One of the objectives of many studies conducted by breeding programs is to characterize and select rootstocks well-adapted to drought conditions. In recent years, field high-throughput phenotyping methods have been developed to characterize plant traits and to identify the most water use efficient varieties and rootstocks. However, none of these studies have been able to quantify the behavior of crop evapotranspiration in almond rootstocks under different water regimes. In this study, remote sensing phenotyping methods were used to assess the evapotranspiration of almond cv. “Marinada” grafted onto a rootstock collection. In particular, the two-source energy balance and Shuttleworth and Wallace models were used to, respectively, estimate the actual and potential evapotranspiration of almonds grafted onto 10 rootstock under three different irrigation treatments. For this purpose, three flights were conducted during the 2018 and 2019 growing seasons with an aircraft equipped with a thermal and multispectral camera. Stem water potential (Ψstem) was also measured concomitant to image acquisition. Biophysical traits of the vegetation were firstly assessed through photogrammetry techniques, spectral vegetation indices and the radiative transfer model PROSAIL. The estimates of canopy height, leaf area index and daily fraction of intercepted radiation had root mean square errors of 0.57 m, 0.24 m m–1 and 0.07%, respectively. Findings of this study showed significant differences between rootstocks in all of the evaluated parameters. Cadaman® and Garnem® had the highest canopy vigor traits, evapotranspiration, Ψstem and kernel yield. In contrast, Rootpac® 20 and Rootpac® R had the lowest values of the same parameters, suggesting that this was due to an incompatibility between plum-almond species or to a lower water absorption capability of the rooting system. Among the rootstocks with medium canopy vigor, Adesoto and IRTA 1 had a lower evapotranspiration than Rootpac® 40 and Ishtara®. Water productivity (WP) (kg kernel/mm water evapotranspired) tended to decrease with Ψstem, mainly in 2018. Cadaman® and Garnem® had the highest WP, followed by INRA GF-677, IRTA 1, IRTA 2, and Rootpac® 40. Despite the low Ψstem of Rootpac® R, the WP of this rootstock was also high.