Linking sources and sinks of organic contaminants is a major challenge in contemporary environmental science. Chemicals can be released to the environment when leaving their field of application, intended or accidentally. It is a challenge to relate the origin of spills, transport and subsequent distribution in the environment and to analyse potential sinks and elimination pathways at a local, regional and global scale. Isotope analysis offers a unique opportunity to obtain information of sources, transport, degradation pathways and sinks of contaminants in the environment which will be urgently needed in the future. Multi-element isotope fingerprinting of chemically complex substances can be used to elucidate transformation pathways making use of isotope fractionation processes altering the reactive position and to analyse the isotope composition of an organic molecule to track sources. Concepts and applications are available for the more simple organic contaminants such as BTEX, chlorinated ethenes and MTBE but not for more complex organic contaminants such as pesticides, brominated flame retardants, persistent organic chemicals (POPs) and emerging chemicals.