The rare stable carbon isotope, 13C, has been used previously to partition CO2 fluxes into land and ocean components. Net ocean and land fluxes impose distinctive and predictable fractionation patterns upon the stable isotope ratio, making it an excellent tool for distinguishing between them. Historically, isotope constrained inverse methods for calculating CO2 surface fluxes—the ‘double deconvolution’—have disagreed with bottom-up ocean flux estimates. In this study, we use the double deconvolution framework, but add, as a constraint, independent estimates of time histories of ocean fluxes to the atmospheric observations of CO2 and 13CO2. We calculate timeseries of net land flux, total disequilibrium flux and terrestrial disequilibrium flux from 1991 to 2008 that are consistent with bottom-up net ocean fluxes. We investigate possible drivers of interannual variability in terrestrial disequilibrium flux, including terrestrial discrimination, and test the sensitivity of our results to those mechanisms. We find that C3 plant discrimination and shifts in the global composition of C3 and C4 vegetation are likely drivers of interannual variability in terrestrial disequilibrium flux, while contributions from heterotrophic respiration and disturbance anomalies are also possible.