Due to the physiological connection with photosynthesis, sun-induced chlorophyll fluorescence (SIF) provides a promising indicator of vegetation physiological changes caused by environmental stress (e.g. water deficiency). SIF response to crop physiological alterations under water stress is complicated by concurrent non-physiological changes. The non-physiological variation stems from crop structure, leaf optical traits (i.e. pigments, leaf water content, and dry matter), and sun-target geometry. This study aims to disentangle the physiological effect from the non-physiological effect on SIF variations caused by water stress, providing more direct insights into the mechanism of SIF response to stress. We parameterized the radiative transfer model (RTM) SCOPE with top-of-canopy (TOC) reflectance and SIF measurements to decouple the joint effects on TOC SIF in sugar beet. SIF and reflectance data were acquired over irrigated and water-stressed plots using an Unmanned Aerial Vehicle (UAV) on two consecutive days. The non-physiological response was quantified with SCOPE by fitting the model parameters to the TOC reflectance measurements. Subsequently, fluorescence emission yield (