This study proposes a framework for estimating pollutant flux in an estuary. An efficient method is applied to estimate the flux of pollutants in an estuary. A gauging station network in the Danshui River estuary is established to measure the data of water quality and discharge based on the efficient method. A boat mounted with an acoustic Doppler profiler (ADP) traverses the river along a preselected path that is normal to the streamflow to measure the velocities, water depths and water quality for calculating pollutant flux. To know the characteristics of the estuary and to provide the basis for the pollutant flux estimation model, data of complete tidal cycles is collected. The discharge estimation model applies the maximum velocity and water level to estimate mean velocity and cross-sectional area, respectively. Thus, the pollutant flux of the estuary can be easily computed as the product of the mean velocity, cross-sectional area and pollutant concentration. The good agreement between the observed and estimated pollutant flux of the Danshui River estuary shows that the pollutant measured by the conventional and the efficient methods are not fundamentally different. The proposed method is cost-effective and reliable. It can be used to estimate pollutant flux in an estuary accurately and efficiently.