<p>Eddy-covariance (EC) is a widely used method for measuring ecosystem-scale fluxes of various gases. The sensor placement height is typically constrained by the canopy height and area of interest size. We studied the carbon dioxide fluxes over a hemiboreal mixed forest with two EC measurement systems located at 30 m and 70 m. The lower system NEE (NEE30) values were more positive (smaller sink or higher source) than the NEE of the higher one (NEE70), but this difference was prevalent in low light conditions and in May–November of all studied years. The nighttime and early morning difference (ΔNEE) increased with wind speed until ~2 m s<sup>-1</sup> and friction velocity until ~0.35 m s<sup>-1</sup> and linearly decreased after. ΔNEE was irregularly distributed over the wind direction sectors with high values overlapping the directions of South-East and South-West guy wire tunnels. Moreover, the shape of the NEE30 seasonal cycle was closer to that of a clear-cut area, and the difference between the systems increased with air temperature. The forest under study varied between a weak net sink and a strong net source on the annual scale. Directional heterogeneity correction shifted the annual NEE towards more negative values, but neither removed the difference between the systems nor changed the shape of the seasonal cycle. More studies are needed to assess the impact of clearcutting on the carbon accumulation under the measurement point.</p>