Irrigated areas are major vectors of agricultural development and components of ecosystems. The groundwater level maintains the irrigated areas’ ecology safety and sustainable development. Under the influence of irrational irrigation practices—such as flood irrigation or extreme water saving without consideration of ecological impact—different areas within an irrigation district may experience anomalies in groundwater levels (either too deep or too shallow). It is of great significance to carry out research on water resource allocation and future water-saving strategies, taking into consideration groundwater depths. In this study, a method for the optimal allocation of irrigation water resources that considered groundwater level was used to regulate irrational irrigation practices and to reveal the future direction of water saving. Helan County in Ningxia province, an ecologically fragile and arid irrigated area, was selected as a case study. Multiple scenarios of different water use and different degrees of water-saving were analyzed. The results showed that non-engineering water-saving measures (such as adjusting the planting structure and controlling the amount of irrigation for rice) had better benefits compared to engineering measures (such as efficient water-saving irrigation and channel lining). When implementing only one water-saving measure, the strategy of replacing 75% of the rice area with corn yielded the best results. This approach can reduce the irrigation water shortage rate to 11% and increase by 4.58% the acreage where the groundwater level is reasonable. When multiple water-saving measures are implemented together, the most effective strategy for future water-saving efforts involves the joint implementation of several measures: replacing 75% of the rice area with corn, limiting irrigation for rice to no more than 11.85 thousand m3/ha, adopting high-efficiency water-saving irrigation in 90% of the pump-diverted water irrigation region and 40% of the channel-diverted water irrigation region, and maintaining the channel’s water utilization coefficient at 0.62. This strategy can keep the irrigation water shortage below 3.66% and increase the acreage where the groundwater level is reasonable, by 4.58% per year. The conclusions and research approaches can provide references for the formulation of water-saving measures for irrigated areas’ sustainable development.