This paper presents a numerical simulation of the three-dimensional flow in the discharge object with welded siphon and the free water level, which is commonly used in real pumping stations. The simulation is solved by the meshless numerical method Smoothed Particle Hydrodynamics (SPH), which is briefly introduced here. All numerical results are performed with the SPH solver DualSPHysics. The influence of selected individual numerical parameters and various configuration strategies of the DualSPHysics solver are presented and discussed. Based on the sensitivity analyses, numerical parameters that play a crucial role in modelling similar problems are evaluated. The presented results of the flow and velocity field are compared with the experimental data and also with the results obtained by various more or less conventional numerical methods. The acquired data show a good agreement with the experiment and exceed the results obtained by the numerical methods.