Hydraulic structures, such as bridges, dikes, engineered logs, rock weirs and vanes, are common in engineering practice. Their existence presents a disturbance to the flow field in rivers and coastal regions. As a result, the sediment transport around these structures is disturbed and consequently results in scour and erosion. This work aims to simulate the sediment transport and bed morphological changes induced by complex structures in real world. Previously we have developed Arbitrary-Lagrangian-Eulerian (ALE) method to track the deformed bed, which is useful for scour around simple geometries. It is difficult and sometime fails to model scour around complex structures. We present a new model which uses an Immersed Boundary Method (IBM) to dynamically track the geometrical deformation of the bed. This method eliminates the need of mesh deformation or remeshing in an ALE approach. The model is developed in the open source computational fluid dynamics platform OpenFOAM.