Water deficit is a significant abiotic stress that severely limits rice growth and production. Therefore, developing drought-tolerant rice genotypes is essential, especially under current water shortage conditions. In this study, eleven SSR markers revealed substantial genetic variation among parental genotypes, identifying 27 alleles with an average of 2.45 per locus and a high polymorphism information content (PIC) of 0.44. Based on this diversity, three specific crosses were generated. Five populations from each cross, including P1, P2, F1, F2, and F3, were evaluated in two separate experiments under normal and water deficit conditions. The results showed that the overall mean values for all generations were higher under normal conditions than under water deficit conditions for most studied traits. The first cross (Sakha 107 × Nerica 7) was the best for the most studied traits under water deficit, while the third cross (Sakha Super 300 × Moroberekan) was the best under normal conditions. Scaling test results indicated that the evaluated traits did not align well with the additive-dominance model, suggesting the possibility of epistasis in trait inheritance. Dominance effects were notably high for 100-grain weight, water use efficiency, and grain yield per plant, suggesting that selection for these traits should be postponed to late generations to ensure homozygosity. The importance of additive and dominance effects varied by trait and cross under normal and water stress conditions. Among the epistatic components, the dominance effect was more significant in magnitude than the additive × additive ones in most studied traits.