Ecological network analysis (ENA) is a helpful tool to study complex ecosystem processes. The diverse species interactions are described as flows of energy providing a simplified representation of the natural system based on attributes and features. In the Wadden Sea, a unique ecosystem along the coastline of Denmark, Germany and the Netherlands, physical forces form the vast intertidal areas to diverse habitat types that differ in their species composition and abundance. Those habitats are important foraging areas for top predators such as birds. In the present study the food web of six habitats characteristic for the Wadden Sea (cockle field, razor clam field, mud flat, mussel bank, sand flat and seagrass meadow) were analyzed in a modelling approach. The functional and structural properties of the food webs were compared to assess differences and similarities in the system functioning. Although all systems revealed a good balance between their degree of organization and their robustness against external perturbations, they differed in their detailed features. The cockle field and the mussel bank both exhibited a strong dependence of their efficiency on external imports. The razor clam field, dominated by the introduced species Ensis directus, appeared to be a rather small and stressed system with low energy transfer. The mud flat system was characterized by a high use of microphytobenthos and appeared to be not fully developed yet. Bird predation was most pronounced in the sand flat and the seagrass meadow and led to an increase in energy transfer, parallel pathways and pathways lengths in these habitats. Each system shows characteristic features and plays a different role in the Wadden Sea ecosystem by contributing significantly to the whole system functioning.