Benthic communities are key components in marine ecosystems as they contribute considerably to nutrient cycling and provide a mayor food resource for higher trophic levels. In this study we examined if adjacent benthic assemblages that differ in faunal structure also differ in their trophic composition. Infauna, epifauna, demersal fish and the possible primary food sources (suspended organic matter and particulate organic matter) were sampled from the Bathyporeia-Tellina (BT) community, i.e. the shallow Dogger Bank, and the deeper northern Central North Sea (CNS) community in the German Bight, and were analyzed for their δ15Ν and δ13C composition. Results provide evidence that trophic composition between communities were different and similar at the same time: Regarding the food web structure of the BT and CNS communities, there was an overlap in their wider trophic niches, and food chain length and sequence of feeding groups were similar. However, their core areas of trophic niche did not overlap and CNS had a broader trophic niche and slightly longer food chain than the BT community. Deposit feeders were the dominant feeding group in the CNS and suspension feeders in the BT community. Dissimilarities between the two assemblages were linked to food availability, which is influenced by the sediment type, current circulation and wave activity of each site. Our study clearly shows that faunal differences do not necessary lead to trophic differences indicated by the overall similar trophic composition. However, it also demonstrates that local environmental settings cause slight adaption of the fauna to the environment, leading to local trophic differences. This knowledge on local food web differences is important to refine marine management of habitats and benthic fish stocks that are often based on faunal but not trophic analysis as fundamental concepts.