We performed an atmospheric inversion of the CO2 fluxes over Iowa and the surrounding states, from June to December 2007, at 20 km resolution and weekly timescale. Eight concentration towers were used to constrain the carbon balance in a 1000×1000 km2 domain in this agricultural region of the US upper midwest. The CO2 concentrations of the boundaries derived from CarbonTracker were adjusted to match direct observations from aircraft profiles around the domain. The regional carbon balance ends up with a sink of 183 Tg C± 35 Tg C over the area for the period June–December, 2007. Potential bias from incorrect boundary conditions of about 0.55 ppm over the 7 months was corrected using mixing ratios from four different aircraft profile sites operated at a weekly time scale, acting as an additional source of uncertainty of 24 Tg C. We used two different prior flux estimates, the SiBCrop model and the inverse flux product from the CarbonTracker system. We show that inverse flux estimates using both priors converge to similar posterior estimates (20 Tg C difference), in our reference inversion, but some spatial structures from the prior fluxes remain in the posterior fluxes, revealing the importance of the prior flux resolution and distribution despite the large amount of atmospheric data available. The retrieved fluxes were compared to eddy flux towers in the corn and grassland areas, revealing an improvement in the seasonal cycles between the two compared to the prior fluxes, despite large absolute differences due to representation errors. The uncertainty of 34 Tg C (or 34 g C m2 ) was derived from the posterior uncertainty obtained with our reference inversion of about 25 to 30 Tg C and from sensitivity tests of the assumptions made in the inverse system, for a mean carbon balance over the region of −183 Tg C, slightly weaker than the reference. Because of the potential large bias (∼24 Tg C in this case) due to choice of background conditions, proportional to the surface but not to the regional flux, this methodology seems limited to regions with a large signal (sink or source), unless additional observations can be used to constrain the boundary inflow.