The rising backwater, which occurs due to the confluence of the Takahashi River and the Oda River, makes the water level rather higher during flood in the upstream of those rivers. The higher water level endangers embankments of those rivers. One of the possible means to reduce the water level is to relocate the present confluence site with the Oda River to the downstream site of the Takahashi River. This study aims to investigate the effect of the relocation of the confluence site using two-dimensional flow analysis. Numerical results under present river course condition were compared with the measured water level, and the effectiveness of the proposed analytical model was confirmed. It is also shown that the relocation of the confluence site has an effect to reduce the water levels of rivers considerably.