The objective reality of uneven water resource distribution and imbalanced water demand of the human society makes it inevitable to transfer water. It has been an age-old method to adopt the inter-basin water transfers (IBTs) for alleviating and even resolving the urgent demand of the water-deficient areas. A number of countries have made attempts and have achieved enormous benefits. However, IBTs inevitably involve the redistribution of water resources in relevant basins and may cause changes of the ecological environment in different basins. Such changes are two-sided, namely, the positive impacts, including adding new basins for water-deficient areas, facilitating water cycle, improving meteorological conditions in the recipient basins, mitigating ecological water shortage, repairing the damaged ecological system, and preserving the endangered wild fauna and flora, as well as the negative impacts, including salinization and aridification of the donor basins, damage to the ecological environment of the donor basins and the both sides of the conveying channel system, increase of water consumption in the recipient basins, and spread of diseases, etc. Because IBTs have enormous ecological risk, it is necessary to comprehensively analyze the inter-basin water balance relationship, coordinate the possible conflicts and environmental quality problems between regions, and strengthen the argumentation of the ecological risk of water transfer and eco-compensation measures. In addition, there are some effective alternative measures for IBTs, such as attaching importance to water cycle, improving water use efficiency, developing sea water desalination, and rainwater harvesting technology, etc.