The Yangtze River Estuary (YRE) is the largest estuary in China, with three-order bifurcations and four outlets into the sea. In recent years, issues of saltwater intrusions have received increased attention due to the increased levels and frequencies of the intrusions. The saltwater intrusions into the YRE resulting from river discharges were investigated in this study based on river discharge levels at the Datong station. A hydrodynamic and salinity transport model (MIKE21) was used to quantify the influences of the river discharges on the saltwater intrusions in the YRE. The model was effectively validated through observational data of the tidal and salinity levels. The 25%, 50% and 70% frequencies of the river discharges during the dry seasons were determined to be 18,112, 16,331 and 14,832 m3
/s, respectively. A multi-year averaged river discharge of 27,856 m3
/s was used to simulate the salinity level changes resulting from the different river discharges. The results revealed the following: (1) the salinity of the South Branch (SB) was distributed as “high–low–high”; and the changes in the salinity levels were greatly affected by the river discharges. A strong correlation was found between the salinity and flow in the North Branch (NB) and SB of between 0.917 and 1; (2) the changes in the river discharges had major impacts on the changes in the salinity levels in the SB. When the runoff was 27,856 m3
/s, the salinity excessive area rate (the ratio between salinity excessive area (>0.45‰) and the SB area) less than 10%. However, when the river discharges were reduced to 16,331 m3
/s, the salinity excessive area rate is more than 50%; (3) As the river discharges decreased, the amplification line (0.2‰) also rapidly decreased, and the amplification lines (0.45‰, 2‰) increased. At points far from the river’s entrance, the effects of the runoff were observed to be weakened, such as the amplification lines gradually becoming reduced; (4) the changes in the river discharges were observed to have significant impacts on the freshwater reservoir water withdrawal. When the river discharges were maintained at 27,856 m3
/s, the salinity of the Baogang, Chenhang, and Qingcaosha Reservoirs remained below 0.45‰. The salinity levels of the four reservoir locations examined in this study were found to exceed the Chinese drinking water standard (0.45‰) for more than 23 days in the 14,832 m3
/s river discharge scenario, which negatively affected the drinking water of the population living near the YRE.