In multiple-inlet coastal systems like the western Dutch Wadden Sea, the tides (and their interaction with the bathymetry), the fresh water discharge, and the wind drive a residual flow through the system. In the current paper, we study the effect of the wind on the residual volume transport through the inlets and the system as a whole on both the short (one tidal period) and long (seasonal or yearly) time scales. The results are based on realistic three-dimensional baroclinic numerical simulations for the years 2009–2011. The length of the simulations (over 2000 tidal periods) allowed us to analyze a large variety of conditions and quantify the effect of wind on the residual volume transport. We found that each inlet has an anisotropic response to wind; i.e., the residual volume transport is much more sensitive to the wind from two inherent preferential directions than from any other directions. We quantify the effects of wind on the residual volume transport through the system and introduce the concept of the system's conductance for such wind driven residual transport. For the western Dutch Wadden Sea, the dominant wind direction in the region is close to the direction with the highest conductance and opposes the tidally driven residual volume transport. This translates in a large variability of the residual volume transport and a dominance of the wind in its long-term characteristics in spite of the episodic nature of storms.