The Wadden Sea and the Ems-Dollard and Western Scheldt estuaries have nationally important navigation channels and globally important ecosystems on tidal flats and coastal wetlands, that also protect the coast against storms. However, dredging costs are escalating, biodiversity is declining, and the sea level is rising. These three threats are magnified by a surplus or deficit of sand and mud, which requires sediment management. The knowledge and tools needed for this pose profound scientific challenges. WadSED will develop the urgently needed system understanding, data analysis tools, and forecasting models for science and expert users, and co-create common ground among stakeholders for future-proof coastal management.