Submarine canyons are morphologically complex systems, acting as major conduits of organic matter along continental shelves, promoting gradients in food resources, habitat heterogeneity, and areas of sediment resuspension and deposition. Often environmental conditions within canyons can be highly distinct, particularly in different parts of the canyon and in contrast to adjacent slopes. Here we examine how biogeochemical drivers shape the differences between canyon and slope infaunal communities in Baltimore and Norfolk Canyons in the U.S. Mid-Atlantic Region. Specific comparisons included macrofaunal communities in Norfolk canyons and adjacent slope, hard substrate associated macrofaunal communities in Norfolk Canyon, macrofaunal communities associated with chemosynthetic habitats (e.g., microbial mats and mussel beds) near Baltimore and Norfolk Canyon, and meiofaunal communities in Baltimore Canyon and the adjacent slope. Replicate sediment cores were collected in each habitat and assessed for infaunal abundance, diversity, and community composition in relation to sediment biogeochemical parameters, including grain size, organic content, stable isotopes, and chlorophyll a. Canyon macrofaunal and meiofaunal communities exhibited differences in abundance, diversity, and community assemblages within the canyon in contrast to the slope, in relation to enrichment patterns of organic matter within the canyon. Chemosynthetic communities differed between habitat types, with microbial mat habitats exhibiting high density but low diversity communities. Macrofaunal communities associated with hard substrates had higher diversity than canyon axis communities and significantly contribute to the overall canyon biodiversity. This study provides a complete benthic infaunal appraisal of two canyon systems in the western Atlantic, highlighting the importance of canyons and their associated environments to host unique ecosystems, enhancing our understanding of the drivers of communities in submarine canyons, and providing regional baseline information for nearby canyon and chemosynthetic systems.