Using eddy covariance method, net ecosystem exchange (NEE) of CO 2 (F CO 2 ), H 2 O (LE), and sensible heat (H) can be approximated as the sum of eddy flux (F C ) and storage flux term (F S ). Depending on strength and distribution of sink/source of scalars and magnitude of vertical turbulence mixing, the rates of changes in scalars are different with height. In order to calculate F S accurately, the differences should be considered using scalar profile measurement. However, most of flux sites for agricultural lands in Asia do not operate profile system and estimate F S using single-level scalars from eddy covariance system under the assumption that the rates of changes in scalars are constant regardless of the height. In this study, we measured F C and F S of CO 2 , H 2 O, and air temperature (T a ) using eddy covariance and profile system (i.e., the multi-level measurement system in scalars from eddy covariance measurement height to the land surface) at the Chengmicheon farmland site in Korea (CFK) in order to quantify the differences between F S calculated by single-level measurements (F S_single i.e., F S from scalars measured by profile system only at eddy covariance system measurement height) and F S calculated by profile measurements and verify the errors of NEE caused by F S_single . The rate of change in CO 2 , H 2 O, and T a were varied with height depending on the magnitudes and distribution of sink and source and the stability in the atmospheric boundary layer. Thus, F S_single underestimated or overestimated F S (especially 21% underestimation in F S of CO 2 around sunrise and sunset (0430-0800 h and 1630-2000 h)). For F CO 2 , the errors in F S_single generated 3% and 2% underestimation of F CO 2 during nighttime (2030-0400 h) and around sunrise and sunset, respectively. In the process of nighttime correction and partitioning of F CO 2 , these differences would cause an underestimation in carbon balance at the rice paddy. In contrast, there were little differences at the errors in LE and H caused by the error in F S_single , irrespective of time.