To understand and explain mechanism of the stones moving in streams is required for among natural and artificial environment, such as flushing bypass channel design, debris flows and sediment-laden flow in rivers. This paper deals with three-dimensional computational method for stones moving in streams taking in to account the shape of stones and mechanical interaction between stones and streams. The method is applied to a real scale experiment in concrete channel in which stones moving in streams were measured. In the case of one stone in streams, validation of the model has been checked by the experimental results. And the importance of stones shape for their moving is demonstrated by the analysis. In the case of a cloud of stones in streams, the present model seems to under-estimate the effect of moving stones and to need the improvement of the model.