When river management is focusing flood mitigation, water resources utilization and ecosystem conservation, vegetation in riparian area recently is a key and it is represented by fluvial process. Recently 2D depth-averaged analysis has become popular and powerful, and one expects its applicability to even a stream with vegetation. However, there must be some restriction for application in 2D depth-averaged model for flow with vegetation. In this paper, as for flow with non-submerged vegetation, several points necessary to be modified are theoretically discussed. From the check along the 2D modelling, the friction resistance law should be reasonably considered and the concept of “bed roughness boundary layer” is proposed and formulated against the vegetation density. Based on this concept, the shear flow structure in this layer is discussed and formulated. It brings the reasonable evaluation of the shear stress and subsequently the kinematic eddy viscosity as important parameter for discussion of sediment transport. In addition, vertical profile of suspended sediment concentration is discussed to relate the depth-averaged concentration to the bottom concentration of suspended sediment. By using the results of this paper, we are able to apply the 2D depth-averaged analysis for flow and fluvial process reasonably for flow and fluvial process in a stream with variable density of vegetation.