Potential impacts of climate change on water quality and ecosystem, as a newly emerged problem and challenge, is of great concern by scientists and governments. However, scientific researches and practices are still facing big challenges in these issues because of their complexity and uncertainty. This paper reviews the most recent literatures on this topic at first, and proposes some research gaps between published results and what needs to be known in practice. Additionally, basing on our knowledge and results of some recent case studies of the two representative rivers which are Huai River and Hanjiang River in China, it should be addressed that if the impact of climate change on the water quality and ecosystem has been taken concern, water pollution and related water environmental problem caused by human activities and economic development must be addressed firstly. It has also been recognized that water quality and ecosystem can be significantly impacted by climate change under the condition of human activities. Climate change can alter water temperature and hydrological regimes and thus influence the water quality and ecosystem. Then, the contents and principles of adaptation options and adaptability construction are discussed. The present study is expected to make clear of conceptions and to give directions for further relevant researches.