It is well known that terrestrial photosynthesis and 13C discrimination vary in response to a number of environmental and biological factors such as atmospheric humidity and genotypic differences in stomatal regulation. Small changes in the global balance between diffusive conductances to CO2 and photosynthesis in C3 vegetation have the potential to influence the 13C budget of the atmosphere because these changes scale with the relatively large one-way gross primary production (GPP) flux. Over a period of days to years, this atmospheric isotopic forcing is damped by the return flux consisting mostly of respiration, Fire, and volatile organic carbon losses. Here we explore the magnitude of this class of isotopic disequilibria with an ecophysiological model (SiB2) and a double deconvolution inversion framework that includes time-varying discrimination for the period of 1981–1994. If the net land carbon sink and plant 13C discrimination covary on interannual timescales at the global scale, consistent with El Niño-induced drought stress causing a decline in global GPP and C3 discrimination, then less interannual variability in ocean and land net carbon exchange is required to explain atmospheric trends in δ13C and CO2 as compared with previous studies that assumed discrimination was invariant.