While the eddy covariance technique has become an important technique for estimating long-term ecosystem carbon balance, under certain conditions the measured turbulent flux of carbon at a given height above an ecosystem does not represent the true surface flux. Profile systems have been deployed to measure periodic storage of carbon below the measurement height, but have not been widely adopted. This is most likely due to the additional expense and complexity, and possibly also the perception

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... given that net storage over intervals exceeding 24 hours is generally negligible – that these measurements are not particularly important. In this study, we used a three year record of net ecosystem exchange of carbon and simultaneous measurements of carbon storage to ascertain the relative contributions of turbulent carbon flux, storage and advection (calculated as a residual quantity) to the nocturnal carbon balance, and to quantify the effect of neglecting storage. The conditions at the site are in relative terms highly favourable for eddy covariance measurements, yet we found a substantial contribution (~ 40 %) of advection to nocturnal turbulent flux underestimation. The most likely mechanism for advection is cooling-induced drainage flows, the effects of which were observed in the storage measurements. The remaining ~ 60 % of flux underestimation was due to storage of carbon. We also showed that substantial underestimation of carbon uptake (approximately 80 gC m^−2 a^−1, or 25 % of annual carbon uptake) arose when standard methods of nocturnal flux correction were implemented in the absence of storage estimates. These biases were much larger than quantifiable uncertainties in the data. Neglect of storage also distorted the relationships between the carbon exchange processes (respiration and photosynthesis) and their key controls (light and temperature, respectively). We conclude that addition of storage measurements to eddy covariance sites with all but the lowest measurement heights should be a high priority for the flux measurement community.