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Water stress may greatly limit plant functionality and growth. Stomatal closure and consequently reduced transpiration are considered as early and sensitive plant responses to drought and salinity stress. An important consequence of stomatal closure under water stress is the rise of leaf temperature (Tleaf), yet Tleaf is not only fluctuating with stomatal closure. It is regulated by several plant parameters and environmental factors. Thermal imaging and different stress indices, incorporating actual leaf/crop temperature and reference temperatures, were developed in previous studies toward normalizing for effects unassociated to water stress on Tleaf, aiming at a more efficient water stress assessment. The concept of stress indices has not been extensively studied on the model plant Arabidopsis thaliana. Therefore, the aim of this study was to examine the different indices employed in previous studies in assessing rosette transpiration rate (E) in Arabidopsis plants grown under two different light environments and subjected to salinity. After salinity imposition, E was gravimetrically quantified, and thermal imaging was employed to quantify rosette (Trosette) and artificial reference temperature (Twet,Tdry). Trosette and several water stress indices were tested for their relation to E. Among the microclimatic growth conditions tested, RWSI1 ([Trosette − Twet]/[Tdry − Twet]) and RWSI2 ([Tdry − Trosette]/[Tdry − Twet]) were well linearly‐related to E, irrespective of the light environment, while the sole use of either Twet or Tdry in different combinations with Trosette returned less accurate results. This study provides evidence that selected combinations of Trosette, Tdry, and Twet can be utilized to assess E under water stress irrespective of the light environment. [ABSTRACT FROM AUTHOR]