Enclosure aquaculture (EA) in lakes is one of the primary types of inland freshwater aquaculture, making significant contributions to food security, employment, and economic growth. However, with the rapid booms in EA intensity, the ecological balance of lakes is gradually being disrupted. Thus, it is crucial to profoundly understand the spatiotemporal dynamics of EA for lake ecosystem preservation and restoration. Compared to field surveys, satellite remote sensing offers advantages such as large-scale coverage, traceability, and cost-effectiveness, making it the optimal choice for monitoring lake EA. This study developed an automatic algorithm for monitoring EA based on Sentinel-1 SAR data and the U-Net model. The algorithm was validated on 10 selected typical lakes, and it achieved a classification accuracy of over 80% in all cases. Additionally, the algorithm was used for monitoring EA lakes in the Yangtze-Huaihe River Basin, providing insights into the spatiotemporal evolution of EA from 2016 to 2023. The results show that a total of 48 lakes (larger than 10 km2) in the Yangtze-Huaihe River Basin engaged in aquaculture activities. From 2016 to 2023, the area of EA in these lakes significantly decreased, with the total area shrinking from 2118.72 km2 to 462.94 km2. Among these lakes, 36 (approximately 77%) have completely removed their enclosure nets. Our findings offer crucial support for evaluating the dynamics of lake water environments and the transformation of aquatic ecosystems pre- and post-enclosure EA removal. Additionally, they offer a scientific basis for formulating measures aimed at lake ecosystem restoration, environmental protection, and sustainable development.