Over the last decades, the rapid expansion of man-made structures (MMS) in the marine environment has generated increased attention by industry, scientists and legislators. In the North Sea, these hard substrates host fauna that is different from the naturally occurring widespread soft sediment communities. These new areas are expected to have an ecological footprint on the environment. To investigate the potential trophic changes through carbon flows caused by MMS, we built an Ecopath with Ecosim (EwE) model focusing on the benthic community. The challenge here was to combine meaningful ecological compartments that are both representative of the benthic functional biodiversity and can detect potential changes in energy flow patterns due to MMS. We adapted a framework developed in terrestrial systems for our analysis whereby the selection of categories was based on functional traits representative of the North Sea fauna, with emphasis on their trophic behaviour, the preferred sediment and environmental position. This method yields a simple, yet effective conceptual trophic network that was then tested under various scenarios. A ‘typical soft bottom’ reference was used to compare the effect of three hard structure scenarios (e.g. ‘offshore wind farm’, ‘oil and gas’ and ‘wrecks’). Temporal assessments of each of these scenarios were also considered (i.e. immediately after construction vs 5 years old structures). The results of these simulations can aid further understanding of the wider effects of man-made structure across the marine food-web, improving the limited knowledge available to date with regards to MMS in these systems.