Pathogens are present in our urban water system, and may pose a health risk to swimmers and playing children. Although the knowledge of pathogens has increased over recent years, little is known about their behaviour in the urban water system. The goal of this thesis is to investigate this. First, the behaviour of pathogens under the influence of environmental variables such as sunlight intensity and temperature was investigated. Then, this was incorporated into a hydrological model to simulate the movement of pathogens through a water system. The removal of pathogens from the water column was found to be caused mostly by the sedimentation and not so much by pathogen decay. The effect of this is that in an equilibrium state, the concentration of pathogens in the sediment is much higher than that in the water column. As sedimentation is the largest factor when considering the removal of pathogens from the water column, any measures that decrease the flow velocity decrease pathogen concentrations. However, pathogens are still present in the system, and care should be taken that the water column is not reinfected through resuspension.