Convective turbulence within the atmospheric boundary layer (ABL) and movement of the ABL over the surface results in a large spatial (104–105 km2) integration of surface fluxes that affects the CO2 and water vapor mixing ratios. We apply quasi-equilibrium concepts for the terrestrial ABL to measurements of CO2 and water vapor made within the ABL from a tall tower (396 m) in Wisconsin. We suppose that CO2 and water vapor mixing ratios in the ABL approach an equilibrium on timescales longer than a day: a balance between the surface fluxes and the exchange with the free troposphere above. By using monthly averaged ABL-to-free-tropospheric water vapor differences and surface water vapor flux, realistic estimates of vertical velocity exchange with the free troposphere can be obtained. We then estimated the net surface flux of CO2 on a monthly basis for the year of 2000, using ABL-to-free-tropospheric CO2 differences, and our flux difference estimate of the vertical exchange. These ABL-scale estimates of net CO2 flux gave close agreement with eddy covariance measurements. Considering the large surface area which affects scalars in the ABL over synoptic timescales, the flux difference approach presented here could potentially provide regional-scale estimates of net CO2 flux.