The impact of urban water fluxes on the river system outflow of the Grote Nete catchment (Belgium) was studied. First the impact of the Waste Water Treatment Plant (WWTP) and the Combined Sewer Overflow (CSO) outflows on the river system for the current climatic conditions was determined by simulating the urban fluxes as point sources in a detailed, hydrodynamic river model. Comparison was made of the simulation results on peak flow extremes with and without the urban point sources. In a second step, the impact of climate change scenarios on the urban fluxes and the consequent impacts on the river flow extremes were studied. It is shown that the change in the 10-year return period hourly peak flow discharge due to climate change (−14% to +45%) was in the same order of magnitude as the change due to the urban fluxes (+5%) in current climate conditions. Different climate change scenarios do not change the impact of the urban fluxes much except for the climate scenario that involves a strong increase in rainfall extremes in summer. This scenario leads to a strong increase of the impact of the urban fluxes on the river system.