To assess the exposure of fish to dioxins and polychlorinated biphenyls in Swiss water bodies, more than 1300 fish analyses data sets covering 20 years were compiled by Swiss authorities. We present body burden data of fish from the investigated sites including the newest available data. For a risk assessment, the concentrations found in Swiss fish were compared to biologically effective concentrations derived from toxicological studies from literature. For this, potentially adverse aryl hydrocarbon receptor-mediated effects in fish were evaluated causing responses with regard to induction of biotransformation enzymes, endocrine, reproductive, immunological endpoints, stress responses and histological endpoints.