A good water ecological environment is crucial for the sustainable development and ecological civilization of China. However, various problems remain for China’s water ecological environment, including eutrophication, pollution of drinking water sources, contamination of groundwater and coastal waters, emerging pollutants, and shortage of ecological water. In this study, we analyzed the overall situation of the water ecological environment in China, pinpointed the major challenges, and proposed the strategic thinking and several basic principles. These principles focus on improving the water ecological environment and comprehensively consider water quality improvement, water ecological protection, and water environmental risk prevention and control. Three major scientific and technological projects were proposed pertaining to (1) coordinated governance and overall restoration of mountains, rivers, forests, fields, lakes, grasses, and sand in key basins, (2) overall improvement of water environment and water ecology in the Beijing-Tianjin-Hebei Collaborative Development Area, and (3) assurance of drinking water safety in the new era. Furthermore, we proposed the following four countermeasures: (1) revising the Environmental Quality Standards for Surface Water to strengthen its leading role in the construction of water ecological civilization in China; (2) evaluating the spatial and temporal differences of nitrogen and phosphorus nutrients in China’s lakes and implementing differentiated nutrients standards; (3) assessing the current status of water ecology in China and promoting water ecology monitoring and assessment; and (4) establishing an intelligent supervision platform for drinking water safety based on big data fusion.