As one of the regions with the most concentrated distribution of freshwater lakes in China, the middle and lower reaches of the Yangtze River has seen significant improvements in water ecological environment in the past decade. However, the trend of lake eutrophication has not been fundamentally contained; the water environment quality and eutrophication of some lakes continue to deteriorate. Current analyses of lake pollution are limited by inadequate samples, making it challenging to discern regional characteristics among lake groups. In this paper, the characteristics of nitrogen and phosphorus pollution in surface sediments of 23 major lakes in middle and lower Yangtze River were analyzed. Results reveal that the average total nitrogen (TN) concentration in river-connected lakes and half-connected lakes are the highest, with no significant differences observed, followed by suburban lakes and urban lakes in descending order. Conversely, the mean total phosphorus (TP) concentration features notable differences, with urban lakes ranking the highest, followed by suburban lakes, river-connected lakes, and half-connected lakes in descending order. Although improvements have been made in the eutrophication status of regional urban and suburban lakes, the comprehensive pollution degree classification suggests that most lakes in the area still face severe pollution challenges. Therefore, there is still an urgent need to strengthen efforts in controlling nitrogen and phosphorus eutrophication. The results provide an overall understanding of the eutrophication of lakes in the middle and lower reaches of the Yangtze River, and support the prevention and control of eutrophication of lakes in the Yangtze River basin.