Demersal and benthivorous fish depend on prey availability in benthic habitats for their diet. Prey availability may in turn be affected by bottom trawling. Our study attempted to link the prey consumed by fish directly to those available in the benthic environment. We test the hypothesis that bottom trawling significantly affected the trait composition of fish diets with a strong link to benthic habitats. Stomach content data were analysed for seven demersal and benthivorous fish species in the southern and central North Sea and were related to habitat fauna collected by grab and epi-benthic trawl data across the same spatial extent. Biological trait analysis was used to avoid taxonomic bias in large-scale comparisons across habitats and to quantify the effect of bottom trawling, which tends to shift prey diversity in favour of small, opportunistic and short-lived species and traits. The diets of two demersal omnivores (whiting, Merlangius merlangus and Atlantic cod, Gadus morhua) and two opportunistic benthivores (haddock, Melanogrammus aeglefinus and long-rough dab, Hippoglossoides platessoides) did not appear to reflect either infaunal or epifaunal traits that were abundant in the benthic environment. The diets of European plaice (Pleuronectes platessa) and Dover sole (Solea solea), however, showed strong links with infaunal prey trait composition in shallow sand to muddy sand habitats located in the eastern North Sea and the Dogger Bank. Such strong links were also observed for the diets of Common dab (Limanda limanda) and plaice in similar habitats in deeper waters. Plaice targeted small to medium sized infaunal burrowers and deeper dwelling infaunal species. Its diet was significantly affected by bottom trawling, which caused a reduction in prey biomass in their stomachs rather than a shift in trait composition. Our study showed that the diets of benthivorous fish across large spatial scales are strongly linked with the prey trait availability in their benthic habitats and that bottom trawling significantly affected the diet of plaice, a species with strong habitat-diet associations.