Hydraulic and environmental engineering projects often utilize side channels. The water flow through the lateral intake of channels and rivers is turbulent including separation zone and lateral eddies. This causes many problems, the transfer and deposition of sediments to the sub-channel, being the most serious. In the current work, a hydrodynamic model using the Navier–Stokes equation for the flow of incompressible fluids was studied. Using the CFD software, ANSYS FlUENT 19.2, 3D flow patterns were simulated at a diversion channel. First, the simulation results were confirmed in this study utilizing the experimental data performed by earlier investigation. The results showed good agreement using the comparison between the experimental and numerical results when the k-omega turbulence viscous model was employed. Simulation of the flow pattern was then done at the lateral channel junction using a variety of geometry designs. These improvements include changing the intake's inclination angle and chamfering and rounding the inner corner of the intake mouth instead of the sharp edge.The flow parameters at the diversion including velocity streamlines, bed shear stress, and separation zone dimensions were computed in the current study. The findings demonstrated that changing the 90° lateral intake geometry can improve the flow pattern and bed shear stress at the intake junction. Consequently, sedimentation and erosion problems are reduced.According to the conclusions of this study, a branching angle of 30° to 45° is the best configuration for increasing branching channel discharge, lowering branching channel sediment concentration and lowering Scour depth at the junction region. It was also discovered that modifying the intake inlet's sharp interior corner with specific conditions has a favorable effect on reducing the size of the separation zone. The intake of chamfered inner edge with 30° angle to flow direction (α) and c value of 0.75b was found to be the best model for lowering separation area in this investigation. In addition, the separation area and stress distribution are negatively influenced by the Configuration E model (chamfered edge at 60° angle with the horizontal), notably the greater chamfer size by increasing chamfered vertical distance (c).