Even moderately complex topography can lead to significant horizontal and vertical advection and a consequent underestimation of nocturnal CO2 effluxes derived from eddy covariance measurements on a single tower. The standard approach to select nighttime eddy flux data uses a threshold in friction velocity to exclude periods when advection is important but this is problematic in situations where turbulence is intermittent. van Gorsel et al. [van Gorsel, E., Leuning, R., Cleugh, H.A., Keith, H., Suni, T., 2007. Nocturnal carbon efflux: reconciliation of eddy covariance and chamber measurements using an alternative to the u*-threshold filtering technique. Tellus 59B, 397–403] have developed an alternative method that estimates the CO2 flux from the maximum of the eddy flux plus change in storage term in the period after sunset when stable stratification develops. During this time the advection terms do not contribute significantly to the mass balance of the air layer below the eddy flux instruments at the Tumbarumba flux station (SE Australia). Advection dominates only later in the night, following the development of large horizontal and vertical gradients of CO2. As net nighttime and daytime fluxes are often of similar magnitude but opposite in sign, underestimation of respiration can lead to large errors in annual ecosystem carbon budgets.