Understanding the mechanisms limiting and facilitating salt marsh vegetation initial establishment is of widespread importance due to the many valuable services salt marsh ecosystems offer. Salt marsh dynamics have been investigated by many previous studies, but the mechanisms that enable or disable salt marsh initial establishment are still understudied. Recently, the “windows of opportunity” (WoO) concept has been proposed as a framework providing an explanation for the initial establishment of biogeomorphic ecosystems and the role of physical disturbance herein. A WoO is a sufficiently long disturbance-free period following seedling dispersal, which enables successful establishment. By quantifying the occurrence of WoO, vegetation establishment pattern can be predicted. For simplicity sake and as prove of concept, the original WoO framework considers tidal inundation as the only physical disturbance to salt marsh establishment, whereas the known disturbance from tidal currents and wind waves is ignored. In this study, we incorporate hydrodynamic forcing in the WoO framework. Its spatial and temporal variability is considered explicitly in a salt marsh establishment model. We used this model to explain the observed episodic salt marsh recruitment in the Westerschelde Estuary, Netherlands. Our results reveal that this model can significantly increase the spatial prediction accuracy of salt marsh establishment compared to a model that excludes the hydrodynamic disturbance. Using the better performing model, we further illustrate how tidal flat morphology determines salt marsh establishing elevation and width via hydrodynamic force distribution. Our model thus offers a valuable tool to understand and predict bottlenecks of salt marsh restoration and consequences of changing environmental conditions due to climate change.