A better understanding of the responsiveness of grain phenotypic indices to terminal water stress (TWS) in wheat might help explain grain weight variations and determine which grain traits are most affected. A two-year field experiment (2020–2021 and 2021–2022) was conducted to identify how TWS and exogenous cytokinin application might affect grain weight and grain dimensions in three bread wheat cultivars using high-throughput digital image phenotyping. The results showed that the effects of growing seasons, irrigation, and cultivars were significant on grain weight and phenotypic indices. In our study, TWS significantly reduced thousand grain weight (24.62%, 14.65%) and grain development in the width directions MinFeret, i.e., minimum caliper diameter (10.70%, 6.64%) and Minor, i.e., the minor axes of the best fitted ellipses to the grains (10.91%, 6.65%), or synthesized indices including Area/Perim. (9.01%, 5.42%), Area × Circ. (17.30%, 10.13%), Minor/Solid. (10.26%, 6.32%), MinFeret/Solid. (10.01%, 6.11%), Area × Solid (13.94%, 7.96%), Perim. × Circ. (9.07%, 5.42%), A1 (29.99%, 17.09%), and A2 (30.20%, 17.27%) in each growing season, respectively. Regardless of the factors causing these variations, a sustained relationship was found between thousand grain weight and phenotypic indices, with significant positive correlations. The stronger positive correlation between thousand grain weight and grain width indices (r ≥ 0.965) showed important implications for grain development and filling. The Torabi cultivar performed better than the Sirvan and Pishgam in both growing season conditions. In addition, the technical advantages of developing phenotyping approaches, the present study could contribute to a better physiological evaluation of wheat cultivars in multivariate environments.