We report the characteristics of the mixing ratios and fluxes of atmospheric carbon dioxide, observed in the period from July 2015 to December 2019. Measurements were noted for three different levels (60 m, 140 m, and 300 m above ground level (a.g.l.)) on a very tall (~300 m) tower in the Boseong Standard Weather Observatory (BSWO), located at the center of barley–rice double-crop fields in Boseong-gun, Jeolla-do, South Korea. The averaged CO2 mixing ratios show 420.7 ± 18.8 (60 m), 410.9 ± 16.7 (140 m) and 403.4 ± 16.7 ppm (300 m). The mixing ratios measured at the 140-m and 300-m heights display a typical seasonal pattern that is lower in the summer due to vegetation uptake and higher in the winter due to plant decaying combined with fossil-fuel emissions, but those at 60 m presented higher values in the spring and autumn, mainly owing to agricultural activities. During the study period, the averaged CO2 fluxes are −0.28 ± 8.81 (60 m), 0.34 ± 8.08 (140 m), and 0.79 ± 9.08 μmol m-2 s-1 (300 m). The monthly averaged fluxes show two dominant negative peaks, one in April and another in August, mainly caused by CO2 uptake during the barley and rice growing periods, respectively. The fluxes represent a strong correlation between daytime solar radiation and photosynthesis and between nighttime air temperatures and respiration. Directional analysis of the fluxes revealed dominant anthropogenic CO2 sources from not only the main industrial areas in the NE directions using geographic information system (GIS), but also from the aquaculture industry in the SE. We compare our measured CO2 fluxes (top-down) with a few bottom-up emissions datasets, which reveal an underestimation of the range from 31% to 69% within the footprint areas. The application of direct measurements of CO2 fluxes, combined with estimation of potential vicinity sources, can be a useful tool to detect local unknown or missing sources and supplement the gap between top-down and bottom-up approaches.