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As the global climate continues to change, plants will increasingly experience abiotic stress(es). Stomata on leaf surfaces are the gatekeepers to plant interiors, regulating gaseous exchanges that are crucial for both photosynthesis and outward water release. To optimise future crop productivity, accurate modelling of how stomata govern plant–environment interactions will be crucial. Here, we synergise optical and thermal imaging data to improve modelled transpiration estimates during water and/or nutrient stress (where leaf N is reduced). By utilising hyperspectral data and partial least squares regression analysis of six plant traits and fluxes in wheat (Triticum aestivum), we develop a new spectral vegetation index; the Combined Nitrogen and Drought Index (CNDI), which can be used to detect both water stress and/or nitrogen deficiency. Upon full stomatal closure during drought, CNDI shows a strong relationship with leaf water content (r2 = 0.70), with confounding changes in leaf biochemistry. By incorporating CNDI transformed with a sigmoid function into thermal‐based transpiration modelling, we have increased the accuracy of modelling water fluxes during abiotic stress. These findings demonstrate the potential of using combined optical and thermal remote sensing‐based modelling approaches to dynamically model water fluxes to improve both agricultural water usage and yields. Summary statement: Using both trait and flux measurements, we have designed a new vegetation index: the combined nitrogen and drought index. This index describes changes in leaf optical properties during nitrogen and or drought stress that can be used to improve transpiration modelling during abiotic stress. [ABSTRACT FROM AUTHOR]