This data set provides Level 4 daily estimates of Net Ecosystem Exchange (NEE) of CO2 at a spatial resolution of 30 arc-seconds (~1 km) for seven of the sites covered by the Airborne Microwave Observatory of Subcanopy and Subsurface (AirMOSS) flights, each site spanning ~2500 km2. The daily NEE estimates are generally available from October 2012 through October 2014, although the exact time ranges vary by site. The AirMOSS L4 daily NEE were produced by the Ecosystem Demography Biosphere Model (ED2) augmented by the AirMOSS-derived L2/3 root zone soil moisture data as an additional input. The AirMOSS soil moisture data were used to estimate the sensitivity of carbon fluxes to soil moisture and to diagnose and improve estimation and prediction of NEE by constraining the model's predictions of soil moisture and its impact on above- and below-ground fluxes.