Stable CO2 isotope measurements are increasingly used to partition the net CO2 exchange between terrestrial ecosystems and the atmosphere in terms of nonfoliar respiration (FR) and net photosynthesis (FA) in order to better understand the variations of this exchange. However, the accuracy of the partitioning strongly depends on the isotopic disequilibrium between these two gross fluxes, and a rigorous estimation of the errors on FA and FR is needed. In this study, we account for and propagate uncertainties on all terms in the mass balance and isotopic mass balance equations for CO2 in order to get accurate estimates of the errors on FA and FR. We apply our method to a maritime pine forest in the southwest of France. Nighttime Keeling plots are used to estimate the 13C and 18O isotopic signature of FR (δR), and for both isotopes the a priori uncertainty associated with this term is estimated to be around 2? at our site. Using δ13C-CO2 and 2> measurements, we then show that the uncertainty on instantaneous values of FA and FR can be as large as 4 ¿mol m-2 s-1. Even if we could get more accurate estimates of the net CO2 flux, the isoflux, and the isotopic signatures of FA and FR, this uncertainty would not be significantly reduced because the isotopic disequilibrium between FA and FR is too small, around 2--3?. With δ18O-CO2 and 2> measurements the uncertainty associated with the gross fluxes lies also around 4 ¿mol m-2 s-1 but could be dramatically reduced if we were able to get more accurate estimates of the CO18O isoflux and the associated discrimination during photosynthesis. This is because the isotopic disequilibrium between FA and FR is large, of the order of 12--17?. The isotopic disequilibrium between FA and FR and the uncertainty on δR vary among ecosystems and over the year. Our approach should help to choose the best strategy to study the carbon budget of a given ecosystem using stable isotopes.