Natural ecosystems are rarely structurally or functionally homogeneous. This is true for the complex coastal regions of Magdalena Bay, Baja California Sur, Mexico, and the Barrow Peninsula on the Arctic Coastal Plain of Alaska. The coastal region of Magdalena Bay is comprised of the Pacific coastal ocean, eutrophic lagoon, mangroves, and desert ecosystems all adjacent and within a few kilometers, while the Barrow Peninsula is a mosaic of small ponds, thaw lakes, different aged vegetated thaw-lake basins (VDTLBs) and interstitial tundra which have been dynamically formed by both short- and long-term processes. We used a combination of tower- and small environmental research aircraft (SERA)-based eddy covariance measurements to characterize the spatial and temporal patterns of CO_, latent, and sensible heat fluxes along with MODIS NDVI, and land surface information, to scale the SERA-based CO_ fluxes up to the regional scale. In the first part of this research, the spatial variability in ecosystem fluxes from the Pacific coastal ocean, eutrophic lagoon, mangroves, and desert areas of northern Magdalena Bay were studied. SERA-derived average midday CO_ fluxes from the desert showed a slight uptake of -1.32 _mol CO_ m__ s__, the coastal ocean also showed uptake of -3.48 _mol CO_ m__ s__, and the lagoon mangroves showed the highest uptake of -8.11 _mol CO_ m__ s___ Additional simultaneous measurements of NDVI allowed simple linear modeling of CO_ flux as a function of NDVI for the mangroves of the Magdalena Bay region. In the second part of this research, the spatial variability of ecosystem fluxes across the 1802 km_ Barrow Peninsula region was studied. During typical 2006 summer conditions, the midday hourly CO_ flux over the region was -2.04 x 10_ kgCO_ hr__. The CO_ fluxes among the interstitial tundra, Ancient and Old VDTLBs, as well as between the Medium and Young VDTLBs were not significantly different. Combined, the interstitial tundra and Old and Ancient VDTLBs, represent ~67% of the Barrow Peninsula surface area, accounting for ~59% of the regional flux signal. Though the Medium and Young VDTLBs represent ~11% of the surface area, they account for a large portion, ~35%, of the total regional flux. The remaining ~22% of the surface area are lakes and contributed the remaining ~6% of the total regional flux. Previous studies treated vegetated areas of the region as a single surface type with measurements from a few study sites; doing so could underestimate the regional flux by ~22%. The San Diego State University Sky Arrow 650TCN Environmental Research Aircraft proved to be an effective tool in characterizing land-atmosphere fluxes of energy, CO_ and water across heterogeneous landscapes at the scale of 1 km, and was capable of discriminating fluxes from the various ecosystem and land surface types a few kilometers distant. Here, we demonstrate that SERA-based approaches have the ability to cover large spatial scales while measuring the turbulent fluxes across a number of surfaces and combined with ground- and satellite-based measurements provide a valuable tool for both scaling and validation of regional- scale fluxes.