This chapter analyses the impacts of discontinuous pollution sources on the water quality of receiving water bodies and offers the possibility to solve such type of water management problem by numerical modelling way. Typical examples of such pollution sources are the combined sewer overflows (CSOs), but generally also different types of storm water management in urban areas. There were designed and performed numerical simulations for four feasible alternatives of storm sewer management (different mixing ratio, different size of storm tanks) in the town Banská Bystrica at the Hron River (Slovak republic). The model MIKE11 was used for numerical simulations of water quality. Results of each modelled alternatives were analysed. Simulation was performed in two alternatives – for Qa and Q355, whereas Qa is the yearly average discharge and Q355 is a discharge, which exceeded 355 days in a year. Results of the study show practical implications and impacts on the receiving water body quality depending on the type of the storm water management.