Environmental DNA (eDNA) methodology has emerged as a groundbreaking tool for non-invasive biodiversity assessment, particularly in aquatic ecosystems. Although slightly lagging behind the progress made on other organismal groups, recently researchers started to recognise the great potential of using eDNA for parasite detection. Although eDNA-based methods show great potential for studying aquatic parasites, they are still neither routinely used nor implemented in a regular biomonitoring. In this chapter we review current applications of eDNA-based methods for research approaches in aquatic parasitology. Then we critically discuss the challenges and limitations of eDNA methodology for studying aquatic parasites and propose solutions for overcoming them. Finally, we provide an outlook and guidelines for future implementation of the eDNA methodology for bioassessment of aquatic parasites. With that, we show that eDNA is a very capable tracer for studying aquatic parasites and can be a promising solution for both biodiversity surveys of aquatic parasites and more effective risk assessment strategies.