Abstract: In recent decades, submerged macrophytes recession has become a prevalent environmental problem in shallow lakes in the middle and lower reaches of the Yangtze River affected by human disturbance and other factors. Bao’an Lake is located in the middle reaches of the Yangtze River. To understand the characteristics of submerged macrophytes community and the impacts of eutrophication and fishery production on the succession of macrophytes community, we analyzed the changes of the submerged macrophytes community, water quality and fishery resources in Bao’an Lake in the recent 40 years. The data were collected from our long-term monitoring, literature and the local lake management department. The results showed that: (1) During 1970s—1980s, there were about 10 common species of submerged macrophytes, mainly including Myriophyllum spicatum, Potamogeton maackianus and Potamogeton crispus, the annual average biomass was 1005—5954 g/m². In 1990s, there were about 7 common species of submerged macrophytes, mainly Potamogeton maackianus and Potamogeton crispus, and the biomass decreased to 209—877 g/m². During 2000s—2010s, the structure of submerged macrophytes was simplified, and Potamogeton crispus became the monodominant species, and the biomass changed greatly, fluctuated between 1 and 1478 g/m². Since 2021, submerged macrophytes have basically disappeared. (2) From the 1980s to now, the nutrients content of Bao’an Lake exhibited an upward trend. Total phosphorus content (TP) during 1980s—1990s was about 0.03 mg/L, which was much lower than the regime shift threshold in shallow lakes. Eutrophication has little effect on submerged macrophytes at this time. In the 21^st century, the nutrients content in lake water increased rapidly. In 2003, TP was 0.07 mg/L, which was close to the regime shift threshold. Since then, it was maintained at a relatively high level, which was one of the important reasons resulting in the decline of submerged macrophytes. (3) During 1980s—1990s, Ctenopharyngodon idellus and Eriocheir japonica sinensis were mainly stocked, and the fish yield fluctuated between 0.62×10⁴ and 1.01×10⁴ kg. The Ctenopharyngodon idellus was cultured at high density during 1986—1989 (about 2.6×10⁴ kg), which was the main reason for the decline of submerged macrophytes during this period. In the 21^st century, the fishery output has increased greatly, up to 500×10⁴ kg. Hypophthalmichthys molitrix and Aristichthys nobilis have been the dominant species farming in the lakes, and there were so many Eriocheir japonica sinensis, which has adverse effects on the survival and development of submerged macrophytes. After the fishery withdrawal in 2018, the fishery resources have been greatly reduced, and only Hypophthalmichthys molitrix and Aristichthys nobilis were stocked, which has little direct impact on submerged macrophytes. The results indicated that in past 40 years, the biodiversity of submerged macrophytes in Bao’an Lake has decreased considerably, and the community structure has tended to be simplified. The succession of submerged macrophytes was mainly regulated by fishing (grazing pressure from Ctenopharyngodon idellus) during 1980s—1990s, while suffered with dual pressure from eutrophication and excessive aquaculture at the beginning of the 21^st century. In recent years, eutrophication become the key factor influencing submerged macrophytes community. This research clarified the effects of eutrophication and excessive aquaculture on the succession of submerged macrophytes communities in isolated lakes, and provided theoretical basis for the ecological management for comparable shallow lakes located in the middle and lower reaches of the Yangtze River.