River dunes, dynamic bedforms in the river bed, limit navigable depths during low flows and increase bed roughness. To predict the navigable depth or where maintenance dredging is needed, a numerical dune development model can be a powerful tool. To study the effect of sediment transport on dune shape and propagation, four different sediment transport models were applied in an existing dune development model. Each sediment transport model was able to simulate dune propagation, while only sediment transport models based on the shear stress reshaped the river dunes. The tested sediment transport models can simulate dune celerity similar to observations and realistic, though different, dune shapes for low and median discharges. Implementation of a gravitational bed slope effect combined with a critical shear stress results in low angle dunes, which are representative for river dunes during low river flows. Sediment transport models with spatial relaxation, also result in low angle dunes. However, the relaxation parameters need to be redefined for low flow situation to prevent transition to upper stage plane bed at too low flow velocities. Further analysis of the resulting dune shapes shows that the sediment transport model determines the dune shape in terms of slope angles, while the dune height is related to the total transport capacity.