Examination of food webs and trophic niches provide insight into organisms’ functional ecology, yet few studies have examined the trophodynamics within submarine canyons, where the interaction of morphology and oceanography influences food deposition. Stable isotope analysis and Bayesian ellipses documented deep-sea food web structure and trophic niches in Baltimore Canyon and the adjacent open slopes in the U.S. Mid-Atlantic Region. Results revealed isotopically diverse feeding groups, comprising approximately 5 trophic levels. Regression analysis indicated that consumer isotope data are structured by site (canyon vs. slope), feeding group, and depth. Benthic feeders were enriched in 13C and 15N relative to suspension feeders, consistent with consuming older, more refractory organic matter. In contrast, canyon suspension feeders had the largest and more distinct isotopic niche, indicating they consume an isotopically discrete food source, possibly fresher organic material. The wider isotopic niche observed for canyon consumers indicated the presence of feeding specialists and generalists. High dispersion in δ13C values for canyon consumers suggested that the isotopic composition of particulate organic matter changes, which is linked to the depositional dynamics, resulting in discrete zones of organic matter accumulation or resuspension. This heterogeneity results in higher trophic diversity in canyons. Hence, given their abundance in the world’s oceans, submarine canyons represent important havens for trophic diversity.