Quantification of the physical and biological factors that influence the spatial structuring of food webs is central to inform effective resource management. We used baseline‐corrected stable isotope ratios (δ13C and δ15N) of 63 invertebrate and fish to investigate food web structure across a continental shelf gradient—the Celtic Sea Shelf in the Northeast Atlantic Ocean. Hierarchical clustering on δ13C and δ15N showed that the shelf food web is characterized by four trophic levels with trophic groups spread across pelagic and benthic trophic pathways. Four biomass‐weighted isotopic diversity metrics provided indicators on the status of the system, showing a relatively complex food web with high trophic redundancy at intermediate trophic levels suggesting resilience to disturbances. Two sets of statistical models, at the community scale and for each trophic group, identified five distinct trophic assemblages associated with different chlorophyll a concentrations, water depth, and bottom temperature. A cold, vertically mixed‐water assemblage over the outer shelf comprised the largest habitat and most diverse assemblage, highlighting the importance of cold productive conditions in the Celtic Sea. Trophic group model results were used to generate spatial area predictions to compare functioning of groups using isotopic overlap (similarity and nestedness) metrics. Isotopic niche area was larger (spanning two trophic levels) in shallow habitats, but not in habitats underlying high primary production or nutrient‐rich water masses, suggesting stronger benthic‐pelagic trophic coupling in inner shelf habitats. Results suggest that depth and intensity of pelagic production are major drivers of trophic structure and functioning of Celtic Sea communities.