Current estimates of biogenic carbon fluxes over North America based on top-down atmospheric inversions are subject to considerable uncertainty. This uncertainty stems to a large part from the uncertain prior fluxes estimates with the associated error covariances and approximations in the atmospheric transport models that link observed carbon dioxide mixing ratios with surface fluxes. Specifically, approximations in the representation of vertical mixing associated with atmospheric turbulence or convective transport and largely under-determined prior fluxes and their error structures significantly hamper our capacity to reliably estimate regional carbon fluxes. The Atmospheric Carbon and Transport – America (ACT-America) mission aims at reducing the uncertainties in inverse fluxes at the regional-scale by deploying airborne and ground-based platforms to characterize atmospheric greenhouse gas mixing ratios and the concurrent atmospheric dynamics. A skillful ensemble system was built to achieve the research goals of ACT-America. This ensemble system allows us to detangle the uncertainties from difference source and in turn to quantify the uncertainties in transport, fluxes, and boundary condition.