The impact of the interannual variability (IAV) of atmospheric transport on atmospheric CO2 observations is often ignored in carbon cycle studies. We use 8 years of analyzed European Centre for Medium-Range Weather Forecasts (ECMWF) wind fields from 1985–1992 to demonstrate the effect of IAV of the circulation on modeled CO2 concentrations for fossil and biosphere CO2 sources. The wind fields are used to drive the Melbourne University Tracer Model. The modeled annual mean CO2 values at observing locations show little IAV in the fossil case. In the biosphere case the IAV of the annual mean is considerably larger, especially in the high northern latitudes. Simulated baseline selection using modeled radon concentrations does not reduce the IAV. In both cases, surface layer interhemispheric differences show small interannual variations indicating small changes in interhemispheric transport. Source fields from a mass balance inversion using 1985–1992 ECMWF winds are compared with those from inversions using a single year of winds repeated for each year of observations. We find differences in semi-hemispheric sources of up to 0.6 Gt C yr−1 at some times. However, 8 year mean sources show smaller differences, mostly less than 0.2 Gt C yr−1 at regional scales. This indicates that the variability in the circulation is a second order factor in determining the sources from inversion calculations.