In order to find out the annual variations in the marine ecosystem of the East China Sea, temperature, salinity, nutrients, chlorophyll-a, suspended solids, and suspended particulate organic carbon were extensively investigated in the northern East China Sea during the Summer of 2003 and 2006. During the Summer of 2003, the northern East China Sea was not significantly affected by the input of fresh waters from the Changjiang River. During the Summer of 2006, however, fresh waters of the Changjiang River intruded into the western part of the study area where temperature, nitrate, and phosphate in the surface waters were higher than in the other areas, and salinity, silicate, and suspended solids in the surface waters were lower. As a result of the increase in nitrate and phosphate concentrations, concentrations of chlorophyll-a and suspended particulate organic carbon increased in the western part compared with the other areas. However, the depth-integrated chlorophyll-a concentrations measured during the Summer of 2003 were rather similar to those during the Summer of 2006, and not considerably different from those measured in the East China sea during the Summer of 1994 and 1998. Therefore, the depth-integrated chlorophyll-a concentrations have not significantly changed in the East China Sea over the last 12 years. The lower concentrations of silicate and suspended solids in the western part may be related to construction of the Three-Gorges Dam since the concentrations of silicate and suspended solids in fresh waters of the Changjiang River have significantly decreased after construction of the Three-Gorges Dam in June 2003.