Several subhabitats (e.g. intertidal and subtidal soft substratum or saltmarsh creeks) have been defined within the estuarine reaches of the Westerschelde and the Oosterschelde. This complex system can serve as spawning ground, nursery area, feeding ground and as a pathway in diadromous migrations. This study concentrated on the significance and role of these selected habitats in the life cycle of fishes and macrocrustaceans. Therefore, both habitat availability and habitat use were quantified. The importance of estuarine biotopes as habitats for fish was evaluated through a Habitat Utilisation Index. Next to the ecological guilds, also feeding guilds were developed to assess the relationship with the lower consumers. A generalised food web structure within the Westerschelde was defined, which proved the importance of mysids and other crustaceans in the food of juvenile fish and shrimps. The results were compared with other systems to examine if the Westerschelde and the Oosterschelde comply with what is inspected in European estuaries.