Estuaries are crucial habitats in the life history of many species; they are nurseries to juveniles of marine and freshwater fish. Resident species complete their life cycle in estuaries while diadromous species pass estuaries on their way to their spawning grounds. The community structure in estuaries is highly dependent on migrations of fish between the coastal nurseries and the estuarine feeding grounds. This research projects aims to clarify the spatial and functional role estuaries perform for juvenile marine fish. In particular, we address the question which proportion of estuarine migrants relative to marine residents contribute to the next cohort. In order to be able to do this, fish have to be assigned to populations and habitats, and exchange rates have to be determined. We use stable isotopes to trace migrations and genetic markers to investigate the metapopulation structure.