The objective of this study is to develop a numerical computation method based on depth integrated model for sand waves varying with hydraulic conditions. To calculate depth scale flow structures with sand dunes, we developed the general bottom velocity computation method based on a depth integrated model, in which bottom velocity and pressure acting on bed surface are calculated without taking the assumption of the shallow water flow, such as the hydrostatic pressure distribution. The flow separation behind the dune crest, which has been found to play an important role of the dune formation, is evaluated by the production terms of the depth integrated vorticity equations. Non-equilibrium sediment transport is calculated by using momentum equation of the sediment motion with the relaxation length of the particle movement. We applied the model to experimental results on sand dunes in a narrow channel and discussed the performance of the model.