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The Southern Ocean (SO) contributes most of the uncertainty in contemporary estimates of the mean annual flux of carbon dioxide CO2between the ocean and the atmosphere. Attempts to reduce this uncertainty have aimed at resolving the seasonal cycle of the fugacity of CO2(fCO2). We use hourly CO2flux and driver observations collected by the combined deployment of ocean gliders to show that resolving the seasonal cycle is not sufficient to reduce the uncertainty of the flux of CO2to below the threshold required to reveal climatic trends in CO2fluxes. This was done by iteratively subsampling the hourly CO2data set at various time intervals. We show that because of storm‐linked intraseasonal variability in the spring‐late summer, sampling intervals longer than 2 days alias the seasonal mean flux estimate above the required threshold. Moreover, the regional nature and long‐term trends in storm characteristics may be an important influence in the future role of the SO in the carbon‐climate system. fCO2and air‐sea flux of CO2strongly modulated by intraseasonal variability in the SOUncertainty of the mean seasonal or annual air‐sea flux is sensitive to sampling resolutionA sampling resolution <2 days is necessary in 30–40% of the SO to reduce the uncertainty to <10%