Carbon dioxide flux measurements in ecosystem sciences are mostly conducted by eddy covariance technique or the closed chamber method. Also some comparisons have been performed. But there is a lack of detailed assessment of present differences and uncertainties. To determine underlying processes, a ten–day, side–by–side measurement of the net ecosystem exchange with both techniques was evaluated with regard to various atmospheric conditions during the diurnal cycle. It was found that, depending on the particular atmospheric condition, the chamber carbon dioxide flux was either: (i) equal to the carbon dioxide flux measured by the reference method eddy covariance, by day with well developed atmospheric turbulence, (ii) higher, in the afternoon in times of oasis effect, (iii) lower, predominantly at night while large coherent structure fluxes or high wind velocities prevailed, or, (iv) showed less variation in the flux pattern, at night while stable stratification was present. Due to lower chamber carbon dioxide fluxes at night, when respiration forms the net ecosystem exchange, and higher chamber carbon dioxide fluxes in the afternoon, when the ecosystem is still a net carbon sink, there are two complementary aspects resulting in an overestimation of the ecosystem sink capacity by the chamber of 40 % in this study.