Abstract. The capture of carbon by aquatic ecosystems and its sequestration in sediments has been studied as a potential method for mitigating the adverse effects of climate change. However, the evaluation of in situ atmospheric CO₂ fluxes is challenging because of the difficulty in making continuous measurements over areas and for periods of time that are environmentally relevant. The eddy covariance (EC) method is the most promising approach to address this concern with the measurement of atmospheric CO₂ fluxes. However, methods to process the data obtained from EC measurements are still being developed, and the estimated air-water CO₂ fluxes have large uncertainties and differ from those obtained using conventional methods. In this study, we improved the post-processing procedure for the EC method to reduce the uncertainty in the measured air-water CO₂ fluxes. Our new procedure efficiently removes erroneous fluxes using a combination of filtering methods based on the received signal strength indicator of the EC sensor, the normalized standard deviation of atmospheric CO₂ and water vapor concentrations, and a high-pass filter. Our procedure is easier to apply to EC measurements than existing correction methods. The improved EC fluxes did not always agree with those obtained by using conventional methods (e.g., the bulk formula method), but this difference was attributable to the difference of measurement heights and the effect on the measured fluxes of the physical and biological properties of the water surface (e.g., the presence of vegetation on the water surface and the temperature gradient in the overlying atmospheric layer). Because the measurement height and the spatiotemporal scales of the flux measurement depend on the applied method, it is essential to select the appropriate method for studies related to CO₂ fluxes and to the determination of ecosystem-atmospheric CO₂ interactions and the role of aquatic ecosystems in mitigating the adverse effects of climate change.