This study was carried out at the Experimental Farm of Sakha Rice Research Station, Kafr El-Sheikh, Egypt, during the 2021, 2022, and 2023 growing seasons. The objective was to evaluate heterosis, inbreeding depression, allelic and non-allelic interactions, and genetic advance for root, physiological, and yield-related traits in rice using a six-population approach: P1, P2, F1, F2, BC1, and BC2. Two rice crosses, Sakha106 × Nerica7 (CI) and Giza177 × GZ 10848-1-2-2-1 (Giza183) (CII), were investigated. Field trials were conducted in a randomized complete block design with three replications. The results revealed highly significant and positive heterosis, as a deviation from both mid-parent and better-parent values, for most traits under both irrigation conditions. Most traits displayed incomplete dominance to over-dominance. Both additive and dominance genetic effects played important roles in trait control, with additive × additive, additive × dominance, and dominance × dominance interactions also contributing to the genetic regulation of most traits, with a few exceptions. High values of Broad-sense heritability and predicted genetic advance were estimated for most traits in the studied crosses. However, narrow-sense heritability was generally moderate to low in most traits of both crosses. Based on these findings, Giza 177 × GZ 10848-1-2-2-1 (Giza183) is recommended for cultivation under water deficit conditions for most of the studied traits.