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It is very important to construct a reasonable and efficient basin management system to meet the ecological water demand in arid areas with natural vegetation, and to maintain the integrity and stability of fragile ecosystems. However, how to assess the effect of basin management on ecological protection in arid areas as well as how to achieve the optimal control and efficient use of ecological water are major issues for many researchers and river basin managers. To address these two questions, we investigated the comprehensive management system for the Tarim River basin in China as a typical case study. The results showed that the natural vegetation coverage degree, the ecological water supply, temperature vegetation dryness index (TVDI), and the tree-ring chronology of Populus euphratica increased, whereas the disturbance of water resources by human activities decreased. Therefore, the effects of ecological protection were obvious after comprehensive "large basin" management. Based on an innovative application of tree-ring chronology to estimate the water leakage from the river, we determined the minimum runoff level (43.1 x 10(8) m(3)) when the natural vegetation needs to overflow. To further improve the effect of comprehensive management, the optimal regulation mode (i.e. maintaining the groundwater depth at 2-6 m, and the frequency and duration of overflowing at 2-3 times per year for a duration of 15-20 days during July to September) for the ecological sluices was formulated from the perspective of the efficient utilization of ecological water. These results provide a scientific reference for constructing reasonable management systems for similar river basins in arid areas. (C) 2018 Elsevier B.V. All rights reserved.