Lake and reservoir ecosystems face varying degrees of eutrophication and cyanobacterial bloom against the background of global climate change, which threatens the safety of drinking water supply. In this study, we reviewed the current status of eutrophication and water quality of lake and reservoir water sources in China, and explored the challenges from the aspects of water source protection, purification process, pipe network distribution, and guarantee mechanism. Four targeted suggestions were recommended for guaranteeing drinking water safety: (1) strengthening environmental protection and ecological restoration of lake and reservoir drinking water sources, (2) promoting the construction of a scientific and technological support system for guaranteeing drinking water safety in the entire process, (3) building an intelligent supervision platform based on big data fusion, and (4) accelerating the system and mechanism innovation for guaranteeing lake and reservoir drinking water safety.