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Observation‐based quantification of ocean carbon dioxide (CO2) uptake relies on synthesis data sets such as the Surface Ocean CO2ATlas (SOCAT). However, the data collection effort has dramatically declined and the number of annual data sets in SOCATv2023 decreased by ∼35% from 2017 to 2021. This decline has led to a 65% increase (from 0.15 to 0.25 Pg C yr−1) in the standard deviation of seven SOCAT‐based air‐sea CO2flux estimates. Reducing the availability of the annual data to that in the year 2000 creates substantial bias (50%) in the long‐term flux trend. The annual mean CO2flux is insensitive to the seasonal skew of the SOCAT data and to the addition of the lower accuracy data set available in SOCAT. Our study highlights the need for sustained data collection and synthesis, to inform the Global Carbon Budget assessment, the UN‐led climate negotiations, and measurement, reporting, and verification of ocean‐based CO2removal projects. The Surface Ocean CO2ATlas (SOCAT) data set plays a crucial role in estimating the ocean carbon sink component of the Global Carbon Budget. However, the number of data sets available in SOCAT each year has drastically decreased since 2017. This study shows that the uncertainty in the data‐based ocean CO2flux estimate has increased by 65% due to this decline in data availability. The estimated fluxes, especially the long‐term flux trend, are remarkably affected by the data availability in SOCAT, reducing the reliability of ocean CO2uptake estimates in years and regions with sparse observations. Lower surface ocean fCO2data availability leads to higher uncertainty in data‐based estimates of ocean CO2uptakeThe long‐term trend in the ocean CO2flux increases by 1.5 times for subsequent years if the data availability is reduced to that in 2000The annual mean CO2flux is not sensitive to the seasonal skew in the data and to the addition of low accuracy data Lower surface ocean fCO2data availability leads to higher uncertainty in data‐based estimates of ocean CO2uptake The long‐term trend in the ocean CO2flux increases by 1.5 times for subsequent years if the data availability is reduced to that in 2000 The annual mean CO2flux is not sensitive to the seasonal skew in the data and to the addition of low accuracy data

Air‐sea carbon dioxide (CO2) flux is generally estimated by the bulk method using upper ocean CO2fugacity measurements. In the summertime Arctic, sea‐ice melt results in stratification within the upper ocean (top ∼10 m), which can bias bulk CO2flux estimates when the seawater CO2fugacity 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 CO2flux measurements to infer sea surface CO2fugacity (fCO2w_surface) in the Arctic Ocean. In sea‐ice melt regions, fCO2w_surfacevalues are consistently lower than fCO2w_bulkby an average of 39 μatm. Lower fCO2w_surfacecan 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 CO2uptake. The Arctic Ocean is considered to be a strong sink for atmospheric CO2. The air‐sea CO2flux is almost always estimated indirectly using bulk seawater CO2fugacity 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 CO2flux estimates if the bulk water CO2fugacity 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 CO2uptake 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 CO2uptake. Seawater CO2fugacity (fCO2w) vertical gradients are generated by fresh and cold sea‐ice melt water, which lowers surface fCO2wAir‐sea CO2fluxes are biased when estimated using fCO2wobservations 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 CO2uptake Seawater CO2fugacity (fCO2w) vertical gradients are generated by fresh and cold sea‐ice melt water, which lowers surface fCO2w Air‐sea CO2fluxes are biased when estimated using fCO2wobservations from the sub‐surface (6 m depth) in sea‐ice melt areas Summertime sea‐ice melt potentially results in a 6%–17% (with high uncertainty) underestimate of annual Arctic Ocean CO2uptake