Background: Ten improved upland rice lines presently grown in dry upland rice field of Jharkhand, Odisha, and Bengal, the three most significant rice yielding states of eastern India, were screened under varying induced water stress to reveal their physiological and biochemical performance followed by rice microsatellite-based genotyping and detection of SNPs for a selected genetic loci (OsLEA3) associated with drought responses in higher plants. Results: For physiological screening changes in plant height and external appearance of mature plant particularly greenish appearance were considered. Quantitative estimation of six biochemical compounds (chlorophyll, carotenoids, catalase, peroxidase, ascorbate peroxidase), commonly associated with normal physiological processes of plants, showed variable response under induced water stress. Variety Vandana and CRdhan 40 were identified to be the most potent drought-avoiding genotypes, whereas variety Sneha and Kalinga III showed least degree of drought tolerance for the studied screening parameters under drought. In post stressed period, both the variety Vandana and CRdhan 40 showed best performance to recover by virtue of regular water supply for a month tenure. In SSR-based genotyping, RM3825 and RM242 showed highest degree of polymorphism, whereas RM321 was monomorphic across the selected rice lines. Genomic DNA of only four lines (Vandana, Anjali, CR dhan 40, and Sahabhagidhan) were amplified with the primer pairs designed from OsLEA3 gene sequence which resulted three distinct allelic forms. Vandana and CR Dhan 40 shared a common allele of mol. wt. 1173 bp size, whereas other two allelic forms were detected by Anjali and Sahbhagi of mol. wt. 1210 bp and 1036 bp respectively. A total number of 23 SNPs were detected for amplified sequence of OsLEA3 gene sequence in CR Dhan 40 of which 12 were transitions and 11 were transversions. Conclusion: From this study, it could be concluded that var. CR Dhan 40, Vandana, and Sahabhagidhan performed better, both physiologically and biochemically under induced drought stress.