Hypoxia has become an overwhelming phenomenon in the coastal environment off the Changjiang (Yangtze River) estuary. Seasonal data were obtained in the Changjiang estuary during 2003, 2004, 2005, and 2009 and during an additional cruise between April and May in 2007 on the dissolved oxygen distribution of the bottom water, on hypoxic events, and on their potential causes. Dissolved oxygen was less than 3.0 mg L⁻¹ in the summer and less than 5.0 mg L⁻¹ in the spring and autumn in the topographic trough and was generally lower than that in the surrounding bottom water of the Changjiang estuary. In the summer, there was a positive correlation (r²  =  0.57) between dissolved oxygen concentration and temperature, contrary to the observations in the autumn and winter. A strong halocline and thermocline appeared in the spring and summer. A change in temperature structure was observed in an additional cruise in 2007; the vertical transport of dissolved oxygen flux, which was restricted by stratification, reached 2.77 g m⁻² d⁻¹. Large nutrient inputs and phytoplankton seem to contribute to hypoxia in the Changjiang estuary.