Drought stress (DS) is one of the most critical environmental abiotic stresses for wheat production in the arid environments. Selection of high-yielding genotypes tolerant to DS can play a significant role in mitigation the negative impacts associated with DS. In the present study, generation means analysis (GMA) was used to study the performance of two crosses under well irrigation (WI) and deficit irrigation [cross I (Line 44 × Shandweel-1) and cross II (Line 20 × Sakha 93)]. Significant differences were observed for days to heading (DH), days to maturity (DM), plant height (PH), spike length (SL), number of spikes per plant (NS/P), number of grains per spike (NG/S), thousand-grain weight (TGW), grain yield per plant (GY/P), and proline content (PC) in the six populations of the two crosses within each irrigation level. Cross II had early maturity and the highest PC, NS/P, TGW, and GY/P regardless of the irrigation level. Cross I showed positive significant relative heterosis and heterobeltiosis for GY/P under the two irrigation levels. The inheritance of characters of cross I revealed additive, dominant, and epistatic effects, which varied with trait and stress. Additive genetic effects predominated in DH, SL, and PC, while non- additive were found in DM, NS/P, NG/S, and GY/P. Narrow-sense heritability estimates (h2n) were high for DH and PC, moderate to high for PH and SL, moderate for DM, NG/S, NS/P, and TGW, and low for GY/P. Based on different drought indices the populations BC1, BC2, F1, and P1 of cross II and BC1 of cross I were more tolerant to drought stress. Therefore, PC, TGW and DH can be used as selection indicators to improve wheat for drought tolerance in early generations and other yield components traits in late generations. The second cross (Line 20 × Sakha 93) shows promise and is of interest to a drought tolerance breeding program, where wheat breeders can use recombinant breeding strategies to construct desirable drought stress genes. Correlation and path coefficient revealed that TGW and PC were the main contributor in grain yield in both environments.