Interannual and seasonal variations in atmospheric transport to a measuring site in western Siberia were studied using three-dimensional 5-day back-trajectories. We identified large differences in transport between summer and winter, but also some differences between the years. Westerly flow was dominating during winter, whereas the transport in summer also had a contribution from the high Arctic and central Siberia. Cluster analysis was applied to the trajectory data to determine systematically to what degree different atmospheric flow patterns influence the variability of the atmospheric CO2. We found that during July, the short-term variability in CO2 was primarily determined by the interplay between planetary boundary layer dynamics and surface fluxes in the region within tens to one hundred kilometers from the measuring site. The weaker biogenic fluxes during winter, resulted in mixing ratios more clearly influenced by long-range transport of CO2. However, the highest CO2 concentrations were not associated with westerly winds reflecting transport of polluted air from Europe but periods characterized by stagnant flow conditions. It was suggested that these high mixing ratios were due to respired CO2 accumulated in the lowest one hundred meters of the atmosphere. The mean duration of the identified flow patterns was about two days, implying a sampling frequency not less than every other day in order to monitor variations in atmospheric CO2 due to air mass changes. This study demonstrates that the flux footprint of a site is variable which must be considered when making comparisons between different seasons or years for a measurement location.