Over the past 50 years, the burgeoning socioeconomic development in Xiamen has led to a significant decrease in the area and the tidal influx of its coastal waters, resulting in the degradation of its marine ecosystem. Nonetheless, through the implementation of comprehensive management measures such as causeway openings and coastal dredging, Xiamen Bay has seen marked improvements in the water quality of various local waters: dissolved oxygen (DO) levels have stabilized, inorganic nitrogen and reactive phosphate levels have decreased, and the diversity index of large benthic organism communities has increased. These results well demonstrate the effectiveness of Xiamen’s comprehensive coastal waters management in improving its marine ecosystem and environment.