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The river is an essential part of water resources, which has unique ecological structure and function. With the rapid socio-economic development, the improper use of water resources has led to a series of structural and functional decline of the river system, such as water pollution, environmental degradation and river shrinkage. How to restore damaged river ecosystems to an ecologically healthy status has become one of the important environmental issues, which is the key to achieve the goal of productivity improvement, ecosystem balance and sustainable development. And also, the structure and function of the river ecosystem should be pre-assessed before the restoration. In this paper, the Liangshui River, a tributary of Daling River in the arid region of western Liaoning Province, is selected as a study site. An assessment index system involving 21 defined indices on structure and function of river ecosystem is firstly established. A mathematical method for comprehensive assessing the structure and function of river ecosystem is proposed based on the Set Pair Analysis (SPA) and Quadrant Method. Then, the evaluation value is gained at the ecosystem level. The result shows that the assessment value of structure and function is -0.513 and -0.208, respectively, which means that the Liangshui River ecosystem is defective in structure and sub-healthy in function. It is necessary to choose potential development emphasized on the structurally rehabilitating of the Liangshui River ecosystem. Based on the above, ecological engineering measures and suggestions are recommended to preserve the health of river ecosystem. (C) 2014 Elsevier B.V. All rights reserved.