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One of the dominant uncertainties in inverse estimates of regional CO₂ surface-atmosphere fluxes is related to model errors in vertical transport within the planetary boundary layer (PBL). In this study we present the results from a synthetic experiment using the atmospheric model WRF-VPRM to realistically simulate transport of CO₂ for large parts of the European continent at 10 km spatial resolution. To elucidate the impact of vertical mixing error on modeled CO₂ mixing ratios we simulated a month during the growing season (August 2006) with different commonly used parameterizations of the PBL (Mellor-Yamada-Janjić (MYJ) and Yonsei-University (YSU) scheme). To isolate the effect of transport errors we prescribed the same CO₂ surface fluxes for both simulations. Differences in simulated CO₂ mixing ratios (model bias) were on the order of 3 ppm during daytime with larger values at night. We present a simple method to reduce this bias by 70–80% when the true height of the mixed layer is known.