Brazilian Pantanal is the largest seasonal wetland in the world and it plays an important role in regulating the local and global water cycle and energy balance. The Pantanal landscape consists of a mosaic of temporary and permanent aquatic habitats, floodable and non-floodable pastures, and forests; however, patterns of energy exchange are poorly understood, especially for seasonally flooded forests. Thus, the main objective of this research was to assess the variability of evapotranspiration (ET) and to evaluate biophysical controls on ET for a seasonally flooded scrub-forest. We used eddy covariance to measure latent (LE) and sensible (H) heat fluxes and linked both micrometeorological and remote sensing data to assess the connection between water dynamics and phenology. Our data suggest that 72% of the net radiation (Rn) was consumed by LE + H, even during the dry season, indicating that trees can access deep water when surface water is limiting. The decoupling factor (0.63 ± 0.08) suggests that the canopy is decoupled from the atmosphere and ET is essentially sensitive to Rn. The patterns of ET and vapor pressure deficit suggest that ET was more dependent on the Rn received and less dependent on stomatal control, but still exhibited a strong relationship with biotic factors such as enhanced vegetation index (EVI), which is sensitive to seasonal variations in leaf area index and canopy cover. Stomatal limitations of this seasonally flooded forest appear to be minimal, even in the dry season, presumably due to the relatively high-water table, the ability of trees to acquire subsurface water, and the predominance of secondary species with high rates of leaf gas exchange. These data indicate that seasonally flooded tropical forests of the Pantanal are consistent sources of water vapor to the atmosphere even during seasonal drought.