Anthropogenic contamination of water resources remains a severe environmental concern on a global scale. Radiogenic and stable isotope measurements (especially for light elements) constitute well-known tools for the identification of pollution sources and thus have considerable potential in prevention and remediation efforts. Recent instrumental and methodological advances have extended the isotope ‘toolbox’ to include a significant number of new stable isotope systems, which in turn resulted in rapid growth of studies using these novel tracers in the field of environmental forensics. Isotopic fractionation, occurring during post-release transformation of contaminants, offers an additional benefit of possibility to study the fate of pollutants in aquatic systems. This review will focus on selected relevant studies in the field and present future trends and development.