The aim was to assess the usefulness of spectral data to detect structural and physiological changes in Citrus crops tinder water and saline stress. Multispectral images were acquired from a fixed-wing Unmanned Aerial Vehicle (UAV) while concomitant measurements of gas exchange, plant water status, leaf structural traits and chlorophyll were taken in a commercial farm located in southeast Spain with two Citrus species, grapefruit and mandarin irrigated for eight years with saline reclaimed water (RW) combined with regulated deficit irrigation (RDI). Measurements at leaf scale and airborne flights were carried out twice a day, at 7 and 10 GMT. Irrigation with RW decreased gas exchange and leaf dry mass per unit area (LMA) on grapefruit. However, salinity from RW resulted in an increase in pressure potential (gyp) on mandarin and allowed maintaining net photosynthesis (A) and stomatal conductance (g(s)) when vapour pressure deficit increased. On both crops, leaf total chlorophyll (ChlT) concentrations were significantly reduced by RW. Moreover, RDI decreased A, gs and stem water potential (psi s) on grapefruit, independently of water quality. Regarding spectral data, red wavelength (R) was significantly correlated with Chl T (p < 0.001), except when mandarin was subjected to stressful climatic conditions (at 10 GMT); since R was influenced, in addition to Chl T, by the plant water and gas exchange status. Near infrared (NIR) was a useful indicator of psi s, A and gs on both crops. The normalized difference vegetation index (NDVI) was clearly related to gas exchange in both species and to psi s only on mandarin. Finally, we combined data from both Citrus species and the best indicators were NIR and R. The novelty of this study was to show that diurnal changes in physiological and structural traits of Citrus irrigated with RW combined with RDI can be determined by multispectral images from UAVs. (C) 2016 Elsevier B.V. All rights reserved.