Shelf mud patches represent major sinks for fine-grained particles on continental shelves, as well as for carbon and contaminants of continental origin. The West Gironde Mud Patch (WGMP) is an interesting example of such offshore marine systems as it is an active mud deposition area located offshore the Gironde estuarine mouth (France) at depths between 30 and 70 m. It is known to be the trap of fine particles coming from the estuary, but the contribution of this material to the total mass of the depocenter is poorly quantified. In addition, despite the economic and ecological issues at stake, the response of such subtidal sedimentary structure to the combination of tidal currents, waves, and river supply remain poorly understood. Thus, using a realistic 3-D hydrodynamic and mixed (mud/sand) sediment transport model, this study aims at investigating the sediment dynamics of the WGMP under different hydrometeorological conditions. The analysis of the residual fluxes at the estuarine mouth exhibited large discrepancies between the different sediment classes as well as for contrasted hydro-and meteorological conditions induced by different dominant transport mechanisms. During winter, the reinforced density gradients drive strong up-estuary baroclinic circulation at the bottom that dominates the sediment dynamics over the barotropic export of mud particles. The model also reproduced the signature of a subtidal mud accumulation area over the continental shelf around 30–40 m water depth, on the proximal side of the observed WGMP. On average over two years, 26% of the mud mass accumulating on the simulated subtidal mudflat comes from the estuary. The trapping efficiency of this mud patch is negatively correlated with the significant wave height. Moreover, due to the estuarine turbid plume being more concentrated and developed at the surface during high river discharge, the trapping efficiency of the mud body is enhanced compared to lower discharge. This study highlights the sensitivity of mud and sand fluxes to vertical and horizontal residual circulation, and points out the uncertainties associated with the simulation of short-term (i.e., years) fine particle deposits compared to long-term (i.e., centuries) sediment accumulation trends. In addition, these results show the primordial effects of both wave action and riverine sediment supply on the dynamics of such subtidal muddy structures, which raises concern about their fate facing climate change and human activities in the future.