Deepening of estuarine tidal channels often leads to tidal amplification and increasing fine sediment import. Increasing fine sediment import, in turn, may lower the hydraulic drag (due to a smoother muddy bed and/or sediment-induced damping of turbulence), and therefore, further strengthen tidal amplification, setting in motion a process in which the sediment concentration progressively increases until the river becomes hyper-turbid (Winterwerp and Wang, Ocean Dyn 63(11–12):1279–1292, 2013). To advance our understanding of the relative role of bed roughness and bed topography on sediment import mechanisms and sediment concentration, a Delft3D numerical model has been setup for an estuary which has been deepened and as a consequence experienced a strong increase in suspended sediment concentration: the lower Ems River. This model is calibrated against present-day hydrodynamic and sedimentary observations, and reproduces the basic sediment transport dynamics despite simplified sedimentological formulations. Historic model scenarios are semi-quantitatively calibrated against historic high and low water observations, revealing that changes in hydraulic roughness and deepening are probably equally important for the observed tidal amplification. This model is subsequently used to better understand historic changes in the hydrodynamic and sediment transport processes in the lower Ems River. Import of fine sediment has increased because of larger tidal transport, even though the degree of tidal asymmetry may not have significantly changed. The resulting rise in suspended sediment concentration reduced hydraulic drag, amplifying the tidal range. Export of fine sediment became less because the river-induced residual flow velocity decreased with deepening of the channel.