Stable isotopes of CO2 contain unique information on the biological and physical processes that exchange CO2 between terrestrial ecosystems and the atmosphere. In this study, we developed an integrated modeling system to simulate dynamics of stable carbon isotope of CO2, as well as moisture, energy, and momentum, between a boreal forest ecosystem and the atmosphere, as well as their transport/mixing processes through the convective boundary layer (CBL), using remotely sensed surface parameters to characterize the surface heterogeneity. It has the following characteristics: (i) it accounts for the influences of the CBL turbulent mixing and entrainment of the air aloft; (ii) it scales individual leaf-level photosynthetic discrimination up to the whole canopy (Δcanopy) through the separation of sunlit and shaded leaf groups; (iii) it has the capacity to examine the detailed interrelationships among plant water-use efficiency, isotope discrimination, and vapor pressure deficit; and (iv) it has the potential to investigate how an ecosystem discriminates against 13C at various time and spatial scales. The monthly mean isotopic signatures of ecosystem respiration (i.e. δ13CR) used for isotope flux calculation are retrieved from the nighttime flask data from the intensive campaigns (1998–2000) at 20 m level on Fraserdale tower, and the data from the growing season in 1999 are used for model validation. Both the simulated CO2 mixing ratio and δ13C of CO2 at the 20 m level agreed with the measurements well in different phases of the growing season. On a diurnal basis, the greatest photosynthetic discrimination at canopy level (i.e. Δcanopy) occurred early morning and late afternoon with a varying range of 10–26‰. The diurnal variability of Δcanopy was also associated with the phases of growing season and meteorological variables. The annual mean Δcanopy in 1999 was computed to be 19.58‰. The monthly averages of Δcanopy varied between 18.55‰ and 20.84‰ with a seasonal peak during the middle growing season. Because of the strong opposing influences of respired and photosynthetic fluxes on forest air (both CO2 and 13CO2) on both the diurnal and seasonal time scales, CO2 was consistently enriched with the heavier 13C isotope (less negative δ13C) from July to October and depleted during the remaining months, whereas on a diurnal basis, CO2 was enriched with the heavier 13C in the late afternoon and depleted in early morning. For the year 1999, the model results reveal that the boreal ecosystem in the vicinity of Fraserdale tower was a small sink with net uptake of 29.07 g 12C m−2 yr−1 and 0.34 g 13C m−2 yr−1.