A junction structure of the greatest combined sewers of Budapest (Hungary) was under hydrodynamic and water quality examinations. The selected junction performs an important role in the operation of a combined sewer overflow. The main environmental effects are on the receiving water body, on the biggest main sewer and on the wastewater treatment plant. In the first step, one-dimensional hydrodynamic simulation was executed for the main and lateral inflow sewers. The simulation results were presenting the open surface elevations of the water flow. In the next step, a 3D fluid flow model was built based on a steady state simulated flow assumption. The resulting velocity and turbulence distribution were showing the critical points of the structure and the joining conduits. The simulation without the lateral inflow highlighted the negative effect of the lateral inflow. The high velocity of the inflowing water is forcing the main branch flow to slow down. The water level and the sedimentation are increasing upstream in the main sewer. Historical sediment volumes data and frequent flooding complaints are confirming the simulation results. Suggestions based on 3D model simulations are given for the improvements.