Harmful algal blooms (“red tides”) occur primarily in a confined region on the inner shelf off the Changjiang River in the East China Sea during May–August. The areal extent of these blooms has increased dramatically in the last decade, and is thought to be associated with the rapid increase in nutrient supply via the Changjiang River. An interdisciplinary survey conducted in August 2000 identified three areas of high chlorophyll-a concentration in this region: the near-surface Changjiang River plume with high dissolved oxygen and pH, the thermocline above Taiwan Warm Current (TWC) water, and near the bottom north of the Zhoushan Island complex, an area of strong sediment deposition from the Changjiang River with low dissolved oxygen and pH. These results imply that the formation of phytoplankton blooms is controlled by a complex interplay of physical, geological, biological, and chemical processes associated with the Changjiang River discharge, sediment deposition, and TWC intrusions. The predicted increase in nutrient loading in the Changjiang River due to further economic development of Shanghai and reduction in sediment discharge due to the Three Gorges dam suggest that this part of the East China Sea could become an ecosystem disaster, with possible downstream contamination of Korea and Japan, unless the nutrient loading from Shanghai and surrounding cities and aquaculture activities along the coast are reduced.