The current study tried to investigate the hydrodynamic characteristics and the pollution mixing and dispersion from the sub-branch through the river confluence using the numerical model of Flow3D. A numerical model was used with length, width, and height of (7 × 1 × 1) m. Also, the nested mesh was used in the junction to refine the modeling and result depiction. It was observed that if there is a water level difference on both sides of the junction, the mixing will occur much faster, and only longitudinal mixing will prevail downstream of the junction. Therefore, it was concluded that to reduce the contamination effect through the river networks, the water level in the main channel should be higher than the subbranch. In the flow separation zone, several clockwise vortices were observed, which become weaker by moving towards the outer wall of the channel. Also, the most significant velocity vectors and also the highest contaminant concentration was observed in this region. Moreover, the vertical distribution of pollution concentration showed that the contaminant concentration would be higher at large distances above the channel bed. The highest values of turbulent intensity and turbulent Kinetic energy were also observed in flow recirculation zone. It was concluded that by increase of concentration gradient through the shear layers, the required mixing length for complete transvers pollution mixing would be decreased.