Water exchangeability is an indicator for evaluating the self-purification ability of estuary. To study the influence of shoreline changes and sea level rise on water exchange in the Pearl River Estuary，we establish a two-dimensional hydrodynamic-conservative mass transport model，compare the results of water level and flow direction simulated by the model with the measured data，and use the Euler method to calculate the water residence time variation of the Pearl River Estuary due to coastline changes and sea-level rise under the condition of wet and dry seasons and high and low tides. The results show that the impact of shoreline changes on water exchange in the Pearl River Estuary is different，for example from the 1970s to 2010，the average water residence time of the Lingding Bay first remains almost unchanged and then decreases slightly，while the water average water residence time of the Huangmao Bay and Modao Bay vary depending on the situation. Sea level rise is not conducive to water exchange，the water residence time increases with the rise of sea level，and the time increases in the dry season is longer than that in the wet season.