This paper is the result of hydrogeological survey engineering. [Objective] The southern Xinjiang is characterized by an important mineral and energy base and a key area of many national strategies. Water resources shortage is a key factor that hinders the social and economic developments as well as ecological protection and restoration in the southern Xinjiang where the climate is arid. To secure sustainable water resources development and environmental protection, identifying water- related issues and taking countermeasures are required. [Methods] Through a systematic synthesis on previous studies, the current status, issues and countermeasures of water resources development will be discussed. [Results] Water resources originate from the mountainous regions where rivers receive precipitation and snow (glacier) melting water contribution. The interaction between groundwater and surface water is frequent after rivers flow out of the mountains and water resources are consumed by evaporation finally at lowest reaches. The mean annual water resources are 4.51 × 10¹⁰ m³ among which surface water resources are 4.32×10¹⁰ m³, groundwater resources are 2.68×10¹⁰ m³, and the overlapping resources are 2.49 × 10¹⁰ m³. The consumption in recent years reaches 3.27 × 10¹⁰ m³, corresponding to a development level of over 70% that significantly exceeds the alarming level. The development rate indicates that water resources are over-used currently. Surface water quality is good in general, water quality superior to the third category accounts for 94%. Groundwater water quality becomes worse from the piedmont plains to the heart of the basin, and decreases from Ⅰ-Ⅲ level to Ⅳ-Ⅴ level (high total dissolved solids). In some areas, common elements and organic pollutants exceed the safety levels. The main problems related to water resources development are low efficiency and output of water resources, salinization and desertification due to unreasonable water development, high uncertainty on ecological water use and limited studies on the impact of climate change on water resources. [Conclusions] Aiming to solving these questions, water-saving agriculture and saline water use should expand, the water allocation among different reaches (upper, middle and lower) and sectors (human, ecology and production) should be considered and detailed studies on the impact of climate change on water resources and on the ecological water demand should be carried out.