The urban aquatic environment is increasingly polluted by low concentrated but potentially harmful compounds such as pharmaceuticals and endocrine disruptors - so-called xenobiotics. These substances are mainly carried by waste water. Up to now information with regard to their impact on the urban ecosystem and human health exist for only few of them. Within an interdisciplinary project on risk assessment of water pollution, we work on the identification of the fluxes of these substances. In a first step, we used a runoff formation model representing the city of Halle (Germany) and the Saale river. The Saale river acts as surface water system collecting slope inputs along the city traverse and sewer outflows. We investigated the anthropogenic effect on the urban water system using indicators such as hydrological parameters, selected complex organic substances, isotopic signatures and dissolved substances (sulphate, nitrate). A first balance modelling showed that main ions are not very sensitive concerning the diffuse urban input into the river. However, the concentration pattern of fragrances (tonalid, galaxolid), rare earth elements (gadolinium) and endocrine disrupters (t-nonylphenol) point to a different pollution along the city traverse: downstream of the sewage plant a higher load was observed in comparison to the upstream passage. Various substance concentrations in groundwater along the city traverse showed increasing trends.