Secondary currents and flow separation at the intake lead to sedimentation and erosion at the lateral and main channels, resulting changes in bed topography. In the separation zone, circular flow with low velocity causes sediment’ s accumulation happens in this area, the consequences of which would be reduction of intake efficiency. Hence, determining the optimum conditions of the impoundment has been one of the concerns for the researchers. In this study, the effects of bed topography on the flow separation dimensions in the 55-degree water intake with the sharp and rounded edge entrances were assessed. Four different discharge ratios: 0. 2, 0. 4, 0. 6 and 0. 8 were tested in this experimental study and the results were compared with those issued in previous papers. Additionally, the effects of bed roughness and submerged vanes on shear stress within water intake were tested in sharp edge and rounded edge entrances. The results showed that in high diversion flow ratio and in round edge entrance, comparing to sharped edge entrance, about 97% of separation dimensions were reduced. In sharp edge entrances, increasing the diverted flow ratio, caused the length of the separation zone increased about 20% and its width reduced about 70%. Furthermore, the bed topography and roughness reduced the width of the separation zone. Also, the shear stress in rounded edge entrance was less than that in sharp edge entrance. The shear stress, in case of absence of submerged vanes, was more than that when submerged vanes were installed. By installation of submerged vanes with parallel and zigzag arrangements and with angles equal to 10 and 30 degrees, shear stress in transverse happened to be uniform, indicating that vanes have helped rotational flow being reduced and velocity being changed.