Abstract: Hypoxia is one of the environmental problems existing in the Pearl River estuary (PRE).In this paper a coupled 3-D hydrodynamic-ecological numerical model is used to investigate the distribution and causes of the hypoxia phenomena in the PRE in summer.Hypoxia at the bottom layer of the major regions is well reproduced by this model,and in complete agreement with the observed pattern.The main results of the simulation show that the hypoxia phenomena in the PRE are caused mainly by the coupled dynamics of the water stratification and biochemical processes.The simulated hypoxia phenomena develop during the neap tide and disappear during the spring tide.The front and salinity stratification impact greatly on the range and intensity of the low oxygen water in the PRE.