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Summer near-surface seawater sampling in the Canadian Arctic revealed potential for significant errors (nearly 0.1mol(m(-2) s(-1))) in CO2 fluxes calculated from measured air-sea CO2 gradients. River runoff and sea ice melt strongly stratify these waters, often resulting in surface mixed layers only a few meters thick and isolated from waters sampled by shipboard underway systems. Samples collected with the underway system, rosette, and small boats exposed substantial near-surface gradients in CO2 partial pressure (pCO(2)) over the top 7m at many stations. Distributions of temperature, salinity, and fluorescence indicated that the sources of the CO2 system gradients varied between stations, precluding simple corrections to align subsurface data with shallower conditions. Overall, the strong summertime sink of atmospheric CO2 implied by the underway data was not supported by shallower data.

Plain Language Summary Large quantities of sea ice melt and river runoff in the Arctic Ocean form thin layers of fresh water at the surface that are isolated from deeper water. However, standard methods of sampling surface waters from ships draw water from 2 to 7m below the surface, which can cause errors in air-sea CO2 fluxes calculated from measured seawater CO2 concentrations. We have quantified the potential error for waters of the coastal Arctic Ocean by measuring CO2 concentrations in samples collected near the surface using different methods from both large ships and small boats. We found that large errors could result from shipboard sampling at some stations. In particular, measuring the CO2 concentration from automated instruments that draw water from below the ship's hull systematically overestimated atmospheric CO2 absorption by the ocean.