In hyperturbid estuaries, fine sediment accumulation frequently generates fluid mud layers that pose major challenges to ecology and navigation. Few studies have addressed the relation between fluid mud and residual sediment transport mechanisms to date. Here, we present Acoustic Doppler Current Profiler (ADCP) and water-sampling observations from the hyperturbid Emden Fairway (Ems Estuary), collected under three river discharge conditions (45–200 m³ s^-1), including two 13 h tidal-cycle surveys with full-depth suspended sediment concentration (SSC) profiles. The thickness of the fluid mud layers differed among surveys with contrasting discharge in the research area, exceeding 2 m at high discharge (200 m³ s^-1), whereas no fluid mud was present at low discharge. When a thin fluid mud layer was present (∼1 m), the net landward sediment flux per unit width over around 12 h observation windows reached 200 t m^-1, which is one order of magnitude larger than that measured when the fluid mud was absent. The presence of a fluid mud layer coincided with a two-layer estuarine circulation, and enhanced tidal pumping through elevated near-bed SSC, which both promote landward sediment transport. In contrast, when the fluid mud layer has retreated, the residual flow is seaward over the full water depth, likely due to a sediment-induced density gradient opposing that of salinity, weakening estuarine circulation. The net landward transport relies mainly on tidal pumping. During the highest-discharge survey, near-bed sediment-induced density gradients were larger than the salinity gradient, indicating that fluid mud is not merely passively advected but may exert a control on the near-bed residual flow. Our results show that resolving the full near-bed layer is essential for quantifying sediment transport and understanding the discharge-driven redistribution of sediment in hyperturbid estuaries.