This data set contains carbon flux measurements recorded by an aircraft at the Duke, Harvard, and Howland Forest sites during the summers of 2012-2014 as part of the Airborne Microwave Observatory of Subcanopy and Subsurface (AirMOSS) project. Frequent measurements of CO2 and H2O were obtained using a cavity ring down spectrometer on board the Airborne Laboratory for Atmospheric Research, operated by Purdue University. Estimates of surface CO2 flux, sensible and latent heat fluxes, their corresponding uncertainties, and average wind speed and direction are provided for each of the 26 flights.