This investigation focused on assessing heterosis, genetic variability, and the key physiological and biochemical indicators associated with drought tolerance in rice at water-limited environments. Seven rice accessions were utilized in a half-diallel pattern, resulting in the development of twenty-one F1 hybrid combinations. Molecular divergence among the parental lines was analyzed through eleven SCoT polymorphism primers, generating 149 DNA fragments, out of which 71 were polymorphic, representing (47.6%) polymorphism. PIC value was 0.40, with SCoT-02, SCoT-08, and SCoT-09 showing the highest polymorphism. Genetic distances ranged from 0.81 to 0.90, with SK-101 and GZ-179 being the most divergent. Cluster separated the rice accessions into two main groups. Several hybrids, notably GZ-179×IET-1444, IET1444×HR-5824, and SK-106×SK-107, displayed significant heterosis for yield-related traits across environments. Under normal circumstances, there was a strong correlation between marker-based genetic distance (GD) and heterosis, especially for sterility. Traits such as thousand-grain weight, weight panicle, sterility, and yield/plant-1 exhibited strong positive correlations with better-parent heterosis under water regime, indicating that SCoT-based genetic distance can predict hybrid performance under stress. Multivariate analyses (Bi-plot PCA and heatmap) revealed that grain yield was positively associated with photosynthetic rate, membrane stability, water-use efficiency, and proline content, while negatively correlated with oxidative stress indicators. PCA effectively discriminated drought-tolerant hybrids, especially GZ-179×IET-1444, IET1444×HR-5824, and GZ-179×HR-5824, which combined superior photosynthetic capacity, membrane integrity, and biochemical resilience along highly production and related features.