Abstract. 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 CO2 at a given height above an ecosystem does not represent the true surface flux. Profile systems have been deployed to measure periodic storage of CO2 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, given that net storage over intervals exceeding 24 h is generally negligible, that these measurements are not particularly important. In this study, we used a 3-year record of net ecosystem exchange of CO2 and simultaneous measurements of CO2 storage to ascertain the relative contributions of turbulent CO2 flux, storage, and advection (calculated as a residual quantity) to the nocturnal CO2 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 CO2. 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 (u∗ filtering) of nocturnal flux correction were implemented in the absence of storage estimates. These biases were reduced to approximately 40–45 gC m−2 a−1 when the filter was applied over the entire diel period, but they were nonetheless large relative to quantifiable uncertainties in the data. Neglect of storage also distorted the relationships between the CO2 exchange processes (respiration and photosynthesis) and their key controls (light and temperature respectively). We conclude that the 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.