The pollution baseline values for different elements in the Changjiang Esturary and its adjacent areas were measured by investigation data obtained in 2000, 2006 and 2013, of which the abnormal data were first excluded and then normal distribution test was carried out. Trends of pollution baseline values from 2000, 2006 and 2013 were discussed, which showed that the pollution baseline values of phosphate increased while Cu, Cd and As decreased obviously. The results showed that the concentrations and fluctuation degree of parameters were different, and as a whole, the spatial distribution of different elements shows higher concentration in estuarine area, and the concentration decreases with the distance from the estuary. Factor analysis results show that the pollution source of nutrient is changing obviously, and the DIN contains two major pollutant sources recently. The source of metal is simple and unique, and the transformation of different metal elements in seawater is different.