Hyperspectral sensing offers a quick and non-destructive alternative for assessing phenotypic parameters of plant physiological status and salt stress tolerance. This study compares the performance of published and modified spectral reflectance indices (SRIs) for estimating and predicting the growth and photosynthetic efficiency of two wheat cultivars exposed to three salinity levels (control, 6.0, and 12.0 dS m−1). Results show that individual SRIs based on visible- and near-infrared (VIS/VIS, NIR/VIS, and NIR/NIR) estimate and predict measured parameters considerably more efficiently than those based on shortwave-infrared (SWIR/VIS and SWIR/NIR), with the exception of some modified indices (the water balance index (WABI-1(1550, 482), WABI-2(1640, 482), and WABI-3(1650, 531)), normalized difference moisture index (NDMI(1660, 1742)), and dry matter content index (DMCI(1550, 2305)), which show moderate to strong relationships with measured parameters. Overall results indicate that modified SRIs can serve as rapid and non-destructive high-throughput alternative approaches for tracking growth and photosynthetic efficiency of wheat under salt stress field conditions.