Due to increasing reliance on pumping stations for water level management, and emerging knowledge of their adverse ecological impacts on whole fish communities, it is important we manage these structures effectively. Recent eel specific policy means we must implement mitigation measures, however knowledge gaps with regard to species distribution in pumped catchments prevent targeted management. This study validates Environmental DNA (eDNA) metabarcoding as a high sensitivity method to uncover priority species distribution and fish community structure in pumped river catchments.