This chapter on urban water in large population centres like Halle/Saale and Leipzig (Germany) focuses on the source, distribution and transport behaviour of xenobiotics as indicator substances for anthropogenic impacts on urban water systems. The xenobiotics reported here are micropollutants including pharmaceuticals, personal care products (collectively known as PPCPs) and industrial chemicals, which show low concentrations in urban waters. Such chemicals can be endocrine disrupters or are otherwise eco-toxic. The concepts presented herein required a new methodology for assessing the impact of human activities on the urban water system and processes in urban watersheds. To this end, we used different approaches in relation to the hydrogeological and hydrodynamic settings of the cities of Halle and Leipzig. For the Halle urban area, a conceptual flow and transport model was developed based on interaction between the river Saale and groundwater, and mass fluxes were computed, based on water balance calculations. For Leipzig, as a first approach, we established a monitoring program that involved various urban land use types and investigated their influence on the urban water system. Multivariate statistics and integral pumping tests were applied to account for the spatially highly heterogeneous conditions and time-varying concentrations. At both sites, we demonstrated the use of indicators consisting of physico-chemical parameters, ions, isotopes and compound-specific patterns of xenobiotics. The chosen indicators of pH, temperature, electrical conductivity, redox conditions, nitrate, sulphate, chloride, boron, the isotopes of hydrogen, nitrogen, oxygen, sulphur and boron, as well as bisphenol A, carbamazepine, technical 4-nonylphenol (t-nonylphenol), galaxolide, tonalide, and gadolinium, helped to balance urban substance fluxes and assess urban effects on surface water quality. From our current quantification, it is clear that predicting contaminant behaviour in urban areas demands a detailed process understanding which cannot be derived from laboratory experiments or phenomenological analyses at the catchment scale. Through an installation of measuring equipment at the interfaces between the unsaturated and saturated zone as well as between ground- and surface water, in situ contaminant transport and fate can be quantified from the cm- up to the m-range.