A study at Sakha Agricultural Research Station examined the impact of water deficit on wheat grain yield using a randomized complete block design in a split-plot arrangement. Drought-tolerant wheat genotypes were identified using stress tolerance indices and factor analysis scores. Results showed a significant effect on all studied traits and the interaction for the shortage of water and genotypes. Alterations in agronomic and physiological characteristics lead to a decrease in grain yield from 29.4% to 61.8% under water deficit. Based on grin yield only under normal and stress conditions (two irrigations), Stress tolerance indices (STI) indicated that Line2, Line4, Line5, Line6, Line8, Line10, Line11, Line12, Gemmeiza 11, Giza 171, Sakha95, and Misr 3 were drought tolerant overall the two seasons. The results indicate significant positive correlations between stress tolerance indices. TOL and SSPI showed an egalitarian relationship when ranking genotypes, and strong positive associations were found between SSI, RD, and CV. These indices are equally effective for ranking genotypes for stress tolerance and can be used interchangeably to save time and effort. In addition, Line 2, Line4, Line6, Line7, Line8, Line9, Line10, Line11, and Giza 171, Sakha95, and Misr 3 were the best genotypes from the Factor Analysis Score method, with the highest grain yield parameters, NDVI, and the lowest increase in canopy temperature at two irrigations so, recommended involvement in the drought breeding program. Two irrigations are recommended for early cultivation of genotypes, as they are sufficient to yield valuable crops with minimal loss under water scarcity challenges.