Water samples were collected at approximately 0.3 m depth at all stations in Hudson Bay during the the 2010 cruise from Kuujjuarapik, PQ to Churchill, MB. We collected samples at basic, mooring and CTD (conductivity-temperature-depth) stations, as well as along two transects made by Zodiac near the mouth of the Rivière de la Grande Baleine and off Cape Tatnam, located at ca. 100 km East of the Nelson River. All water samples were filtered on board, and subsamples were retained for analysis for dissolved and particulate organic carbon and nitrogen, as well as for phosphate, total soluble salts (TSS), chlorophyll a, CDOM (absorbtion and fluorescence spectra), oxygen-18 and salinity. At each station, water column profiles were recorded, each to the bottom or at least 30 m depth, using an Idronaut CTD with conductivity, temperature, depth and turbidity sensors, and a WetLabs ECO Fluorometer for CDOM fluorescence. In addition,we made several water column profiles of absorption and attenuation spectra off the mouth of the Rivière de la Grande Baleine, using a WetLabs hyperspectral absorption and attenuation meter (WetLabs acs). We also recorded miscellaneous water surface reflectance spectra, using a Satlantic HyperSAS instrument mounted on the ship's bow, near Rivière de la Grande Baleine, near the mouth of James Bay and in the outer estuary of the Nelson River.

Field observations were made in the southern Beaufort Sea and the Amundsen Gulf as part of CASES 2003 expedition. Samples were collected during the first two legs of the expedition from 13 September to 14 October 2003 (open water) and from 15 October to 25 November 2003 (newly formed sea ice) onboard the Canadian icebreaker CCGS Amundsen. Temperature and salinity profiles were obtained using a SeaBird 911 Conductivity¿Temperature¿Depth (CTD) probe. Nutrient concentrations (nitrate plus nitrite, phosphate, and silicate) were determined on fresh samples (within 1 h of sampling) using standard colorimetric methodologies adapted for use on an Auto-Analyzer 3 (Bran þ Luebbe). A RAMSES ASC scalar hyperspectral irradiance sensor (TriOS) was mounted on the flight bridge to measure downwelling irradiance with 1 nm intervals during the day. A total of 50 and 102 discrete water samples were collected over the euphotic zone at 13 and 20 stations for legs 1 and 2, respectively for fluorometrically chlorophyll a measurements and absorption analysis of phytoplankton, non-algal particules (NAP) and colored dissolved organic matter (CDOM). Water samples (preserved in acidic Lugol solution) were enumerated and identified to the lowest possible taxonomic rank using an inverted microscope. Concentrations of chlorophyll a and chlorophyll b were obtained by HPLC measurements and these two pigments were used for the calculation of the ratios of chl b to chl a.

Samples were collected from nine sites distributed across the study region in 2008 and 2009. To avoid confounding influence of seasons, the same sites were sampled in the same season each year. Sampling was conducted onboard the CCGS Amundsen between July and October during the Circumpolar Flaw Lead Study, ArcticNet expeditions in collaboration with the Canadian Healthy Ocean Network and the Malina project. Locations were chosen to study both hotspots and coldspots in the Canadian Arctic. At each sampling station, an USNEL box corer was deployed for seafloor sediment collection. From each box core, three to five sub-cores of 10 cm diameter and approximately 20 cm sediment depth were taken for assessing benthic remineralisation function in shipboard microcosm incubations. After incubation, the same sediment cores were passed through a 0.5 mm mesh sieve under slow running seawater. The sieve residues were preserved in a 4% seawater-formaldehyde solution for later analyses of species diversity and abundance under a dissection microscope.

The datasets present new data from microscopic counts and selected nutrient and physical data assembled from the following missions. Aboard the CCGS Louis St-Laurent: IPY Canada's Three Oceans 2007. Aboard the CCGS Amundsen: International Polar Year (IPY) Circumpolar Flaw Lead Study 2008; ArcticNet 2008. Temporal coverage is July-September. Cell density of the three sub-clades MAST-1A, MAST-1B and MAST-1C was measured by cell-counts using fluorescent in situ hybridization with taxa-specific probe. Biomass of phototrophic organisms, of different size classes, was obtained by counts of DAPI-stained cells under epifluorescence microscopy. Samples for total chlorophyll a (chl a) were filtered onto GF/F filters, extracted in either ethanol or acetone and analysed by spectrofluorometry. Chl a was also measured for the < 3 µm size fraction, and chl a in the < 3 µm size fraction was calculate by simple substraction. CCGS Amundsen data: Temperature, salinity, transmissivity, oxygen, and photosynthetically active radiation were provided by Dr. Y. Gratton (Institut National de la Recherche Scientifique, Québec). Nitrate and Phosphate concentrations were provided by Dr. J.-É. Tremblay (Université Laval, Québec). CCGS Louis St-Laurent data were supplied by Drs. E.C. Carmack and J. Nelson (Institute of Ocean Sciences, Sidney, B.C.). Distance to ice edge was obtained from the Canadian Ice Services (http://ice-glaces.ec.gc.ca).

The datasets present new data from microscopic counts and selected nutrient and physical data assembled from the following cruises. Aboard the CCGS Amundsen: ArcticNet Expeditions 2006, 2008, 2009, 2010; International Polar Year (IPY) Circumpolar Flaw Lead Study 2008 and MALINA Project 2009 (French IPY project headed by Dr. M. Babin). Aboard the CCGS Louis St-Laurent: IPY Canada's Three Oceans 2007. Temporal coverage is Feb.-Nov., but varies by year, with the greatest sampling effort in July-Oct. Cryothecomonas abundance was measured by cell-counts using fluorescent in situ hybridization with a taxon-specific probe. Biomass of phototrophic and heterotrophic organisms, of different size classes, was obtained by counts of DAPI-stained cells under epifluorescence microscopy. Samples for total chlorophyll a (chl a) were filtered onto GF/F filters, extracted in either ethanol or acetone and analysed by spectrofluorometry. Chl a was also measured for the < 3 µm size fraction. CCGS Amundsen data: Temperature, salinity, oxygen, and photosynthetically active radiation were provided by Dr. Y. Gratton (Institut National de la Recherche Scientifique, Québec). Nitrate and Phosphate concentrations were provided by Dr. J.-É. Tremblay (Université Laval, Québec). CCGS Louis St-Laurent data were supplied by Drs. EC Carmack and John Nelson (Institute of Ocean Sciences, Sidney, B.C.). Distance to ice edge was obtained from the Canadian Ice Services (http://ice-glaces.ec.gc.ca).