Enclosure aquaculture 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 escalation in enclosure aquaculture intensity, there is an observed disruption to the ecological balance of lakes on a gradual basis. It is imperative to develop a profound understanding of the spatiotemporal dynamics of enclosure aquaculture in order to facilitate the preservation and restoration of lake ecosystems. In comparison with field surveys, satellite remote sensing offers a number of advantages, including large-scale coverage, traceability, and cost-effectiveness, thus rendering it the optimal choice for the monitoring of lake enclosure aquaculture. The present study developed an automatic algorithm for monitoring enclosure aquaculture based on Sentinel-1 SAR data and the U-Net model. The efficacy of the proposed algorithm was assessed through a rigorous evaluation process involving the utilization of validation data from ten representative enclosure aquaculture lakes. The evaluation yielded a remarkable extraction accuracy exceeding 80% across all instances, thereby substantiating the algorithms effectiveness. Moreover, the validation results based on long-term random sampling points demonstrated an overall classification accuracy that exceeded 95%.In addition, the algorithm was employed for the monitoring of enclosure aquaculture lakes in the Yangtze-Huaihe River Basin, thereby providing insights into the spatiotemporal evolution of enclosure aquaculture from 2016 to 2023. The results indicated that a total of 48 lakes (larger than 10 km²) in the Yangtze-Huaihe River Basin were engaged in aquaculture activities. From 2016 to 2023, the area of enclosure aquaculture in these lakes underwent a substantial decrease, with the total area diminishing from 2118.72 km² to 462.94 km². Of the lakes under consideration, 34 (approximately 71%) had successfully removed their enclosure nets. The findings of the present study offer crucial support for the evaluation of the dynamics of lake water environments and the transformation of aquatic ecosystems both before and after enclosure and the removal of enclosure aquaculture. Moreover, they provide a scientific underpinning for the formulation of measures aimed at the restoration of lake ecosystems, environmental protection, and sustainable development.