Abstract. The Dutch Wadden Sea is a region of intertidal flats located between the chain of Wadden Islands and the Dutch mainland. We present numerical model results on the tidal prisms and residual flows through the tidal inlets and across one of the main watersheds. The model also provides insight into the pathways of fresh water originating from the two sluices at the Afsluitdijk (enclosure dike) through the use of passive tracers. All these results are obtained from three-dimensional numerical simulations carried out with the General Estuarine Transport Model (GETM), at a horizontal resolution of 200 m and with terrain-following vertical coordinates with 30 layers. We concentrate on the years 2009–2010, for which we impose meteorological forcing, freshwater discharge, and boundary conditions for tidal forcing and storm surges. Results from the model show an excellent agreement with various observational data sets for sea surface height, temperature, salinity and transport through the Texel Inlet. The simulations show that although tides are responsible for a characteristic pattern of residual transport through the inlets, the wind imposes a large variability on its magnitude and can even invert its direction during strong southwesterly winds. Even though these events are sporadic, they play an important role in the flushing of the Dutch Wadden Sea, as they strongly diminish the flushing time of fresh water. In addition, wind can force a residual transport across the Terschelling watershed of the same order, if not larger, than through any of the main tidal inlets, despite the fact that its tidal prism is much smaller than any of those of the inlets. For the pathways of fresh water, the Terschelling watershed turns out to be more important than was previously thought, while the opposite holds for the Vlie Inlet.