Numerical computation of river flows have been employed the general coordinate system to adjust a river plane form. An adjustment flexibility of the coordinate system is better but it is difficult to generate a grid system in order to compute stably because grid system is not determined uniquely. This study develops a new boundary fitting method introducing the hierarchical quad-tree grid system for computation of confluence and bifurcation in natural rivers. The numerical model with the quad-tree grid system apply to compute flow pattern in experiment flume and in natural river with bifurcation and confluence , the computed results agree with measured result of the flume and natural river well.