Effects resulting from the use of reclaimed waters on mandarins and grapefruits are evaluated by measuring the spectral responses of their canopies and the anatomy and the chlorophyll content of their leaves against control trees irrigated with waters provided by an interbasin transfer. Spectral responses from the red (R) and near-infrared (NIR) wavelength bands, and its normalized ratio (NDVI), were acquired from a hyperspatial flight conducted after a low-moderate exposition to reclaimed waters. Chlorophyll and leaf and palisade/spongy ratio thicknesses were analyzed after a moderate-high exposition. Significant differences between controls and treatments were detected in mandarins in R and leaf chlorophyll, but not in grapefruits, likely because of their higher tolerance to saline waters. Reused waters did not affect either NIR-NDVI or anatomy traits. Hyperspatial sensing techniques are suitable for detecting chlorophyll dynamics, but NIR information and related vegetation indices may mask the detection of periods of saline stress in citrus orchards.