Many estuaries are strongly modified by human interventions, including substantive channel deepening. In the Ems River Estuary (Germany and Netherlands), channel deepening between the 1960s and early 2000s coincided with an increase in the maximum near‐bed suspended sediment concentration from moderate (∼1 kg/m3) to high (>10 kg/m3). In this study the observed transition in the suspended sediment concentration in the Ems is qualitatively reproduced by using an idealized width‐averaged iFlow model. The model is used to reproduce observations from 1965 and 2005 by only changing the channel depth between the years. Model results show an increase in sediment concentrations from approximately 1–2 kg/m3 to 20–30 kg/m3 near the bed between 1965 and 2005 if the river discharge is below 70 m3/s, which holds approximately 60% of the time. Thereby, this study for the first time provides strong evidence for earlier published hypotheses that channel deepening was the main driver of the increased sediment concentrations in the Ems. The results are explained using two aspects: sediment transport (longitudinal processes) and local resuspension (vertical processes). The magnitude of the sediment import increased, because a combination of channel deepening and sediment‐induced damping of turbulence increased the M2–M4 tidal asymmetry. This effect is particularly strong, because the M4 tide evolved to a state close to resonance. All imported sediment is kept in suspension when it is assumed that resuspension is sufficiently efficient, which depends on the value of the erosion parameter used and inclusion of hindered settling in the model.