Regular monitoring of diadromous fishes is critical to inform their management and conservation. Yet, the in situ data collection for these species is challenging due to their complex life cycle and low abundance. Focusing on the sea lamprey ( Petromyzon marinus , Petromyzontidae) and the European shads (allis shad Alosa alosa and twaite shad Alosa fallax , Clupeidae), emblematic diadromous fishes in the Northeast Atlantic region, this study leverages the use of aquatic environmental DNA (eDNA) samples to monitor their distribution range. For that aim, we developed quantitative PCR (qPCR) and digital PCR (dPCR) assays and applied them to detect sea lamprey and European shad DNA in a network of 44 river basins across Spain, France, Ireland and the UK. We found that qPCR efficiently detected presence/absence of European shads, whereas the higher sensitivity of dPCR was essential for detecting sea lamprey, which is likely to occur at lower abundance. Moreover, sea lamprey showed significantly lower eDNA copies per litre of water compared to European shads, probably due to their larvae spending several years burrowed within soft sediments, reducing eDNA shedding into the water column. The integration of previously recorded data as reference datasets with this wide‐ranging snapshot study enhances our understanding of the distribution of sea lamprey and European shads in Northeast Atlantic rivers. Importantly, the lessons learned within this international collaboration are critical towards achieving a prevailing framework for conservation of migratory fishes, highlighting the need of well‐designed sampling strategies coupled with species‐specific assays applied to eDNA samples to boost long‐term monitoring efforts of diadromous species.