Biological invasion is one of the biggest threats to global freshwater diversity, and large transboundary rivers are subject to human impacts. Environmental DNA (eDNA) is a powerful tool as it is both non-invasive and can detect the presence of species at very low population numbers. The current research focuses on the use of eDNA to identify invasive freshwater species in the Euphrates River system through eDNA-based surveillance. This includes a focus on the Shatt al-Hillah channel within the province of Babylon, Iraq. Samples were taken from several sites along the length of the river, and metabarcoding was performed to amplify the mitochondrial genes. Results indicate that the eDNA method produced reliable signals for detecting invasive species and could be used as an early warning tool for monitoring invasive species in Middle Eastern freshwater ecosystems. These results also indicate that molecular monitoring should be integrated into biodiversity conservation strategies in the region and into river basin management frameworks.