Groynes are popular hydraulic structures often used to control the erosion of banks by altering flow and sediment transport. In this paper, the effects of altering groyne orientation and spatial setup (from large to small and vice versa) on flow patterns, bed erosion, and sedimentation are numerically investigated. Studied groynes were parallel to each other, non-submerged, and impermeable. Numerical simulations were conducted in FLOW-3D. A nested mesh configuration combined with Van-Rijn formula on sediment transport yielded more accurate results when comparing numerical results to experiments. Groynes arranged from large to small at an angle of 45° decreased the scour depth by up to 55%, and an arrangement from small to large at an angle of 135° reduced the scour depth by up to 72%. Additionally, it was observed that simulations with an orientation closer to 90 degrees needed more equilibrium time when compared to other simulations.