Submarine canyons transport large amounts of sediment and organic matter (OM) from the continental shelf to the abyssal plain. Three carbon-based food web models were constructed for the upper (300–750 m water depth), middle (2700–3500 m) and lower section (4000–5000 m) of the Nazaré canyon (eastern Atlantic Ocean) using linear inverse modeling to examine how the food web is influenced by the characteristics of the respective canyon section. The models were based on an empirical dataset consisting of biomass and carbon processing data, and general physiological data constraints from the literature. Environmental conditions, most notably organic matter (OM) input and hydrodynamic activity, differed between the canyon sections and strongly affected the benthic food web structure. Despite the large difference in depth, the OM inputs into the food webs of the upper and middle sections were of similar magnitude (7.98±0.84 and 9.30±0.71 mmol C m−2 d−1, respectively). OM input to the lower section was however almost 6–7 times lower (1.26±0.03 mmol C m−2 d−1). Carbon processing in the upper section was dominated by prokaryotes (70% of total respiration), though there was a significant meiofaunal (21%) and smaller macrofaunal (9%) contribution. The high total faunal contribution to carbon processing resembles that found in shallower continental shelves and upper slopes, although the meiofaunal contribution is surprisingly high and suggest that high current speeds and sediment resuspension in the upper canyon favor the role of the meiofauna. The high OM input and conditions in the accreting sediments of the middle canyon section were more beneficial for megafauna (holothurians), than for the other food web compartments. The high megafaunal biomass (516 mmol C m−2), their large contribution to respiration (56% of total respiration) and secondary production (0.08 mmol C m−2 d−1) shows that these accreting sediments in canyons are megafaunal hotspots in the deep-sea. Conversely, carbon cycling in the lower canyon section was strongly dominated by prokaryotes (86% of respiration) and the food web structure therefore resembled that of lower slope and abyssal plain sediments. This study shows that elevated OM input in canyons may favor the faunal contribution to carbon processing and create hotspots of faunal biomass and carbon processing along the continental shelf.