At the ecosystem and global scales, the carbon isotopic compositions of $CO_2$ and methane exchanged between the biosphere and the atmosphere (${delta}_N$ and ${delta}_M$, respectively) have been used to partition net fluxes of $CO_2$ and methane into the source and sink terms. The temporal variations of ${delta}_N$ and ${delta}_M$ were investigated at the same time in a Japanese rice paddy by combining stable isotopes and concentration measurements within and above the canopy. There were close agreements between the measured concentrations and the ${delta}^{13}C$ values of $CO_2$ and methane on both temporal and spatial scales. While atmospheric stability and environmental parameters influencing photosynthetic assimilation were the major controls on variability of [$CO_2$] and ${delta}^{13}CO_2$, atmospheric stability was the predominant factor for driving changes in [$CH_4$] and ${delta}^{13}CH_4$ profiles. We also found strong linear relationships between the measured isotopic compositions and the inverse of concentrations over the time spans of day, night, and whole day. The ${delta}_N$ values determined on the two days contrasting in environmental conditions revealed that the relative contributions of photosynthetic assimilation and ecosystem respiration to the total $CO_2$ exchange did not change significantly. In contrast, the ${delta}_M$ values showed a marked difference between the sampling dates, reflecting a transpiration-induced shift in methane transport.