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A simple aerodynamic-variance method is proposed to fill gaps in continuous CO2 flux measurements in rainy conditions, when open-path analysers do not function. The method requires turbulent conditions (friction velocity greater than 0.1ms−1), and uses measurements of mean wind speed, and standard deviations of temperature and CO2 concentration fluctuations to complement, and at times replace, eddy-covariance measurements of friction velocity, sensible heat flux and CO2 flux. Friction velocity is estimated from the mean wind speed with a flux-gradient relationship modified for the roughness sublayer. Since normalised standard deviations do not follow Monin-Obukhov similarity theory in the roughness sublayer, a simple classification scheme according to the scalar turbulence scale was used. This scheme is shown to produce sensible heat and CO2 flux estimates that are well correlated with the measured values. [ABSTRACT FROM AUTHOR]