Long-lived top predators shape biodiversity structure in their ecosystems and predator-prey interactions are critical in decoding how communities function. Studies on the foraging ecology of seals and Eurasian otters in Western Europe are outdated and most studies solely performed traditional hard part analysis. Molecular metabarcoding can be used as an innovative non-invasive diet analysis tool, which has proven efficient and complementary to hard part analysis, however lacking application in the wider North Sea area. In this study, DNA from digesta, collected between 2014-2020, were used to identify fish species in the diet of 47 Eurasian otters, 54 harbour seals and 21 grey seals by applying a next-generation metabarcoding approach. A newly designed 16S rRNA primer, providing the best coverage of >130 local marine and freshwater fish species, was used to amplify prey DNA from seal scats and otter gut content sampled from the North Sea and regional freshwater bodies. Frequent fish species included tench, ninespine stickleback and white bream in otters; hooknose and common roach in grey seals and Pleuronectidae and sand gobies in harbour seals. Bipartite network analysis showed a strong overlap of harbour and grey seal diets. Otter diet intersected with both seal species in terms of freshwater species. This study provides new knowledge about dietary composition and community assemblage of fish prey in otters and seals in the North Sea and regional freshwaters, and a new molecular tool to elucidate predator-prey interactions and interspecies competition in complex and changing ecosystems under pressure from anthropogenic activities.