Root distribution during rice cultivation is a governing factor that considerably affects soil water content (SWC) and root water uptake (RWU). In this study, the effects of activating root growth (using growth function) and assigning a constant average root depth (no growth during simulation) on SWC and RWU for rice cultivation under four deficit drip irrigation treatments (T90, T80, T70, and T60) were compared in the HYDRUS-2D/3D model version 3.03. A secondary objective was to investigate the effect of applied deficit irrigation treatments on grain yield, irrigation water use efficiency (IWUE), and growth traits of rice. The simulated DI system was designed to reflect a representative field experiment implemented in El-Fayoum Governorate, Egypt, during two successive seasons during 2017 and 2018. The deficit treatments (T90, T80, T70, and T60) used in the current study represent scenarios at which the first irrigation event was applied when the pre-irrigation average SWC within the upper 60 cm of soil depth was equal to 90%, 80%, 70%, and 60% of plant-available water, respectively. Simulation results showed that as water deficiency increased, SWC in the simulation domain decreased, and thereby, RWU decreased. The average SWC within the root zone during rice-growing season under different deficit treatments was slightly higher when activating root growth function than when considering constant average root depth. Cumulative RWU fluxes for the case of no growth were slightly higher than for the case of root growth function for T90, T80, and T70 accounting for 1289.50, 1179.30, and 1073.10 cm2, respectively. Average SWC during the growth season (24 h after the first irrigation event, mid-season, and 24 h after the last irrigation event) between the two cases of root growth was strongly correlated for T90, T80, T70, and T60, where r2 equaled 0.918, 0.902, 0.892, and 0.876, respectively. ANOVA test showed that there was no significant difference for SWC between treatments for the case of assigning root growth function while the difference in SWC among treatments was significant for the case of the constant average root depth, where p-values equaled 0.0893 and 0.0433, respectively. Experimental results showed that as water deficiency decreased, IWUE increased. IWUE equaled 1.65, 1.58, 1.31, and 1.21 kg m−3 for T90, T80, T70, and T60, respectively. Moreover, higher grain yield and growth traits of rice (plant height, tillers number plant−1, panicles length, panicle weight, and grain number panicles−1) were obtained corresponding to T90 as compared with other treatments. Activating the root growth module in HYDRUS simulations can lead to more precise simulation results for specific dates within different growth stages. Therefore, the root growth module is a powerful tool for accurately investigating the change in SWC during simulation. Users of older versions of HYDRUS-2D/3D (version 2.05 and earlier) should consider the limitations of these versions for irrigation scheduling.