AbstractDeltas and estuaries worldwide face the challenge of capturing sufficient sediment to keep up with relative sea‐level rise. Knowledge about sediment pathways and fluxes is crucial to combat adverse effects on channel morphology, for example, erosion which enhances bank collapse and increasing tidal penetration. Here, we construct sediment budgets which quantify annual changes for the urbanized Rhine‐Meuse Delta of the Netherlands, a typical urban delta experiences changing fluvial and coastal fluxes of sediment, engineering works and dredging and dumping activities. The delta shows a negative sediment budget (more outgoing than incoming sediment) since the 1980s, due to anthropogenic intervention. Following a large offshore port expansion, dredging in ports and harbors in the region has doubled in the past 5 years, likely due to the induced change in net sediment fluxes. In addition, the deeper navigation channels, ports, and harbors are now trapping siltier sediment, changing the sediment composition in the mouth. The removal of sediment by 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 at the boundaries of the system and the internal mechanisms of transport. The varied response of the branches has important consequences for navigation, ecology and flood safety and management of the sediment in the system. These effects will be of pivotal importance in coming decades with similar implications for many urbanized deltas worldwide.