The mud dynamics in an estuary are recognized as an important element of estuarine functioning, because increasing suspended sediment concentrations may be both harmful for ecological functions (e.g., biomass production by phytoplankton) and deteriorative for human functions (e.g., by siltation of shipping channels). Considering the potential risk of increase in suspended sediment concentration in the Schelde estuary, this study aims to quantify the mud deposition/erosion in different time periods since 1930 to present, different intertidal ecotope types, and different zones along the Schelde estuary, including the Westerschelde and Zeeschelde. We analyzed the height change, volume change, eroded or deposited mud mass, and the overall mud balance. Our results suggested that net mud deposition occurred in intertidal areas in both the Westerschelde and Zeeschelde in almost all time periods. The mud deposition in stable marshes plays an important role. A large amount of mud deposition is also observed in stable intertidal flats and areas that shifted from intertidal flat to marshes or from subtidal zone to intertidal flat. Over 90% of mud erosion is observed in areas that shifted from intertidal flat to subtidal zone. Mud erosion is also observed in areas that shifted from marsh to intertidal flat.