Considering the feedback in radiation, temperature, and soil moisture with alterations in rainfall patterns, the influence of the changing monsoon on Net Ecosystem CO₂ Exchange (NEE) can be critical to the estimation of carbon balance in Asia. In this paper, we examined CO₂ fluxes measured by the eddy covariance method from 2004 to 2008 in two major ecosystems in the KoFlux sites in Korea, i.e., the Gwangneung Deciduous forest (GDK) and the Haenam Farmland (HFK). Our objectives were to identify the repeatability of the mid-season depression of NEE encountered at the two sites based on the single-year observation, and to further scrutinize its cause, effect, and interannual variability by using multi-year observations. In both GDK and HFK sites, the mid-season depression of NEE was reproduced each year but with different timing, magnitude, and mechanism. At the GDK site, a predominant factor causing the mid-season depression was a decreased solar radiation and the consequent reduction in Gross Primary Productivity (GPP) during the summer monsoon period. At the HFK site, however, the monsoonal effect was less pronounced and the apparent mid-season depression was mainly a result of the management practices such as cultivation of spring barley and rice transplantation. Other flux observation sites in East Asia also showed a decline in radiation but with a lesser degree during the monsoon season, resulting in less pronounced depression in NEE. In our study, the observed depressions in NEE caused both GDK and HFK sites to become a weaker carbon sink or even a source in the middle of the growing season. On average, the GDK site (with maximum leaf area index of ~5) was a weak carbon sink with NEE of −84 gC m⁻² y⁻¹. Despite about 20% larger GPP (of 1321 gC m⁻²y⁻¹) in comparison with the GDK site, the HFK site (with maximum leaf area index of 3–4) was a weaker carbon sink with NEE of −58 gC m⁻² y⁻¹ because of greater ecosystem respiration (of 1263 gC m⁻² y⁻¹). These NEE values were near the low end of the ranges reported in the literature for similar ecosystems in mid-latitudes. With the projected trends of the extended length of monsoon with more intensive rainfalls in East Asia, the observed delicate coupling between carbon and hydrological cycles may turn these key ecosystems into carbon neutral.