The determination of food web structures using Ecological Network Analysis (ENA) is a helpful tool to get insight into complex ecosystem processes. The intertidal area of the Wadden Sea is structured into diverse habitat types which differ in their ecological functioning. In the present study, six different intertidal habitats (i.e. cockle field, razor clam field, mud flat, mussel bank, sand flat and seagrass meadow) were analyzed using ENA to determine similarities and characteristic differences in the food web structure of the systems. All six systems were well balanced between their degree of organization and their robustness. However, they differed in their detailed features. The cockle field and the mussel bank exhibited a strong dependency on external imports. The razor clam field appeared to be a rather small system with low energy transfer. In the mud flat microphytobenthos was used as a main food source and the system appeared to be sensitive to perturbations. Bird predation was the most pronounced in the sand flat and the seagrass meadow and led to an increase in energy transfer and parallel trophic cycles in these habitats. Habitat diversity appears to be an important trait for the Wadden Sea as each subsystem seems to have a specific role in the overall functioning of the entire ecosystem.