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.

Zooplankton samples were collected onboard the research Icebreaker CCGS Amundsen during Leg 1 in 2005 (4 stations) and Leg 1 in 2006 (8 stations) with a vertically towed net frame equipped with a set of 4 adjacent 1-m2 nets (mesh size 200 µm and 500 µm) from near the bottom to the surface and by trawling an oblique rectangular mid-water trawl (mesh size 1600 µm) or an oblique Tucker net (mesh size 2x500 µm) in the surface layer from 100 m depth to the surface. Samples were placed into 30 ml plastic vials and/or whirl-pak bags and were kept frozen at -20 degree Celsius. Representative sub-samples of individual zooplankton genera were placed in 4 ml glass vials for stable isotope analysis. Three keystone zooplankton genus were included in this study: Calanus spp. (mostly adult Calanus hyperboreus), Themisto spp. (mostly adult Themisto libellula) and Euchaeta spp. THg analysis was conducted at the Freshwater Institute with cold vapour atomic absorption spectroscopy (CVAAS). MMHg analysis was conducted at the University of Ottawa by Gas Chromatography Atomic Fluorescence Spectroscopy (GCAFS). Carbon and nitrogen isotopic analyses were performed at the University of Winnipeg Isotope Laboratory by continuous flow ion ratio mass spectrometry (CF-IRMS). Oceanographic data (Hg levels in water column, salinity, 18O) were collected by our team. Water samples were collected with 24 12-L Niskin bottles attached to a rosette sampler equipped with Seabird 911+ CTD (Sea-Bird Electronics, Inc.).

Processed atmospheric ceiling heights were recorded from a CT25K ceilometer. The instrument was mounted on the CCGS Amundsen icebreaker on the port side directly behind the ship's wheelhouse. Data were collected during transit, set transects, 24-hour stations, and multi-day drift stations. The instrument was running continuously during the IPY-CFL project, with only minor interruptions for maintenance activities.

During the ArcticNet annual cruises of the research icebreaker CCGS Amundsen, characteristics of the surface sea water (temperature, salinity, dissolved CO2 and O2) are monitored in conjunction with properties of the near-surface atmosphere (basic meteorological elements, incident radiation, CO2 concentration) to observe the relationship between the surface microclimate and the air-sea exchange, with particular interest in CO2. Central to this project, the following variables were measured continuously at 1 minute intervals using a custom-built pCO2 equilibrator attached to the ship's clean water intake: -pCO2sw (LI7000 gas analyzer) -Equilibrator water temperature

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. As part of this integrated dataset, the following radiation variables were recorded at 1 minute intervals (instrument used to collect each variable is in parentheses): incoming shortwave radiation (Eppley pyranometer, model PSP); incoming longwave radiation (Eppley pyrgeometer, model PIR); incoming photosynthetically active radiation (Kipp & Zonen, PAR-Lite); and, incoming UVa,b (Kipp & Zonen, UVS-AB-T). All instruments were mounted on a meteorological tower on the bow of the research icebreaker CCGS Amundsen.

The LADCP data was obtained during the years 2009, 2010, 2011, 2014, 2015, 2017, 2018 and 2019 aboard the CCGS Amundsen. The following parameters were measured: DEPTH (Depth Below Sea Surface [m]), EWCT (East (true) Component of Current [m/s]), NSCT (North (true) Component of Current [m/s]), and ERRV (Error Velocity [m/s]). This archives contain the final absolute velocity profile for each cast. Quality control procedures are applied to the data. Data are available on Polar Data Catalogue under the format .lad (one cast by file).

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.

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.