Ecosystem conservation has become one of the purposes in river management as well as flood mitigation and water resources management, and understanding of river flow and morphology in a stream with vegetation becomes important. Recently 2D depth averaged analysis is familiar even in a stream with vegetation by taking account of form drag due to vegetation. However, the shear stress in vegetated area is not properly described because the resistance law due to bed roughness is not reasonably modified in vegetated area. In this study, we discussed the bed roughness boundary layer in flow with non-submerged vegetation to deduce a reasonable relation between U and u* in vegetated area toward improving the analysis of sediment transport. The results show that the modification of resistance law using by thickness, velocity distribution in that layer was found to bring significant improvement of accurate estimation of shear velocity and subsequently the sediment transport. The proposed modification is improved by 2D depth averaged analysis based on this concept, and its application is certificated through flume experiment.