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Marine ecosystems are highly dynamic and complex and contribute immensely to human well-being. Spatiotemporal overlaps of marine uses and human activities are constantly pressuring ecosystems, and that in turn impacts the supply quantity and quality of various ecosystem services (ES). This study is the first attempt to use the ES matrix to link marine uses and the capacity to supply ES. Combining expert- and literature-based evaluations, we assessed the relationships of twelve marine uses and five selected ecosystem services in the German North and Baltic Sea and mapped their spatial distribution. Despite a limited data availability and a higher need for simplification, the matrix approach proved to be applicable for the marine realm. Areas used for tourism and those that provide coastal safeguarding show high values of ES supply in comparison to areas used for sediment extraction and areas previously used as ammunition dumping areas. Nature conservation areas tend to have the highest capacity to supply ES. Differences in the ES supply pattern between the North Sea and Baltic Sea were identified. The results show the influence of anthropogenic activities on the spatial distribution of ES supply and can support future marine planning.