The data set is composed of raw files recorded with the Kongsberg Maritime SX90 long-range, low frequency (20-30 kHz) fisheries sonar during the CCGS Amundsen 2011 summer expedition in the Eastern Canadian Arctic. The sonar was operated during a 3 hours opportunistic survey offshore the Labrador coast on July 22nd and during a 18.75 hours opportunistic survey on July 30th. The sonar transducer is lowered 2.5 feet below the hull through a gate-valve. The cylindrical 256-elements transducer allows both a horizontal and a vertical sound transmission, and the omni-directional (horizontal) sonar beam can be tilted from +10 to -60 degrees to scan a large portion of the water column. The raw acoustic data were saved onto an external drive and print screens of interesting targets (fish schools and/or marine mammals) were recorded.

Samples were collected at two sites in the Eastern Canadian Arctic (Figure 1) aboard the scientific icebreaker CCGS Amundsen. The sampling positions at biogenic and non-biogenic habitats were defined during ROV video surveys at the two sites (Figure 2a-d). Positions were carefully selected to avoid overlap between the two types of habitats (i.e., when most of the camera’s field of view was dominated by a single habitat over the course of approximatively 5 meters). At each site, we deployed two box cores (0.5 × 0.5 m) per habitat (i.e., inside the biogenic structures and in the bare sediment; Figure 2e) approximately 200 m apart in FB site and 500 m apart in BB site. From each box core, we collected three sediment cores (i.d = 9.8 cm, H = 30 cm) for a total of six cores per habitat and 12 cores per site. Sediment cores sampled in biogenic structures habitats were visually exempted from biogenic structures. Bottom (10 m above the seafloor) temperature, salinity and oxygen saturation at each site were recorded with a conductivity-temperature-depth (CTD) probe. Sediment cores were incubated in the dark at a temperature-controlled room (2-4°C) until a maximum of 20% of available oxygen was consumed. Sediment samples for chlorophyll a, phaeopigments and sediment properties were also collected from each box core. sediment cores were sieved through a 500 µm mesh sieve to collect infauna. Organisms were fixed with 4% formaldehyde solution. They were sorted under a dissecting microscope in the laboratory and identified to the lowest possible taxonomic level.

A video-survey using a Super Mohawk remotely operated vehicle (ROV) was conducted in July 2017 at Lancaster Sound, Nunavut. The benthic environment was video-recorded and opportunistically photographed using a high-definition camera (1Cam Alpha, Sub C Imaging, 24.1 megapixels), at ~740 m. The ROV recorded transect data for approximately 1 km over a level muddy sand bottom with abundant Umbellula sea pens, Chondrocladia sp. carnivorous sponges, small Virgularia sp. sea pens, and common other sessile, sedentary and mobile epifauna and infauna including cerianthids, sea anemones, large Gorgonocephalus sp., and two common ophiuroid species, small holothurians and sea stars. The most common fish were eelpouts (Lycodes sp.), although several other types of fish were observed. Depth change over the 1 km transect was less than 10 m.

Coral samples were collected in Pond Inlet and Lancaster Sound in Baffin Bay using the CCGS Amundsen’s remotely operated vehicle (ROV). Samples from Agassiz trawl and box-core deployments were also kept as part of this study (11 stations). Samples were collected between 253 and 856 m. Specimens were subsampled aboard and frozen for determination of their carbon and nitrogen stable isotopic composition, as well as for lipids and fatty acids composition, as part of a study focusing on the trophic ecology of cold-water corals. Carbon and Nitrogen stable isotope analysis as well as lipids/fatty acids analysis were performed on tissue samples of soft corals at the Stable Isotopes Laboratory and Lipids Laboratory, Memorial University, respectively.

Membrane inlet mass spectrometer (MIMS) and optode / gas tension device (GTD) gas systems were deployed on the CCGS Amundsen in 2018 and 2019. These autonomous sensors obtained measurements of dissolved O2, Ar, and N2 from the ship's underway seawater supply line at approximately 10-20 sec. intervals (<100 m spatial resolution). Raw and calibrated absolute gas concentrations, supersaturation anomalies, and gas ratios are reported. Data from the underway gas instrumentation were combined with hydrographic observations of surface and depth-resolved temperature and salinity (obtained by the Amundsen Science research group) collected via underway thermosalinograph (TSG) and Rosette-mounted conductivity-temperature-depth (CTD) instrumentation.