Abstract: According to the ecological environment survey data of three subtropical aquaculture bays (Maowei Sea, Dapeng Cove and Baisha Bay) along the northern coast of the South China Sea from 2011 to 2012, and by appling methods of comprehensive grading evaluation of aquaculture area as well as river comprehensive water quality index (I_wq) evaluation, we compared the advantages and disadvantages of ecological environment of the same level quantitatively based on classification of marine environment. The results show that only two of the 12 voyages in the three bays (autumn and winter in Dapeng Cove) had a good environmental rating, and the other 10 were medium. In spring, the rating of the three bays was medium and with simila index. In summer, autumn and winter, the environmental quality of Baisha Bay was the worst. In the past two years, five water environmental factors had been alarmed, and the three bays were at risk of eutrophication. The influence of seasonal change on the bay environment increased with the increase of latitude. It is found that the improved I_wq index is more efficient in comparing the environmental conditions of the same level, but its comparability among different levels is uncertain.