Abstract Genetic data have greatly increased means to understand fish marine migration behaviours at large spatial scale within a quantitative framework. The anadromous sea trout is a prized target of recreational fishery and an important ecosystem component in freshwater and marine coastal habitats in large parts of temperate northern Europe. Nonetheless, little is known about population distributions while feeding at sea. To reconcile notions about feeding migrations being predominantly locally restricted or not, we used SNP data for 3465 trout representing >100 rivers to identify population origins of 903 coastally feeding fish captured throughout the North Sea-Baltic Sea transition area. Across areas, coastal collections generally showed marked stock-mixing and overall 70:30% native:non-native fish with seasonal variation corresponding with spawning run timing. Data revealed strong spatial feeding segregation between trout from the Scandinavian Peninsula and the European continent. This is surprising given the short distances between areas, but is in alignment with strong genetic differentiation between populations in these areas. Estimation of stock complexity of coastal feeding aggregations showed no spatial trend through the North Sea-Baltic Sea transition area otherwise characterized by strong environmental clines. Analyses of scale samples collected in the 1950s indicate that stock-mixing was consistent over almost 70 years.