Based on the marine ecological investigation in the coastal area of Beibu Gulf, Guangxi in September 2009, a GIS-based evaluation was conducted on the present status of ecological environment quality, including seawater quality, nutrient level, biomass, primary productivity, biodiversity, and ecological buffer capacity, in the area in autumn, and the integrated ecological risk index (ERI) was adopted to assess the risk of the coastal ecosystem in the Gulf. In September 2009, the study area had a better ecological environment quality. Most of the risk indicators were at medium or lower level, and the total area was overall at low ecological risk level. The ERI showed that there was an obvious spatial heterogeneity in the distribution of the ecological risk. The nearer to the harbors, the higher the risk was.