Due to the unique geographic location, complex navigation environment and intense vessel traffic, a considerable number of maritime accidents occurred in estuarine waters during recent years which caused serious loss of life, property and environmental contamination. Based on the historical data of maritime accidents from 2003 to 2012, which is collected from Shenzhen Maritime Safety Administration, this paper conducted a risk analysis of maritime accidents by applying Bayesian network and fault tree analysis. First a Bayesian network model was introduced to describe the consequence of accidents based on the accident investigation report. Then fault tree analysis was applied to estimate the probability on the basis of accident statistics and ship traffic flow. Finally the risk of maritime accidents in Shenzhen Waters was depicted through the consequence multiplied by the probability of an accident.