To improve water quality and enhance ecological management, all the net-pen aquaculture facilities in the East Lake Taihu have been removed by the end of 2018. Understanding the impact of this activity on lake ecosystem health is critical to promote efficient ecological management. Aquatic vegetation, especially submerged aquatic vegetation is an essential component of healthy lake ecosystem, as they provide food and shelter, help to secure and stabilize shorelines and modulate nutrient circulation. Additionally, submerged aquatic vegetation can improve water clarity by competing for nutrient with algae. Monitoring submerged aquatic vegetation is fundamental to lake ecosystem health evaluation. In this study, we leverage Sentinel-2 data to map the temporal change of different types of aquatic vegetation types (i.e., emergent vegetation, floating-leaved vegetation and submerged aquatic vegetation), as well as the dominant submerged aquatic vegetation species. We found that the dominant vegetation shifted from submerged to floating-leaved vegetation after the pen aquaculture removal in East Lake Taihu. Meanwhile, the total coverage of submerged aquatic vegetation and its diversity significantly decreased, suggesting environmental degradation in this area. Our research indicated that removing net-pen culture has negative effect on lake ecosystem health. Efficient ecological management of this critical lake system requires comprehensive evaluation before they implement any management activities.