Based on the annual monitoring on the dissolved heavy metal and petroleum hydrocarbon in 2012, the present pollution situation and features were analyzed to clarify the environmental impact caused by the construction and operation of the Yangshan Port. The results indicated that the dominant heavy metal in Yangshan Port was Hg, followed by Cu, Pb and Zn. It can be classified into two stages throughout the year of 2012, that is, the first stage was from January to May and the second stage was from June to December. Contaminant levels were relatively high in the first stage which were mainly caused by construction and drainage based on the time distribution and cluster analysis of pollutants. The results of spatial distribution showed that areas of high concentration appear at the edge of Xiaoyangshan and the southeast region of Dayangshan Island. For the Yangshan Port was in the special stage that construction and operation is simultaneously underway, it was necessary to control the pollution of harbor.It is proposed to take the concept of development coefficient by using the modified GM(1,1) model in order to evaluate the variation tendency and pattern of contamination deeply. The results indicated that, of all heavy metals, Hg, Cr and Cd are difficult to be eliminated in the investigated waters. Measures need to be strengthened to prevent and control these pollutants.