Many submarine canyons are known hotspots of pelagic and benthic biodiversity and productivity. Despite a very limited knowledge of the ecology, biodiversity and ecosystem function of Canada’s West Coast canyons, Barkley Canyon is becoming a relatively well studied system, particularly after the installation of the NEPTUNE seafloor cabled observatory in 2009. Video observations of large densities of overwintering calanoid copepods (likely a combination of Neocalanus plumchrus, N. cristatus, and a small contribution of N. flemingeri) drifting near the bottom at 970 m in the axis of Barkley Canyon motivated our interest in investigating the temporal dynamics of their ontogenetic migration cycle. Particularly, since these large calanoid copepods, and especially Neocalanus plumchrus, comprise up to 50% of of the mesozooplankton biomass in the subarctic NE Pacific, being considered a keystone species in the trophodynamics of pelagic ecosystems in the region. Here we used ∼20-months (May 2013–Jan 2015) of seafloor video imagery combined with acoustic Doppler current and backscatter time-series data from the NEPTUNE observatory to identify the precise timing and seasonal and inter-annual variability in the deep ontogenetic migration of Neocalanus spp. in Barkley Canyon. A total of 33,486 still images were extracted from 1674 × 5-min segment videos, captured at two-hour intervals, and used in a computer-automated image analysis protocol designed to estimate Neocalanus spp. densities near the seafloor. The results from the entire time-series revealed close correspondence with the described developmental and reproductive cycle for Neocalanus spp., with the highest densities of copepodite-5 (C5) and adult individuals present at depth from the late fall and through the winter. The concomitant high-frequency (2 MHz) ADCP backscatter time-series nearly mirrored the patterns obtained from the video imagery, and also highlighted a clear inter-annual variability, with higher copepod densities in 2013 relative to 2014. Such inter-annual variability was also evidenced by ground-truth net tow casts from Line P and La Perouse monitoring stations in the vicinity of Barkley Canyon. The low and high-frequency ADCP (75 KHz and 2 MHz) current data demonstrated an along axis mean flow near the bottom and an up-canyon mean subsurface flow from 70 to 300 m above the seabed, suggesting a recirculation cell at this segment of the canyon. Based on this circulation pattern and on our video and backscatter data, we propose a conceptual model describing how the topographically-constrained currents along the canyon axis and the up-canyon flow may help trap the seasonally migrating biomass of Neocalaus spp. near the core of its overwintering depth at mid-canyon (∼1000 m). Based on a previously calculated 25-yr mean of carbon export flux attributed to N. plumchrus in the NE Pacific (i.e., 5 g C m2 yr−1; min. 1.44, max 8.82C m2 yr−1 – Bradford-Grieve et al., 2001), which considers respiration and mortality at the overwintering depth throughout winter after spawning, we estimated that 35–215 tons of carbon reach Barkley Canyon’s seafloor yearly over an area of approximately 24 km2. Future studies should aim to further constrain the role of submarine canyons in transporting and concentrating deep zooplankton migrating biomass, as there are at least another 230 submarine canyons in the subarctic NE Pacific, a region where zooplankton biomass is heavily dominated by deep ontogenetically migrating calanoid copepods.