The rotor-stator interaction and the corresponding pressure fluctuations represent one of the sources of pressure and load fluctuations on the rotating parts of rotating machineries. The high-Reynolds flow is subject to rotation in the comparably large vaneless space of axial turbines, causing wake interaction and wake dissipation in this region. This increases the level of flow complexity in this region. This study examined the effect of the flow condition entering the spiral casing on the flow condition within the distributor and the runner and the physical source of pressure fluctuations exerted on the runner of a Kaplan turbine model. Simulations were performed within the water supply system, including the upstream tank, penstock, and the Francis turbines, the level of entering the spiral casing; the results were compared with laser Doppler anemometry (LDA) results. The results were considered as the inlet boundary condition for simulation of the turbine model from the spiral inlet to the draft tube outlet to investigate the flow condition within the distributor and the runner. The CFD simulations showed that the water supply system induces inhomogeneity to the velocity distribution at the spiral inlet. However, the flow condition does not affect the pressure fluctuations exerted on the runner blades due to the rotor-stator interactions. Moreover, the dominant frequencies exerted on the runner blades were accurately approximated although the amplitudes of the fluctuations were underestimated.