There are many drainage projects on the left bank of, and intersect with the middle main channel of the South-to-North Water Diversion Project, leading to very complicated inflow conditions. In recent years, severe rainfall-induced floods in Henan and Hebei Province posed significant threats to those drainage works. In this study, a typical example – a drainage culvert adjacent to a spillway of the reservoir with lateral confluence – is used to investigate the hydrodynamic characteristics of the pressurized flow in the culvert and the balance of the outflow, which represents typical situations of outflow confluence and mixing. Numerical simulation was conducted using a RNG k-ε hydrodynamics model covering both the intersection area and the hidden culvert. Different combinations of upstream flood and lateral confluence discharges were modelled to analyze the flow pattern, velocity distribution, turbulent kinetic energy changes and flow characteristics in the intersection area. The simulation results were also compared with the results of physical models. The results show that, with the increase of the left-side junction discharge ratio, the mainstream line gradually shifts to the right, and the maximum difference of the non-uniformity of the single-barrel flow between the left and right sides reaches 0.23. The flow balance and flow capacity of the hidden culvert are significantly disturbed. An array of diversion piles can effectively inhibit the left-side backflow, and the flow balance between culvert barrels is improved significantly. Furthermore, the maximum left-right flow unevenness is reduced by 27.8%, and the local turbulent kinetic energy is reduced by 44%, improving the pressurized culvert's flow capacity.