Interbasin water-transfer schemes provide an engineering solution for reconciling the conflict between water demand and availability. In the context of climate change, which brings great uncertainties to water resource distribution, interbasin water transfer plays an increasingly important role in the global water–food–energy nexus. However, the transfer of water resources simultaneously changes the hydrological regime and the characteristics of local water bodies, affecting biotic communities accordingly. Compared with high economic and technical inputs water-transfer projects require, the environmental and ecological implications of water-transfer schemes have been inadequately addressed. This work selects the largest water-transfer project in China, the South-to-North Water Diversion (SNWD) Project, to critically review its eco-environmental impacts on donor and recipient basins, as well as on regions along the diversion route. The two operated routes of the SNWD Project represent two typical water diversion approaches: The Middle Route uses an excavated canal, while the East Route connects existent river channels. An overview of the eco-environmental implications of these two routes is valuable for the design and optimization of future water-transfer megaprojects.