Abstract: The Dan'ao River is the one with the largest flow and the worst water quality in Daya Bay's rivers flowing into the Southern Ocean. Exploring the hydrodynamic water quality changes of the Dan'ao River is of great significance for coastal environmental risk control and coastal zone remediation. The hydrodynamic water quality model of the tidal reach and the whole estuary area of the Dan'ao River were established based on the EFDC model. The hydrodynamic process in the downstream and estuarine area under the action of runoff and current was mainly researched, and the response relationship between saltwater intrusion and water quality in different water periods was estimated quantitatively. The results showed that the tidal characteristics of Daya Bay were mainly irregular semi-diurnal mixed tide, which was diurnal tide about 8-10 days a month, and semi-diurnal tide about 20-22 days a month. Under the diurnal tide and semi-diurnal tide, the bottom water could invade the upstream of Huzhao section (the national section) about 700-1 100 m, but the surface water could not reach the section. The salt water intrusion in different water periods showed that the salt content was the highest in the low water period, up to 16‰. Based on the hydrologic data of 2019, the boundary of river and sea water mass was preliminarily divided, which could provide the basis for the classification and regulation of fresh water and sea water in the estuary and coastal zone. According to the interaction between salt water and fresh water, the concentration of pollutants in the high water period increased significantly, about 10% higher compared with that in the average water period, and the change of upstream flow directly affected the water quality, especially during the neap tide. It was suggested to optimize the project scheduling to reduce the discharge during the neap tide.