A unsteady, depth-averaged two dimensional simulation model for water quality prediction in estuary is described, and the Galerkin``s finite element technique with the linear interpolating function is used for the analysis of this model. The model consists of two submodels which are flow induced circulation model and pollutant dispersion model. The presented pollutant dispersion model represented only the effect of biodegration by plankton, sedimentation, and diffusion of material into the benthos by a decay term. Two submodels, the flow induced circulation model and the pollutant dispersion model, are tested by comparing computed results with analytical solutions in a one dimensional rectangular channel where analytical solutions are known. The tested results are well agreement with the analytical solutions. Also the above two submodels are examined in a simple two dimensional channel with free boundary. This model is applied to Ulsan estuary to simulate circulation and pollutant dispersion. The flow pattern by the model is shown to be similar to the observed data. It is, thus, concluded that this water quality simulation model may be useful for simulating water quality in estuary.