The Three Gorges Project has been subject to intense debates regarding its benefits and costs. The environmental impacts of this huge project have been an important focus of these debates since the project planning stage. After the operation of the Three Gorges Dam at full capacity at the end of 2008, new environmental and ecological issues are emerging. This paper gives a brief description of the Three Gorges Project and its environmental impact assessment process, as well as major efforts to control environmental problems brought about by the project. From the long and complicated evaluation process, it is clear that there are large uncertainties and competing opinions regarding the benefits and costs, especially the ecological and environmental ones, of the project even after great research effort. Emphasis here is given to the environmental challenges including: (1) water quality control; (2) water and sediment regulation; (3) biodiversity conservation in the riparian and aquatic ecosystems; (4) environmentally friendly dam operation and regional sustainable development. Opportunities often grow out of the challenges. The Three Gorges Project provides opportunities for grand-scale experiments on the environmental, ecological, and socio-economic impacts of large dams. Local, national, and international concerted efforts and concrete actions should be directed to the mitigation and control of the negative impacts as well as securing the positive contributions of the project across scales