Deltas and estuaries worldwide face the challenge of capturing sufficient sediment to keep up with relative sea level rise. Knowledge about sediment pathways and fluxes are crucial to combat adverse effects on channel morphology, e.g. erosion which enhances risk of bank collapse and increasing tidal penetration. We constructed sediment budgets which quantify annual changes for the urbanized delta of the Netherlands affected by fluvial and coastal fluxes of sediment, engineering works and dredging and dumping activities. The Rhine-Meuse delta shows a negative sediment budget in recent decades due to anthropogenic intervention. Following a large offshore port expansion, dredging in ports and harbours in the region has doubled in the past five years, likely due to the induced change in net sediment fluxes. In addition, the deeper navigation channels, ports and harbours are trapping siltier sediment than before, changing sediment composition in the mouth. The removal of sediment from the system through dredging is adverse to the necessity for sediment in heavily eroding branches. To allow for sustainable sediment management in the future and to cope with sea level rise, further measurements are required to properly quantify the amount of incoming sediment from the rivers and the seaward boundary and the mechanisms of transport which are key to solving the sediment issues in the delta. The varied response of the branches has important consequences for navigation, ecology and flood safety and management of the sediment in the system will be of pivotal importance in coming decades and for other deltas worldwide.