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Air‐sea carbon dioxide (CO2) flux is generally estimated by the bulk method using upper ocean CO2 fugacity measurements. In the summertime Arctic, sea‐ice melt results in stratification within the upper ocean (top ∼10 m), which can bias bulk CO2 flux estimates when the seawater CO2 fugacity is taken from a ship's seawater inlet at ∼6 m depth (fCO2w_bulk). Direct flux measurements by eddy covariance are unaffected by near‐surface stratification. We use eddy covariance CO2 flux measurements to infer sea surface CO2 fugacity (fCO2w_surface) in the Arctic Ocean. In sea‐ice melt regions, fCO2w_surface values are consistently lower than fCO2w_bulk by an average of 39 μatm. Lower fCO2w_surface can be partially accounted for by fresher (≥27%) and colder (17%) melt waters. A back‐of‐the‐envelope calculation shows that neglecting the summertime sea‐ice melt could lead to a 6%–17% underestimate of the annual Arctic Ocean CO2 uptake. Plain Language Summary: The Arctic Ocean is considered to be a strong sink for atmospheric CO2. The air‐sea CO2 flux is almost always estimated indirectly using bulk seawater CO2 fugacity measured from the ship's seawater inlet at typically ∼6 m depth. However, sea‐ice melt results in near‐surface stratification and can cause a bias in air‐sea CO2 flux estimates if the bulk water CO2 fugacity is used. The micrometeorological eddy covariance flux technique is not affected by stratification. Here for the first time, we employ eddy covariance measurements to assess the impact of sea‐ice melt on Arctic Ocean CO2 uptake estimates. The results show that the summertime near‐surface stratification due to sea‐ice melt could lead to an ∼10% (with high uncertainty) underestimation of the annual Arctic Ocean CO2 uptake. Key Points: Seawater CO2 fugacity (fCO2w) vertical gradients are generated by fresh and cold sea‐ice melt water, which lowers surface fCO2wAir‐sea CO2 fluxes are biased when estimated using fCO2w observations from the sub‐surface (6 m depth) in sea‐ice melt areasSummertime sea‐ice melt potentially results in a 6%–17% (with high uncertainty) underestimate of annual Arctic Ocean CO2 uptake [ABSTRACT FROM AUTHOR]