The ongoing deforestation process in Amazonia has led to intensified forest fires in the region, particularly in Brazil, after more than a decade of effective forest conservation policy. This study aims to investigate the recovery of two mature sub‐montane ombrophile Amazonian forests affected by fire in terms of energy, water and carbon fluxes utilizing remote sensing (MODIS) and climate reanalysis data (GLDAS). These two forest plots, mainly composed of Manilkara spp. (Maçaranduba), Protium spp. (Breu) (∼30 m), Bertholletia excelsa (Castanheira) and Dinizia excelsa Ducke (Angelim‐Pedra) (∼50 m), occupy areas of 100.5 and 122.1 km2 and were subject to fire on the same day, on September 12, 2010. The fire significantly increased land surface temperature (0.8°C) and air temperature (1.2°C) in the forests over a 3 years interval. However, the forests showed an ability to recover their original states in terms of coupling between the carbon and water cycles comparing the 3‐year periods before and after the fires. Results from a wavelet analysis showed an intensification in annual and seasonal fluctuations, and in some cases (e.g., daily net radiation and evapotrasnspiration) sub‐annual fluctuation. We interpreted these changes to be consistent with overall intensification of the coupling of energy balance components and drivers imposed by climate and solar cycle seasonality, as well as faster time scale changes, consistent with a shift toward greater forest openness and consequent reduction in the interception of incoming solar radiation by the canopy.

• Large-scale eddy-covariance flux datasets need to be used with footprint-awareness • Using a fixed-extent target area across sites can bias model-data integration • Most sites do not represent the dominant land-cover type at a larger spatial extent • A representativeness index provides general guidance for site selection and data use Large datasets of greenhouse gas and energy surface-atmosphere fluxes measured with the eddy-covariance technique (e.g., FLUXNET2015, AmeriFlux BASE) are widely used to benchmark models and remote-sensing products. This study addresses one of the major challenges facing model-data integration: To what spatial extent do flux measurements taken at individual eddy-covariance sites reflect model- or satellite-based grid cells? We evaluate flux footprints—the temporally dynamic source areas that contribute to measured fluxes—and the representativeness of these footprints for target areas (e.g., within 250–3000 m radii around flux towers) that are often used in flux-data synthesis and modeling studies. We examine the land-cover composition and vegetation characteristics, represented here by the Enhanced Vegetation Index (EVI), in the flux footprints and target areas across 214 AmeriFlux sites, and evaluate potential biases as a consequence of the footprint-to-target-area mismatch. Monthly 80% footprint climatologies vary across sites and through time ranging four orders of magnitude from 10 3 to 10 7 m 2 due to the measurement heights, underlying vegetation- and ground-surface characteristics, wind directions, and turbulent state of the atmosphere. Few eddy-covariance sites are located in a truly homogeneous landscape. Thus, the common model-data integration approaches that use a fixed-extent target area across sites introduce biases on the order of 4%–20% for EVI and 6%–20% for the dominant land cover percentage. These biases are site-specific functions of measurement heights, target area extents, and land-surface characteristics. We advocate that flux datasets need to be used with footprint awareness, especially in research and applications that benchmark against models and data products with explicit spatial information. We propose a simple representativeness index based on our evaluations that can be used as a guide to identify site-periods suitable for specific applications and to provide general guidance for data use.