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Bedform-related roughness affects both water movement and sediment transport, so it is important that it is represented correctly in numerical morphodynamic models. The main objective of the present study is to quantify for the first time the importance of ripple- and megaripple-related roughness for modelled hydrodynamics and sediment transport on the wave- and tide-dominated Ameland ebb-tidal delta in the north of the Netherlands. To do so, a sensitivity analysis was performed, in which several types of bedform-related roughness predictors were evaluated using a Delft3D model. Also, modelled ripple roughness was compared to data of ripple heights observed in a six-week field campaign on the Ameland ebb-tidal delta. The present study improves our understanding of how choices in model set-up influence model results. By comparing the results of the model scenarios, it was found that the ripple and megaripple-related roughness affect the depth-averaged current velocity, mainly over the shallow areas of the delta. The small-scale ripples are also important for the suspended load sediment transport, both indirectly through the affected flow and directly. While the current magnitude changes by 10–20% through changes in bedform roughness, the sediment transport magnitude changes by more than 100%.