During the "13th Five-Year Plan" period, the water ecological environment quality of the Yangtze River Basin has improved significantly, but the improvement of lake water quality and eutrophication has lagged behind. As one of the concentrated distribution regions of freshwater lakes in China, the middle reaches of the Yangtze River have the problems of deterioration of water quality and aggravation of eutrophication. This article chosed six typical lakes monitored by national agencies, including Lake Honghu, Lake Futou, Lake Liangzi, Lake Datong, Lake Dongting and Lake Poyang, to scientifically evaluate their spatiotemporal changes, key drivers of water quality and eutrophication from 2016 to 2020, and to discuss the degradation causes and governance countermeasures. The results revealed significant spatiotemporal changes in water quality and eutrophication of those lakes. From 2016 to 2020, the water quality of Datong Lake improved mostly, while Lake Liangzi became worse. TP is the main factor affecting the lake water quality and TLI(SD) is most important in the lake eutrophication evaluation. The eutrophication in Lake Honghu is the most serious, followed by Lake Futou. The lakes in the middle reaches of the Yangtze River widely experienced increasing organic pollution and chlorophyll-a concentration. Such degradation in Lake Honghu, Lake Futou and Lake Liangzi is mainly related to the increase of nitrogen and phosphorus nutrients, while Lake Datong, Lake Dongting and Lake Poyang are greatly affected by non-nutrient factors such as hydrological processes, pollution holding capacity and Lake management. TN and TP are still the main drivers on the water quality and eutrophication of these lakes during the "13th Five-Year Plan" period, and change synergistically in each lake. We propose to put forward the standard limits or assessment targets of nitrogen and phosphorus in rivers and lakes, to improve their environmental quality standards of rivers and lakes and the technical specifications for ecological health impact assessment. At the same time, it is recommended that the lakes in the middle reaches of the Yangtze River should carry out pollution control, endogenous control and ecological restoration. It is important to strengthen watershed management, especially the lakes across administrative regions such as Lake Dongting, Lake Poyang, Lake Liangzi, and Lake Futou to improve the system and integrity of lake governance and restoration.