Environmental parasitology developed as a discipline that addresses the impact of anthropogenic activities related to the occurrence and abundance of parasites, subsequently relating deviations of natural parasite distribution to environmental impact. Metals, often considered pollutants, might occur under natural conditions, where concentrations might be high due to a natural geogenic release rather than anthropogenic activities. We specifically investigated whether naturally occurring high levels of elements might negatively affect the parasite community of the intertidal klipfish, Clinus superciliosus, at different localities along the South African coast. Parasite communities and element concentrations of 55 klipfish (in muscle and liver) were examined. Our results show that parasites can disentangle anthropogenic input of elements from naturally occurring high element concentrations. Acanthocephala, Cestoda and Isopoda were associated with higher concentrations of most elements. Environmental parasitology, applicable to a wide range of systems, is scarcely used on marine ecosystems and can contribute to environmental monitoring programs.