Intertidal shoals are pronounced morphological features found in many estuaries worldwide. Apart from maintaining an ecologically unique intertidal environment, shoals also protect adjacent dyke systems by attenuating waves. The fate of sandy shoals under anticipated sea level rise (SLR) scenarios is underexplored. The current research investigates the long-term morphodynamic evolution of estuarine sandy shoals under forcing by short fetch, locally generated wind-waves, tides, and SLR by means of a numerical, process-based model (Delft3D). The focus lies on a sheltered shoal complex in the Western Scheldt, the Netherlands. Starting from the initial, 1963 bathymetry, we model 50-year morphodynamic development with schematized wind-wave forcing. We analyze in detail the impact of locally generated wind-waves on shoal formation. Finally, we impose regional SLR of 1.10 m and 1.95 m for 100 years. Model results show that, on the spatial scale of intertidal flats, small, locally generated wind-waves lower and widen the shoals while the adjacent channels deepen. However, on the estuarine system scale, wind-waves do not lead to fundamentally different channel–shoal patterns and morphodynamic evolution trends. This suggests that channel–shoal formation is mainly due to tide residual sediment transports, with wind-waves playing a secondary role. SLR leads to a notable intertidal area loss, despite a continuous heightening of the shoals, implying that morphodynamic adaptation lags behind SLR. The inclusion of wind-waves does not fundamentally change the reaction of the estuarine shoal to SLR. Future research may focus on exploring the impact of including multiple sediment classes.