Muddy coastlines cover much of the world’s shores, yet studies on the interaction between mud-affected coasts and estuaries are limited. This study focuses on the Mahury River estuary and its interaction with the muddy coast of the Guianas, primarily fed by the Amazon. A coupled wave–current–sediment transport model is developed to analyze the sediment exchange in an environment with strong interactions between the waves and the fluid mud. Simulations explore how seasonal changes in waves, mud availability, and tides affect sediment fluxes. The main processes influencing suspended particulate matter (SPM) and sediment transport are well emulated, notwithstanding the complexity of the ambient muddy environment. The results show that during the rainy season, strong wave damping and wave refraction zones cause high SPM resuspension in shallow waters (<5 m). In contrast, during the dry season, wave influence shifts to the estuary mouth. Erosion and sedimentation patterns indicate that ebb currents associated with neap tides during the rainy season represent the most favourable conditions for the alongshore migration of mud banks. Neaptide ebb currents also contribute to sedimentation during the dry season but only in the estuary mouth and the nearby coastal area. The abundance of mud leads to an extension of the estuary’s intertidal area during the dry season.