Urban areas are a focus of increasing conflict with regard to water use and water protection. Half of the world’s population and about 73% of Europeans live in cities. Currently, about 82% of the total population growth of the world occurs in the cities of the developing countries. As a direct and/or indirect consequence of human activity, urban water systems are frequently polluted with organic contaminants. Many of these contaminants are related to human behaviour and activity, such as pharmaceuticals, personal care products (collectively PPCPs) and endocrine-active substances, which are increasingly being found in urban water systems. However, the behaviour and the effects of these contaminants in the environment have been widely unknown until now. Consequently, it is important to pay more attention to such substances and to explore new integrated methodologies (including flux calculations as well as chemical and biological investigations) for determining the impact of human activities on urban water systems and on processes within the urban water-shed. The overall goal is to assess the risks to humans and the ecosystem, and to support the development of suitable management strategies.