In arid regions, large-scale water diversion from rivers leads to significant changes in river flow regimes, which may have large impacts on ecological water uses of river-dependent ecosystems, such as river, lake, wetland, and riparian ecosystems. To assess the integrated impact of water diversion on ecological water uses, we proposed a hierarchy evaluation model composed of four layers representing the evaluation goal, sub-areas of the influenced region, evaluation criteria, and water diversion schemes, respectively. The evaluation criteria for different types of ecological water uses were proposed, and the analytical hierarchy process was used for the integrated assessment. For a river ecosystem, the percentage of mean annual flow was used to define the grade of environmental flow. For a lake ecosystem, water recharge to the lake to compensate the lake water losses was used to assess the ecological water use of a lake. The flooding level of the wetland and the groundwater level in the riparian plain were used to assess the wetland and riparian ecological water uses, respectively. The proposed model was applied to a basin in north Xinjiang in northwest China, where both water diversion and inter-basin water transfer projects were planned to be carried out. Based on assessment results for the whole study area and two sub-areas, an appropriate scheme was recommended from four planning schemes. With the recommended scheme, ecological water uses of the influenced ecosystems can be maintained at an acceptable level. Meanwhile, economical water requirements can be met to a great extent.