Environmental gradients and their influence on benthic community structure vary over different spatial scales; yet, few studies in the Arctic have attempted to study the influence of environmental gradients of differing spatial scales on megabenthic communities across continental-scales. The current project studied for the first time how megabenthic community structure is related to several environmental factors over 2000 km of the Canadian Arctic, from the Beaufort Sea to northern Baffin Bay. Faunal trawl samples were collected between 2007 and 2011 at 78 stations from 30 to 1000 m depth and patterns in biomass, density, richness, diversity, and taxonomic composition were examined in relation to indirect/spatial gradients (e.g., depth), direct gradients (e.g., bottom oceanographic variables), and resource gradients (e.g., food supply proxies). Six benthic community types were defined based on their biomass-based taxonomic composition. Their distribution was significantly, but moderately, associated with large-scale (100-1000 km) environmental gradients defined by depth, physical water properties (e.g., bottom salinity), and meso-scale (10-100 km) environmental gradients defined by substrate type (hard vs. soft) and sediment organic carbon content. We did not observe a strong decline of bulk biomass, density and richness with depth or a strong increase of those community characteristics with food supply proxies, contrary to our hypothesis. We discuss how local- to meso-scale environmental conditions, such as bottom current regimes and polynyas, sustain biomass-rich communities at specific locations in oligotrophic and in deep regions of the Canadian Arctic. This study demonstrates the value of considering the scales of variability of environmental gradients when interpreting their relevance in structuring of communities.