China has adopted nuclear power generation as one of the strategic energy sources to resolve the dilemma between its ever-growing energy demand and the associated environmental issues. To achieve the latter, a systematic assessment of the state of the ecosystem near nuclear power plants and its restoration via ongoing recovery actions would be highly desirable and much needed. Current assessment methods are mostly based on the individual components of the ecosystem and the methods are therefore not integrated. In this paper, we report a set of system-based assessment indices to study the restoration of Daya Bay in Guangdong, China where a nuclear power plant has been in operation for 15 years. The results show that decades of intensive exploitation by the various coastal activities have pushed Daya Bay's ecosystem away from its baseline and its structure and functions are impaired; ecosystem restoration does not make up for the weakening of the ecological carrying capacity due to anthropogenic sea-use, nonetheless, the potential for recovery still exists. The case study suggests that the system-based indices can provide integrated information for ecosystem restoration assessment and management.