Bank protection structureis applied generally as acountermeasure of the ank erosin problem. The structures, such as groynes, revetments and so on, will auccess to protect the riverbank locally. However, usually the structures will change the cross-sectional geometry, which lead to change the flow pattern or others hydraulics parameters. Furthermore, the structure will produce another bank erosion problem in another place, especially in case that the flow is a dominant factor in riverbank erosion problem. The horizontal two dimensional bed deformation analysis of the Sesayap River is performed. The adventage of the dredging method is discussed. The dredging of bars is the appropriate choice for the countermeasures of bank erosion of the Sesayap River at Malinau, when we considered the financial efficiency and bed degradation along both banks