Environmental observatory networks (EONs) are coordinated efforts to provide knowledge that ultimately delivers transformational ecological science from regional to global scales. We used ecosystem functional types (EFTs), a time-varying land surface classification, as an alternative way to characterize ecosystem functional heterogeneity based on carbon uptake dynamics. We assessed the representativeness of the eddy-covariance sites of AmeriFlux and NEON, and their combined core sites (i.e., sites with long-term support) across the conterminous United States (CONUS) based on: a) the number of different EFT categories (EFTmode) represented by each network, b) representativeness of the EFT inter-annual variability (EFTint; number of unique EFTs within each pixel during years 2001–2014), and c) the spatial representation of EFTmode and EFTint based on a maximum entropy approach (i.e., spatial functional heterogeneity). AmeriFlux represents 50% of all possible EFT categories, includes most of EFTint values (9 out of 14), and represents 55% of the spatial functional heterogeneity across CONUS. NEON represents 23% of all possible EFT categories, 7 out of 14 possible EFTint values, and 23% of the spatial functional heterogeneity across CONUS. The combined effort of AmeriFlux and NEON core sites represents 33% of all possible EFT categories, 7 out of 14 possible EFTint values, and 46% of the spatial functional heterogeneity across CONUS. We used the NEON ecoclimatic domains to summarize our results within a geographical context. The least represented NEON ecoclimatic domains were Desert Southwest, Southern Rockies and Colorado Plateau, Great Basin, Northern Plains, and Central Plains. Our results provide insights about the potential of AmeriFlux to address questions regarding decadal and inter-annual variability of ecosystem functional heterogeneity across CONUS.