The exchange of carbon between the Earth’s atmosphere and biosphere influences the atmospheric abundances of carbon dioxide (CO2) and methane (CH4). Airborne eddy covariance (EC) can quantify surface-atmosphere exchange from landscape-to-regional scales, offering a unique perspective on carbon cycle dynamics.Weuse extensive airborne measurements to quantify fluxes of sensible heat, latent heat, CO2, and CH4 across multiple ecosystems in the Mid-Atlantic region during September 2016 and May 2017. In conjunction with footprint analysis and land cover information, we use the airborne dataset to explore the effects of landscape heterogeneity on measured fluxes. Our results demonstrate large variability in CO2 uptake over mixed agricultural and forested sites, with fluxes ranging from−3.4 ± 0.7 to −11.5 ± 1.6 μmol m−2 s−1 for croplands and −9.1 ± 1.5 to −22.7 ± 3.2 μmol m−2 s−1 for forests. We also report substantial CH4 emissions of 32.3 ± 17.0 to 76.1 ± 29.4 nmol m−2 s−1 from a brackish herbaceous wetland and 58.4 ± 12.0 to 181.2 ± 36.8 nmol m−2 s−1 from a freshwater forested wetland. Comparison of ecosystem-specific aircraft observations with measurements from EC flux towers along the flight path demonstrate that towers capture ∼30%–75% of the regional variability in ecosystem fluxes. Diel patterns measured at the tower sites suggest that peak, midday flux measurements from aircraft accurately predict net daily CO2 exchange. We discuss next steps in applying airborne observations to evaluate bottom-up flux models and improve understanding of the biophysical processes that drive carbon exchange from landscape to regional scales.