This study investigates interactions between waves, water levels and currents at the mouth of the second largest estuary in Europe (the Tagus Estuary, Portugal) under storm waves, combining field observations and a three-dimensional fully coupled wave-current modelling system. Tidal-induced water depth variations substantially modulate waves over the ebb shoal. During energetic conditions, low tide levels promote depth-limited wave breaking and energy transfer towards higher harmonics (triad interactions), which reduces wave heights and periods. Furthermore, for a given water level, tidal currents also influence wave propagation and drive strong modulations over shallow regions characterized by cross-channel current gradients. Flood currents change the mean wave direction by about 10–15° and tend to focus the wave energy flux towards coastal regions of the southern margin compared to a run without currents (20 to 30% increase of wave heights), while ebb currents reduce the wave heights. In addition, model results suggest that the saturation level associated with wave and current conditions at shallow locations may be close to the threshold where waves start to dissipate by whitecapping. At the peak of the storm, waves become a main driver of the circulation at the mouth scale, even in the 45-m deep main channel. Wave breaking acceleration over the ebb-shoal locally increases flood currents by 50 to 300% and reduces ebb currents by 20 to 50%.