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 2013 summer expedition in the Eastern Canadian Arctic. 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) were recorded.

The navigation data of the Amundsen scientific expeditions between 2003 and 2019 were recorded with the Position and Orientation Systems for Marine Vessels (POS-MV) and C-Nav Differential Global Navigation Satellite System (DGNSS) Precise Point Positioning systems. Two sets of controlled data are provided for each year of expedition. The first set is at time intervals of seconds for every day of the cruise and the second set is at 15 minute intervals. The data consist of Latitude, Longitude, Heading, Roll, Pitch, Heave, Track, Speed and Global Positioning System (GPS) sources at the second time intervals. The vessel's tracks in .kml (Google Earth format) were derived from the 15 minute time intervals dataset and are also provided. Research programs participating in the Amundsen expeditions between 2003 and 2017 were CASES, ArcticNet, IPY-CFL, Solas, Geotraces, Malina, IOL and BP, Jamstec, Netcare, Weston, BREA, iBO and GreenEdge.

The CTD data was obtained during the 2007-2008 ArcticNet scientific cruise #0806. The data were collected from September 5 to 25, 2008, aboard the CCGS Amundsen. There were 83 casts, associated to 44 oceanographic stations, in the Baffin Bay area. The following parameters were measured: temperature, conductivity and pressure (with a Sea-Bird SBE-9plus), dissolved oxygen (Sea-Bird SBE-43), pH (Sea-Bird SBE-18-I), fluorescence (Seapoint chlorophyll fluorometer), nitrate concentration (Satlantic MBARI-ISUS 5T), transmittance (Wetlabs C-Star transmissometer), light intensity (PAR; Biospherical Instruments QCP2300) and surface light intensity (sPAR; Biospherical Instruments QCP2200). Quality control procedures were applied to the data. Data are available on the Polar Data Catalogue and at the Marine Environmental Data Service (MEDS) of Fisheries and Oceans Canada.

The CCGS Amundsen is equipped with a RDI ADCP Ocean Surveyor (RDI os150), a ship-mounted current meter attached to the hull of the ship. The ship is also equipped of ice windows to protect the system while sailing through harsh arctic conditions. The current meter records continuous measures of the current along the ship transit route using a 150KHz sonar capable of covering the first 450m of the arctic water column. Since 2015 data are controlled using the Common Oceanographic Data Access System (CODAS, https://currents.soest.hawaii.edu/home/software/) of the University of Hawai'i, also adopted by the NOAA-National Centers for Environmental Information (NOAA-NCEI) to create the Joint Archive for Shipboard ADCP. Data are provided in NetCDF formats and follow the COARD (Cooperative Ocean/Atmosphere Research Data) convention. Detailed information and metadata are available in the documentation of the archive and in-built metadata files. Raw data since 2004 are available on demand.

Here, we sampled five specimens of Chondrocladia and Cladorhiza as part of the Hidden Biodiversity project, using the SuperMohawk ROV on board the CCGS Amundsen. In October 2015, samples were collected from Scott Inlet and off Qikiqtarjuaq, and retrieved using a custom-built sample elevator. Samples were immediately dissected and processed for DNA and histological analyses. The analysis of these samples is currently in progress.

During the ArcticNet annual cruises of the research icebreaker CCGS Amundsen, characteristics of the near-surface atmosphere (basic meteorological elements, incident radiation, CO2 concentration) are monitored in conjunction with surface sea water properties (temperature, salinity, dissolved CO2 and O2) to observe the relationship between the surface micro-climate and the air-sea exchange, with particular interest in CO2. Central to this integrated dataset, the following meteorological variables were recorded at 1 minute intervals (instrument used to collect each variable is in parentheses, and approximate instrument height above surface is indicated): -Wind speed (RM Young Wind Monitor 05103) - 16m height -Wind direction (RM Young Wind Monitor 05103) -16m height -Air Temperature (Vaisala HMP45C212) - 15m height -Relative Humidity (Vaisala HMP45C212) -15m height -Surface temperature (Everest IR Transducer, 4000.44ZL) - 8m height All instruments were mounted on a meteorological tower on the bow of the research icebreaker CCGS Amundsen.

The data set is composed of raw files recorded with a SIMRAD EK60 three-frequency split-beam echosounder that was operated continuously during the annual ArcticNet (2005-2013) sampling expeditions in the Canadian Arctic and Subarctic aboard the CCGS Amundsen. Three 7° transducers were hull-mounted, two in oil-filled arctic wells protected by a 2.5 cm thick acoustically transparent polycarbonate plate (38 and 120 kHz) and one in a Traveocean piston well in direct contact with water (200 kHz). The acoustic signal was recorded continuously on a PC using ER60 software version 2.0.0. Ping interval was set at 2 or 3 s and the pulse length was set at 1.024 ms.

During the ArcticNet annual cruises of the research icebreaker CCGS Amundsen, characteristics of the near-surface atmosphere (basic meteorological elements, incident radiation) are monitored. Central to this integrated dataset, the following meteorological variables were recorded at 1 minute intervals (instrument used to collect each variable is in parentheses, and approximate instrument height above surface is indicated): wind speed (RM Young Wind Monitor 05106-10) - 16m height; wind direction (RM Young Wind Monitor 05106-10) -16m height; air temperature (Vaisala HMP45C) - 15m height; relative humidity (Vaisala HMP45C) -15m height; and, surface temperature (Apogee IR Transducer SI-111) - 8m height, atmospheric pressure. All instruments were mounted on a meteorological tower on the bow of the research icebreaker CCGS Amundsen, except for the IR transducer SI-111, which was mounted on top of the gunwale at the ship's bow, overlooking the water surface.

Sample collections were made aboard the CCGS Amundsen during the ArcticNet field campaigns in August 2013 (Leg 1), July, August and October 2014 (Leg 1 & 3) and October 2015 (Leg 4). Sediment samples retrieved from box cores were sliced into 0.5 cm increments and frozen separately, while benthic invertebrates were collected using a benthic trawl. Individual species including Gorgoncephelus arcticus, Psilaster andromeda, Ophiopleura borealis and Ctenodiscus crispatus were identified, sorted, packed and stored at -30C and shipped to Winnipeg. At the University of Manitoba samples were freeze-dried and homogenized. Samples were then extracted and analyzed for polycyclic aromatic hydrocarbons (PAHs) and n-alkanes using a LECO Pegasus gas chromatographer with a high resolution time of flight mass spectrometer (GC-HR TOFMS). Supplementary data was also generated, including stable isotope ratios of nitrogen and carbon, as well as lipid (inverts) and total organic carbon (sediment) to calculate biota-sediment accumulation factors (BSAFs). Statistical analysis is currently ongoing.

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.