The challenges of food security are exacerbated by the world's expanding population and diminishing agricultural land. In response, hydroponic cultivation offers a potentially more sustainable approach to growing nutrient-dense crops compared to traditional methods. Motivated by this understanding, we conducted a series of experiments to explore the behavior of Brassica juncea (Pusa Jaikisan) plant roots under various flow configurations within a controlled environment. The flow configurations considered were no-flow/flow (NF/F), continuous flow, flow/no-flow (F/NF), and stagnation. Additionally, we conducted anatomical sectioning of plant roots to study how different flow configurations affect the cellular structure of the plant root cross section. We also performed numerical simulations to investigate the internal stress generated within plant roots under various flow conditions. We observed that an increased number of cortical cells developed in response to higher internal stress in the case of continuous flow, which protected the inner vascular bundle from excessive biological stress. Comparing the designs, we found that continuous flow resulted in a longer root length compared to the F/NF and NF/F configurations. The root length per unit average flow power was highest for the 2 h F/NF case, followed by the 2 h NF/F, 3 h F/NF, and continuous flow cases. This suggests that periodic flow conditions (F/NF and NF/F) with lower average power, a necessary requirement for economical use, led to longer root lengths. Furthermore, we observed that the nitrogen uptake per unit average flow power was higher for the F/NF configuration compared to continuous flow. Consequently, we infer that in hydroponic cultivation, altering the flow configuration to a F/NF type could be more cost-effective with less nutrient solution wastage, promoting better plant root growth compared to a continuous flow scenario.