AbstractIt is observed, during flood events, that bed forms initially grow in height and make the riverbed rougher. But later, under high discharge, the bed forms grow longer with the opposite effect of making the riverbed smoother. After the discharge drops to a lower value, new bed forms regenerate on top of the elongated bed forms. This mechanism leads to a significant variation in the bed roughness and the water stage and hence determines the behavior of floods and the risk of flood disasters. This work presents detailed modeling of bed forms under discharge hydrographs and simulates the conditions under which the bed is flattened out in the upper plane bed regime. The flow was simulated by large‐eddy simulation, and the sediments were considered as rigid spheres and modeled in a Lagrangian framework. The bed morphodynamics were the result of entrainment and deposition of sediment particles. We examined several discharge hydrographs. In the first case, we increased the discharge linearly and then kept it constant after reaching the upper plane bed condition. The dunes were generated and grew during the rising stage of discharge. When the flow conditions reached the upper plane bed regime, high‐frequency ripples were generated and helped to flatten the bed. The results also showed that in contrast with mechanisms in the dune regime, the flattening of the bed was associated with a distinct pattern of sediment transport which deposited sediment mainly in the lee side of the dunes and led to flattening of the bed. After flattening, the sediments were mainly transported in suspension mode. As long as flow conditions stayed in the upper plane bed regime, the bed remained flat with small high‐frequency ripples. We also examined two other scenarios: one with an immediate falling stage of discharge after the rising stage and the other with a period of constant discharge between the rising and falling stages. Dunes were regenerated during the falling stage of discharge for both cases. In the first case, the dunes were regenerated before the bed was flattened because of a time lag between the flow and the bed deformation. Bed flattening was followed by dune regeneration in the second case. Moreover, a significant reduction in the form drag coefficient was observed after the flattening in the second case. The reduction in form drag led to a reduction in the flood intensity. The model showed its ability to reproduce the key phenomena of the development of subaqueous dunes under conditions of a passing flood wave.