With the presence of arbitrary objects, such as gravels, boulders, woody debris, and various hydraulic structures, the hydrodynamics in a river channel are complex. They are of great interest to the understanding of the river hydraulics and geomorphology. On the other hand, due to the arbitrary geometric shapes of the objects, it is extremely difficult to model them using the traditional approach of generating body-fitted meshes. To cope with this, Immersed Boundary Method (IBM) can be used to approximate the effect of objects. However, most previous IBM methods are proposed with structured meshes as the background mesh. Many of them also lack the capability to model the free surface. In this paper, we present a new IBM method under the framework of unstructured mesh, which greatly extends the modeling capability. It also considers the effect of the free water surface using the Volume-of-Fluid (VOF) method. The new method has been implemented in the open source CFD framework Open FOAM. Simulation examples will be shown to showcase the capability of the new method.