Submarine canyons are often morphologically complex features in the deep sea contributing to habitat heterogeneity. In addition, they act as major conduits of organic matter from the shallow productive shelf to the food deprived deep-sea, promoting gradients in food resources and areas of sediment resuspension and deposition. This study focuses on the Baltimore and Norfolk canyons, in the western North Atlantic Ocean, and investigates how different biogeochemical drivers influence canyon and slope macrofaunal communities. Replicated sediment cores were collected along the main axes (~180–1200 m) of Baltimore and Norfolk canyons and at comparable depths on the adjacent slopes. Cores were sorted, assessing whole community macrofaunal (>300 μm) abundance, diversity and standing stocks. Canyon communities were significantly different from slope communities in terms of diversity, abundance patterns and community assemblages, which were attributed to high levels of organic matter enrichment within canyons. There was a significant departure from the expected density-depth relationship in both canyons, driven by enhanced abundances between 800 and 900 m canyon depths, which was characterised as a deposition zone for organic matter. Bathymetric zonation, sediment dynamics, organic enrichment, and disturbance events were clear factors that structured the benthic communities in both Baltimore and Norfolk canyons. Coupling family-level community data, with sediment grain-size and biogeochemistry data explained community dynamics across depth and biogeochemical gradients, providing further evidence that canyons disrupt macrofaunal diversity and density patterns in the deep-sea benthos.