Shipping fairways in estuaries are continuously dredged to maintain access for large vessels to major ports. However, several estuaries worldwide show adverse side effects to dredging activities, in particular affecting morphology and ecologically valuable habitats. We used physical scale experiments, field assessments of the Western Scheldt estuary (the Netherlands), and morphodynamic model runs to analyse the effects of dredging and future stresses (climate and sediment management) on a multi-channel system and its ecologically valuable intertidal flats. All methods indicate that dredging and disposal strategies are unfavourable to long-term morphology because dredging creates and propagates the imbalance between shallow and deeper parts of the estuary, causing a loss of valuable connecting channels and fixation of the tidal flats and main channel positions, while countering adverse effects by disposal strategy has limited effectiveness. Changing the disposal strategy towards main channel scour disposal can be economically and ecologically beneficial for the preservation of the multi-channel system. Further channel deepening will accelerate the adverse side effects, whereas future sea-level rise may revive the multi-channel system.