Abstract: The scarcity of monitoring data and the constrained capacity to detect inter-basin groundwater flows have hindered the definition of endorheic basins in China, while research on sustaining a healthy circulation of water resources within endorheic basin remains exceedingly limited. As a result, relevant management frequently lacks empirical evidence and technical support. To enhance the understanding of the co-evolutionary dynamics of water resources in endorheic basin, this paper used the Bali River Basin, a representative endorheic basin of the Ordos Plateau, as a case study. The MODFLOW model was employed to simulate shallow groundwater dynamics under varying extraction conditions. We investigated the balanced interactions among precipitation recharge, evaporation, artificial extraction, and inter-basin groundwater, and delineated the mechanisms governing the coordinated development of water resources, along with recommendations for their sustainable management. The findings indicate that the groundwater system in the Bali River Basin is overall in a negative equilibrium state of-5.8%. If extraction rates persist at their current levels, shallow groundwater levels in the basin′s middle and lower reaches would markedly decrease by 2035, with certain regions experiencing declines of up to 0.6 m/a. Should a diminished extraction strategy be enacted, groundwater levels are expected to exhibit a two-phase recovery and reach a relatively stable state by 2035. However, the substantial decrease in long-term extraction may potentially increase the risk of salinization in certain downstream regions. An increase in discharge of at least 5.5 million m³/a is required to maintain the stability of the shallow groundwater level downstream and preserve a robust circulation of the water resources system. On the whole, the methods for sustaining healthy water resources in endorheic basins are more intricate than those in full closed-flow environments. Achieving a sustained dynamic equilibrium among basin-wide precipitation recharge, evaporation, artificial extraction, and inter-basin groundwater movement is essential for preserving sustainable water supplies in regional endorheic basins.