Topographic and hydrodynamic complexity in submarine canyons promotes steep gradients in food availability and geophysical parameters which affect ecological assemblages and beta diversity. While habitat heterogeneity in submarine canyons is known to support diverse and abundant megafaunal communities, due to difficulty in sampling little is known about infaunal communities adjacent to hard substrate habitats, their contribution to canyon assemblages, and overall deep-sea diversity. Sediments were collected in three distinct habitat types: within Norfolk Canyon (western Atlantic) adjacent to hard substrate habitats including canyon walls and large boulders, along the main axis of the canyon, and on the adjacent continental slope to quantify macrofaunal (>300 μm) density, diversity and community composition, and sediment geochemical parameters including grain size, organic content, and stable isotope composition. While macrofaunal densities were similar among habitats sampled at comparable depths, diversity was higher near the hard substrate environments. Discrete communities were present in each habitat type, while annelid functional composition was similar between hard substrate adjacent and canyon axis habitats. Although diversity and abundance of hard substrate adjacent sediment communities did not change with depth, communities were driven by sediments with low organic matter content, whereas canyon and slope community assemblages were best explained by depth and higher organic content. Beta diversity among hard substrate adjacent sediments and canyon axis communities was high, with 27% of canyon taxa and 10% of regional taxa only occurring in hard substrate habitats. Given the thousands of submarine canyons worldwide, our results highlight the overall importance of substrate habitat heterogeneity within canyons in supporting deep-sea benthic diversity and suggest that both within-canyon and regional diversity are underestimated.