Shoal margin collapses of several million cubic meters have occurred in the Western Scheldt estuary, the Netherlands, on average five times a year over the last decades. While these collapses involve significant volumes of material, their effect on the channel‐shoal morphology is unknown. We hypothesize that collapses dynamicize the channel‐shoal interactions, which could impact the ecological functioning, flood safety, and navigation in the estuary. The objective is to investigate how locations, probability, type, and volume of shoal margin collapse affect the channel‐shoal dynamics. We implemented an empirically validated parameterization for shoal margin collapses and tested its effect on simulated estuary morphological development in a Delft3D schematization of the Western Scheldt. Three sets of scenarios were analyzed for near‐field and far‐field effects on flow pattern and channel‐shoal morphology: (1) an observed shoal margin collapse of 2014, (2) initial large collapses on 10 locations, and (3) continuous collapses predicted by our novel probabilistic model over a time span of decades. Results show that a single shoal margin collapse only affects the local dynamics in the longitudinal flow direction and dampen out within a year for typical volumes, whereas larger disturbances that reach the seaward or landward sill at tidal channel junctions grow. The direction of the strongest tidally averaged flow determined the redistribution of the collapsed sediment. We conclude that adding the process of shoal margin collapses increases the channel‐shoal interactions and that in intensively dredged estuaries shoal margins oversteepen, amplifying the number of collapses, but because of dredging the natural morphological response is interrupted.