Harbor seal (Phoca vitulina) is one of the most abundant top predator species in the Wadden Sea. Their abundance and distribution can have a large effect on the structure and the functioning of coastal food webs, and assessing their role in the functioning of ecosystems is a central issue in ecology and management. Ecological Network Analysis (ENA) methodologies were developed to assess holistically the complex environmental interactions within an ecosystem. We used trophic marker methods to assess the diet of harbor seals from the Wadden Sea. The results showed that harbor seals use the food resources from the Wadden Sea in higher intensity in the warm seasons than in fall and winter, in accordance with the abundance of their potential prey items in the area. They also revealed a shift from a diet more influenced by pelagic prey items in spring to a diet more influenced by benthic and demersal prey items in summer. The harbor seal compartment was then included in an updated food web model of the Sylt-Rømø Bight. One model per season was constructed and ENA was conducted to assess the seasonal development of the system properties. The whole system indicators were not significantly different across seasons. Seasonal trends were nevertheless observed in the ecosystem size, stability and resistance in front of external disturbances. Opportunistic predators seemed to have a structural role in the food web, increasing the stability and the resistance of the ecosystem in spring and summer, in comparison with fall and winter.