Inter-basin water transfer project is an effective engineering countermeasure to alleviate the pressure of water supply in water-deficient areas and balance the uneven distribution of water resources. To assess the impacts of inter-basin water transfer projects on optimal water resources allocation, an integrated water resources management framework is proposed, and is applied to the middle and lower reaches of the Hanjiang River Basin in China. Firstly, future water demands are analyzed as inputs. Then, a multi-objective water resources allocation model is formulated mitigating the negative impacts of water transfer projects on downstream water quantity and quality by using the non-dominated sorting genetic algorithm-II (NSGA-II). Finally, the indicators of water supply reliability, vulnerability and resilience are evaluated under different scenarios of inter-basin water transfer projects. The results indicate that: (1) the reliability and resilience of the water donor system will be gradually reduced while the vulnerability will be increased with the expansion of water transfer projects and the increase of water demand, (2) water supply risk is likely to increase in all zones (because zones at the boundary cannot obtain sufficient water due to limitations of local inflow and reservoir operation, while the amount of water available in the zones along the mainstream river is directly decreased by the water transfer projects), (3) more water supply measures and compensation measures will need to be implemented in the water donor areas. The framework proposed in this study to evaluate the comprehensive impact of inter-basin water transfer projects is conducive to water resources management. mitigating the uneven distribution of water resources and balancing the inter-basin water resource development [6,7]. Many large-scale inter-basin water transfer projects have been implemented and planned in China, transferring part of the water from water-abundant basins to water-deficient basins, such as the Yellow River Project [8] and the East, Middle and West Route for the South-to-North Water Transfer Project [9][10][11]. The implementation of these water transfer projects involves complex water diversion works, long tunnel construction, large-scale water pumping, and reservoir operation. Their impacts on socio-economic and environmental systems are so great that they cause widespread concern in society. As well as playing an important supporting and safeguarding role in promoting economic and social development in the water receiving areas, any inter-basin water transfer system can also have complex physical, chemical, hydrological and biological implications for both the donor and receiving areas [12,13]. Undoubtedly, it is very important to thoroughly assess the potential impacts of the proposed water transfer projects.Substantial studies have assessed the impacts of inter-basin water transfer projects implemented across the world [14]. However, most of these studies emphasize the impacts on biodiversity conservation [1...