Imperfect representation of vertical mixing near the surface in atmospheric transport models leads to uncertainties in modelled tracer mixing ratios. When using the atmosphere as an integrator to derive surface-atmosphere exchange from mixing ratio observations made in the atmospheric boundary layer, this uncertainty has to be quantified and taken into account. A comparison between radiosonde-derived mixed layer heights and mixed layer heights derived from ECMWF meteorological data during May–June 2005 in Europe revealed random discrepancies of about 40% for the daytime with insignificant bias errors, and much larger values approaching 100% for nocturnal mixed layers with bias errors also exceeding 50%. The Stochastic Time Inverted Lagrangian Transport (STILT) model was used to propagate this uncertainty into CO<sub>2</sub> mixing ratio uncertainties, accounting for spatial and temporal error covariance. Average values of 3 ppm were found for the 2 month period, indicating that this represents a large fraction of the overall uncertainty. A pseudo data experiment shows that the error propagation with STILT avoids biases in flux retrievals when applied in inversions. The results indicate that transport models driven by current generation data assimilation for meteorological fields is by far not sufficient for inversions of continental mixing ratio data. As a solution we suggest the use of better, higher resolution atmospheric models, and a modification of the overall sampling strategy.