Artificial coastal structures associated with coastal defences, energy generation, ports, marinas and other developments, are known to support lower levels of biodiversity than natural coastal environments and tend to be hotspots of invasive non-native species (INNS). In the present study, we attempted to detect INNS through both quantitative (q)PCR and metabarcoding of environmental (e)DNA from seawater samples. A mitochondrial COI based species-specific qPCR assay was developed and deployed to detect Didemnum vexillum, a colonial tunicate that has successfully become established at coastal sites across Europe. Our targeted qPCR assay was able to detect D. vexillum in eDNA seawater samples from all sampled sites where it is currently found in Ireland and Wales. Through metabarcoding of the same eDNA samples, we detected an established INNS at all sites but not D. vexillum even in locations where it is present. We conclude that our qPCR approach is effective for sensitive and targeted screening for specific INNS at coastal sites including those with artificial structures, and while metabarcoding is a less sensitive approach it is a valuable tool to detect a broad taxonomic range of native and non-native species.