also linkages and tradeoffs among services, which is the reason that we cannot manage the services they provide separately. Many reports draw attention to the seriously disrupted state of marine ecosystems, as result of climate change, coastal development, overexploitation of ocean resources, nutrient and chemical pollution and other anthropogenic influences. Ecosystem functioning is strongly affected by this disruption. The publication will provide a synthesis of the current state of knowledge regarding the natural capital of water related ecosystems and will offer an overview of the innovative approaches that can support the analysis of the links between interconnect ecosystems. It will analyze the linkage across coastal ecosystem (as estuaries, mangroves, coral reefs) and the 'value added' in terms of ecosystem services (benefits), provided by the linkage as opposed to the services provided by just one system. The linkages between ecosystems will be examined under consideration of environmental, economic, management and social aspects.