In order to monitor water quality in the Yangtze Estuary, water samples were collected and field observation of current and velocity stratification was carried out using a shipboard acoustic Doppler current profiler (ADCP). Results of two representative variables, the temporal and spatial variation of new point source sewage discharge as manifested by chemical oxygen demand (COD) and the initial water quality distribution as manifested by dissolved oxygen (DO), were obtained by application of the Environmental Fluid Dynamics Code (EFDC) with solutions for hydrodynamics during tides. The numerical results were compared with field data, and the field data provided verification of numerical application: this numerical model is an effective tool for water quality simulation. For point source discharge, COD concentration was simulated with an initial value in the river of zero. The simulated increments and distribution of COD in the water show acceptable agreement with field data. The concentration of DO is much higher in the North Branch than in the South Branch due to consumption of oxygen in the South Branch resulting from discharge of sewage from Shanghai. The DO concentration is greater in the surface layer than in the bottom layer. The DO concentration is low in areas with a depth of less than 20 m, and high in areas between the 20-m and 30-m isobaths. It is concluded that the numerical model is valuable in simulation of water quality in the case of specific point source pollutant discharge. The EFDC model is also of satisfactory accuracy in water quality simulation of the Yangtze Estuary.