Savannas are among the most variable, complex and extensive biomes on Earth, supporting livestock and rural livelihoods. These water-limited ecosystems are highly sensitive to changes in both climatic conditions, and land-use/management practices. The integration of Earth Observation (EO) data into process-based land models enables monitoring ecosystems status, improving its management and conservation. In this paper, the use of the Two-Source Energy Balance (TSEB) model for estimating surface energy fluxes is evaluated over a Mediterranean oak savanna (dehesa). A detailed analysis of TSEB formulation is conducted, evaluating how the vegetation architecture (multiple layers) affects the roughness parameters and wind profile, as well as the reliability of EO data to estimate the ecosystem parameters. The results suggest that the assumption of a constant oak leaf area index is acceptable for the purposes of the study and the use of spectral information to derive vegetation indices is sufficiently accurate, although green fraction index may not reflect phenological conditions during the dry period. Although the hypothesis for a separate wind speed extinction coefficient for each layer is partially addressed, the results show that taking a single oak coefficient is more precise than using bulk system coefficient. The accuracy of energy flux estimations, with an adjusted Priestley–Taylor coefficient (0.9) reflecting the conservative water-use tendencies of this semiarid vegetation and a roughness length formulation which integrates tree structure and the low fractional cover, is considered adequate for monitoring the ecosystem water use (RMSD ~40 W m−2).