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Abstract Agricultural activity is a significant source of greenhouse gas emissions. The fertilizer production process emits N₂O, CO₂, and CH₄, and fertilized croplands emit N₂O. We present continuous airborne observations of these trace gases in the Lower Mississippi River Basin to quantify emissions from both fertilizer plants and croplands during the early growing season. Observed hourly emission rates from two fertilizer plants are compared with reported inventory values, showing agreement for N₂O and CO₂emissions but large underestimation in reported CH₄emissions by up to a factor of 100. These CH₄emissions are consistent with loss rates of 0.6–1.2%. We quantify regional emission fluxes (100 km) of N₂O using the airborne mass balance technique, a first application for N₂O, and explore linkages to controlling processes. Finally, we demonstrate the ability to use airborne measurements to distinguish N₂O emission differences between neighboring fields, determining we can distinguish different emission behaviors of regions on the order of 2.5 km²with emissions differences of approximately 0.026μmol m⁻²s⁻¹. This suggests airborne approaches such as outlined here could be used to evaluate the impact of different agricultural practices at critical field‐size spatial scales.