To address the growing issue of scarce water in the arid and semi-arid areas, it is essential to investigate the potential of drought tolerant crops and implement promising farm management strategies to improve water productivity and yield production. Therefore, a split plot experiment to investigate how different irrigation levels (I-1:100% water requirement (WR), I-2:75%WR, and I-3: 50%WR) and planting methods (P-1: basin, P-2: on-ridge, and, P-3: in-furrow) interact and affect quinoa water use, yield, root growth, and water productivity in southern Iran over two growing seasons. The results showed high seasonal crop evapotranspiration (993–1030 mm) in I-1 as a result of the high advection ratio (α), which ranged from 1.02 to 1.46 from the early vegetative to the seed filling stages. The P-3 increased transpiration rate by 4.5% and 7.7%, and decreased soil evaporation by 17% and 29% compared to P-1 and P-2, respectively. Single (Kc) and dual (Kcb + Ke) crop coefficients varied between 0.41 and 1.38 over the two growing seasons. Grain yield in P-3 were 25%, 34%, and 44% higher compared to P-1 and P-2 under I-1, I-2 and I-3, respectively. The study revealed that nearly 67% and 80% of the total root dry matter was in the 0–30 cm and 0–60 cm of the soil profile in all experimental treatments, respectively. Regardless of irrigation treatment, root length density (RLD) and root mass density (RMD) were found to be 18.9% and 15.7% lower in P-1’s top 0–20 cm of the soil profile than those obtained in P-2 and P-3, respectively. Analyses showed that the increased root length in deeper soil layers contributed to higher soil water uptake, and consequently higher crop water productivity. In addition, root-to-shoot ratio increased as the amount of the applied irrigation water was decreased. Quinoa exhibited the highest acclimation to water stress in P-3 based on water stress sensitivity coefficients (λi) and yield response factor (Ky) values. Crop water productivity (WPC) and irrigation water productivity (WPI) for grain yield varied between 0.17 and 0.28 kg m−3. In conclusion, in terms of grain yield, shoot and root dry matter and water productivity, I-2 and P-3 (75% WR irrigation level and in-furrow planting method treatment) is recommended as the optimum water and planting management strategy for quinoa cultivation in the study area as a measure to address water scarcity and food sustainability. Still, to improve yield and irrigation water efficiency, the effect of soil management practices such as mulching and organic amendments on soil water retention and nutrient availability for quinoa should be investigated.