Abstract. Estimates of CO2 fluxes that are based on atmospheric data rely upon a meteorological model to simulate atmospheric CO2 transport. These models provide a quantitative link between surface fluxes of CO2 and atmospheric measurements taken downwind. Therefore, any errors in the meteorological model can propagate into atmospheric CO2 transport and ultimately bias the estimated CO2 fluxes. These errors, however, have traditionally been difficult to characterize. To examine the effects of CO2 transport errors on estimated CO2 fluxes, we use a global meteorological model-data assimilation system known as "CAM–LETKF" to quantify two aspects of the transport errors: error variances (standard deviations) and temporal error correlations. Furthermore, we develop two case studies. In the first case study, we examine the extent to which CO2 transport uncertainties can bias CO2 flux estimates. In particular, we use a common flux estimate known as CarbonTracker to discover the minimum hypothetical bias that can be detected above the CO2 transport uncertainties. In the second case study, we then investigate which meteorological conditions may contribute to month-long biases in modeled atmospheric transport. We estimate 6 hourly CO2 transport uncertainties in the model surface layer that range from 0.15 to 9.6 ppm (standard deviation), depending on location, and we estimate an average error decorrelation time of ∼2.3 days at existing CO2 observation sites. As a consequence of these uncertainties, we find that CarbonTracker CO2 fluxes would need to be biased by at least 29%, on average, before that bias were detectable at existing non-marine atmospheric CO2 observation sites. Furthermore, we find that persistent, bias-type errors in atmospheric transport are associated with consistent low net radiation, low energy boundary layer conditions. The meteorological model is not necessarily more uncertain in these conditions. Rather, the extent to which meteorological uncertainties manifest as persistent atmospheric transport biases appears to depend, at least in part, on the energy and stability of the boundary layer. Existing CO2 flux studies may be more likely to estimate inaccurate regional fluxes under those conditions.