An ecosystem model was developed to simulate the water quality and plankton dynamics in the Danshuei River estuary, Taiwan. The model simulates the hydrodynamics with a laterally integrated 2-dimensional intratidal numerical model, which supplies the physical transport processes for simulation of water quality and plankton state variables. The application of the model to the Danshuei River estuary indicates that the point source loadings are mainly responsible for the degraded water quality and very high nutrient concentrations in the estuary. The impacts of wastewater discharges are tightly controlled by the transport processes. Frequent occurrence of high river flow and flood events rapidly cleanses the estuary by flushing out both pollutants and plankton populations. The plankton is allowed to grow to significant populations if low river flow lasts for a period much longer than the biological time scale.