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Natural ecosystems are rarely structurally simple or functionally homogeneous. This is true for the complex coastal region of Magdalena Bay, Baja California Sur, Mexico, where the spatial variability in ecosystem fluxes from the Pacific coastal ocean, eutrophic lagoon, mangroves, and desert were studied. The Sky Arrow 650TCN environmental research aircraft proved to be an effective tool in characterizing land-atmosphere fluxes of energy, CO2, and water vapor across a heterogeneous landscape at the scale of 1 km. The aircraft was capable of discriminating fluxes from all ecosystem types, as well as between nearshore and coastal areas a few kilometers distant. Aircraft-derived average midday CO2 fluxes from the desert showed a slight uptake of -1.32 mol CO2 m(-2) s(-1), the coastal ocean also showed an uptake of -3.48 mol CO2 m(-2) s(-1), and the lagoon mangroves showed the highest uptake of -8.11 mol CO2 m(-2) s(-1). Additional simultaneous measurements of the normalized difference vegetation index (NDVI) allowed simple linear modeling of CO2 flux as a function of NDVI for the mangroves of the Magdalena Bay region. Aircraft approaches can, therefore, be instrumental in determining regional CO2 fluxes and can be pivotal in calculating and verifying ecosystem carbon sequestration regionally when coupled with satellite-derived products and ecosystem models.