Understanding the impact of the environment on temporal trends in the composition and abundance of deep-sea species is essential for forecasting evolution of the community in the context of climate change. The recent development of deep-sea observatories enables multidisciplinary studies of long duration and high temporal resolution. We used a platform at the Ocean Networks Canada NEPTUNE Observatory located in the axis of Barkley Canyon between June 2012 and January 2015 to: (1) characterize the megabenthic community and the environmental conditions in the canyon; (2) investigate temporal patterns in the faunal community; and (3) determine the influence of environmental conditions on the observed patterns. The megafaunal epibenthic community, which included commercially important species, was composed of species known to be able to adapt to low oxygen conditions. A strong seasonal pattern characterized wind speed and direction, wave height, temperature, and chlorophyll concentration at the sea surface. The megafaunal epibenthic community exhibited seasonal patterns which were influenced by in-situ benthic boundary layer currents and temperature, weather conditions and chlorophyll concentration at the sea surface. At inter-annual scales, the surface temperature anomaly event observed in 2013 in the region could potentially impact the community structure with significant changes in species’ densities, highlighting the need for long-term monitoring in the region.