Water eutrophication has become one of the most serious aquatic environmental problems around the world. More and more research has indicated climate change as a major natural factor that will lead to the acceleration of eutrophication in rivers and lakes. However, understanding the mechanism of climate change’s effect on water eutrophication is difficult due to the uncertainties caused by its complex, non-linear process. There is considerable uncertainty about the magnitude of future temperature changes, and how these will drive eutrophication in water bodies at regional scales under the effect of human activities. This review collects the existing international and domestic literature from the last 10 years, discussing the most sensitive factors of climate change (i.e., temperature, precipitation, wind, and solar radiation) and analyzing their interaction with water eutrophication. Case studies of serious eutrophication and algal bloom problems in China are discussed to further demonstrate the conclusion. Finally, adaptation countermeasures and related implications are proposed in order to foster the development of sustainability strategies for water management in China.