Using the model of health assessment of a marine coastal ecosystem, we assessed the petrochemical sewage waters in Daya Bay using the ecological survey data of 2011 and 2012. The results showed that the ecosystem health comprehensive index (EHCI) of the petrochemical sewage waters of Daya Bay during the flood season (August 2011) was 0.808, suggesting that the ecosystem health was at a "good" level. Spatial distribution of EHCIs of inshore waters was higher than that of offshore waters, and the comprehensive biodiversity index of benthos was found to be the primary factor that negatively affected ecosystem health. The EHCI of the petrochemical sewage waters in the dry season (January 2012) was 0.767, suggesting that ecosystem health was at a "moderate" level. Spatial distribution of EHCIs of offshore waters was higher than that of inshore waters, and the comprehensive biodiversity indices of phytoplankton and benthos were found to be the primary factors that negatively affected ecosystem health. Compared to 2006 and 2007, health status of the petrochemical sewage waters in Daya Bay was deteriorating and changed from "good" to "moderate".