Effective management is crucial to achieve the high yield potential of quinoa (Chenopodium quinoa Willd.), renowned for its resilience in harsh environments, to meet the rising global demand. The present study examines how varying levels of water and nitrogen affect the agronomic and yield traits of quinoa (cv. Q-36) during the two growing seasons of 2020/2021 and 2021/2022. The experiment was a 3 × 4 factorial laid out in a randomized complete block design with three replications per treatment during the two seasons of the study, as water regimes were considered the main factor, including 100%, 80%, and 60% ETc, whereas nitrogen levels were considered the sub-plot factor, comprising four levels (75, 150, 225, and 300 kgN ha−1). The analysis of variance indicated that nitrogen level, irrigation regime, and irrigation regime × nitrogen level had highly significant effects (p < 0.001) on all studied traits, including plant height, panicle length, dry weight, seed weight, seed yield, and total yield in the two growing seasons under study. For all traits of study, the combined application of 100% ETc with 300 kgN, followed by 80% ETc with 225 kgN, resulted in the highest value of plant height, panicle length, dry weight, seed weight, seed yield, and total yield, whereas the combination of 60% ETc and 75 kgN applications resulted in the lowest value for all of the aforementioned traits. Furthermore, the water regime impacted water productivity at all nitrogen levels as the highest productivity level was recorded under the 80% ETc (0.58 kg/m3), followed by the 100% ETc (0.54 kg/m3), and the 60% ETc (0.52 kg/m3). The highest water productivity rate was observed at 300 kg/ha of the nitrogen levels for 60% and 80% ETc regimes, where water productivity levels were 0.73 and 0.71 (kg/m3), respectively. The results also indicate that the water productivity of quinoa plants is noticeably affected by both water regime and nitrogen level; as the water regimes decrease from 100% to 60% ETc, water productivity increases for all nitrogen levels. The information obtained from these results can be applied to optimize the methods for cultivating quinoa under conditions of water scarcity and minimal nitrogen availability, thus gaining an insight into the impact of these conditions on quinoa growth and yield.