Variations of atmospheric CO2 at regional scales are becoming increasingly important in understanding regional carbon budgets, yet the processes that drive them remain relatively unexplored. A simulation was conducted to test a coupled biosphere-atmospheric model (SiB2-RAMS), by comparing with measurements made at the WLEF-TV tower in Wisconsin, and to investigate some of the mechanisms leading to CO2 variability, both on local and regional scales. The simulation was run for a 5-day period from 26 to 30 July 1997. Multiple nested grids were employed, which enabled mesoscale features to be simulated and which resolved small-scale features in the vicinity of the WLEF tower. In many respects the model was successful at simulating observed meteorological variables and CO2 fluxes and concentrations. The two most significant deficiencies were that excessive nighttime cooling occurred on two of the nights and that late afternoon uptake of CO2 was larger than observed. Results of the simulation suggest that in addition to biological processes causing variations in CO2 concentrations at the WLEF site other factors, such as small nearby lakes, turbulence induced by vertical wind shear, boundary layer thermals, and clouds, also had significant impacts. These factors add to the difficulty of interpreting CO2 measurements. Regional-scale patterns of CO2 variability caused by meteorological processes were also identified. Katabatic winds had a significant effect by causing respired CO2 to pool in valleys and along the shores of the Great Lakes during the night. Furthermore, a large diurnal cycle of CO2 concentration occurred over the lakes, which appeared to be mainly due to the combined action of katabatic winds, ambient winds, and the lake breeze circulation. These results suggest that meteorological processes associated with the complex terrain in this region leads to substantial CO2 advection. Therefore meteorological as well as biological processes are likely to be important causes of regional-scale CO2 variability in the Great Lakes region. A sensitivity test conducted to examine the differences between using a turbulent kinetic energy based subgrid-scale scheme versus a deformation-type subgrid-scale scheme showed advantages and disadvantages to both approaches. Our results suggest that continuous records of CO2 variability measured over heterogeneous continental regions must be interpreted with caution because of the impact of mesoscale circulations on the concentration time series.