In order to understand the flow mechanisms that are important in formation of river-bed and bank morphology for preservation of certain riparian plants, we have conducted a Large Eddy Simulation (LES) of a flood flow in the river where communities of a rare plant species are known to be preserved. The river reach being studied contains sharp bends and there are large rocks and boulders on the bed. The three-dimensional turbulent flow in a reach of about 200 m and a width of about 50 m of this river has been computed on a computational grid that resolves rocks and boulders of dimensions 0.5 m or larger in the horizontal direction and 20 cm in the vertical direction. The results of the flood stage, three-dimensional flow features and the bed drag have been obtained. The results appear to agree with the observation of a recent flood and the results will be useful in identifying the mechanism how the plant community is maintained surviving large floods.