With China’s reform and opening up, rapid economic development, and improvement of people’s living standards, industrial and domestic wastewater discharge as well as fertilizer and pesticide residues in agricultural runoff has increased drastically since 1980’s, leading to the widespread eutrophication of its watersheds, the pervasive outbreak of algae blooms, and the degradation and collapse of its aquatic ecosystems. Therefore, pollution control and aquatic ecosystem recovery has become one of the most critical tasks faced by Chinese authorities. The prevailing view is that only when water pollutant concentration is reduced to the level of the 1980’s can a fundamental improvement in water quality and ecological restoration be achieved. However, the reality in China is that on the one hand pollutant loads have exceeded their environmental capacities in most watersheds, and on the other hand they are hard to reduce due to economic development. Furthermore, even if wastewater has been properly collected and treated so as to meet the strictest wastewater discharge standards in China, its pollutant concentrations far exceed the surface water quality standards (often exceed the Category III surface water quality standard by several or a dozen times). Nevertheless, previous study results have indicated that water quality needs to improve to Category II or better to control algae bloom effectively. There is a loud opinion that exotic species should be eradicated from watersheds besides pollution control to achieve its ecological recovery. So far, China has approved such projects. The above situation seems to indicate that watershed pollution control and ecological recovery has fallen into a deadlock in China. We feel that effective watershed pollution control and ecological recovery in China requires new thinking. First, adjust China’s economy progressively to an environment-friendly industry structure with low emissions. Meanwhile, lifestyle in China should change gradually following the environment-friendly concept. Secondly, solve the issue of current huge difference between China’s sewage treatment discharge standards and surface water quality standards, including raising China’s sewage treatment discharge standards. Thirdly, gradually strengthen the construction of clean water networks by linking water bodies to form stream networks and recovering plant ecosystems so as to increase the carrying capacities and self-purification capabilities of watersheds as well as the health level of ecosystems. Fourthly, we could not and should not pursue a complete restoration of plant communities in the watersheds to those in the 1980’s, because situation changes with time. We should focus on advancing with time and carrying out ecological restoration to establish a new ecological balance. Finally, our research group has conducted several years of research at the Dianchi, one of the most polluted and ecologically degraded lakes in China. In view of its poor water quality of worse than Category V, nearly none vegetation coverage, and highly polluted inflow which is mostly discharge from wastewater treatment plants with pollutant concentrations far exceeding surface water quality standards, we have proposed the concept of spatiotemporal configuration of plants, and have gradually realized the control of algae bloom and recovery of plant communities in our experimental area.