There is increasing interest in the use of nature-based approaches for mitigation of storm surges along coasts, deltas, and estuaries. However, very few studies have quantified the effectiveness of storm surge height reduction by a real-existing, estuarine-scale, nature-based, and engineered flood defense system, under specific storm surge conditions. Here, we present data and modelling results from a specific storm surge in the Scheldt estuary (Belgium), where a hybrid flood defense system is implemented, consisting of flood control areas, of which some are restored into tidal marsh ecosystems, by use of culvert constructions that allow daily reduced tidal in- and outflow. We present a hindcast simulation of the storm surge of 6 December 2013, using a TELEMAC-3D model of the Scheldt estuary, and model scenarios showing that the hybrid flood defense system resulted in a storm surge height reduction of up to half a meter in the estuary. An important aspect of the work was the implementation of model formulations for calculating flow through culverts of restored marshes. The latter was validated comparing simulated and measured discharges through a physical scale model of a culvert, and through a real-scale culvert of an existing restored marsh during the storm surge.