Against the backdrop of global warming, ongoing sea-level rise is known to substantially affect saltwater intrusion processes and ecosystems in estuarine regions. The Qinjiang Estuary was selected as the study area, and a three-dimensional numerical model of saltwater intrusion was developed to investigate dry-season salinity responses under sea-level-rise scenarios of 0~0.4 m. The results show that sea-level rise is associated with accelerated surface-layer flow and decelerated bottom-layer flow, leading to increased bottom salinity and enhanced vertical salinity exchange. A more pronounced salinity response is observed in the river channel reach, where the maximum salinity increase during spring tides reached 210.08%. Ecologically, the minimum salinity in the Maowei Sea mangrove area exceeded the optimal range for seedlings of Kandelia obovata and Aegiceras corniculatum, indicating an elevated risk of salinity stress. At the Qingnian Junction, salinity is increased by 67.17%, suggesting that the saline environment may further intensify the corrosion risk of the lock's metal structures during operation. These findings provide scientific support for ecological conservation in the Qinjiang Estuary, water-resources management and saltwater-intrusion risk control, as well as operation-phase anti-corrosion maintenance decisions for the lock structures at the Qingnian Junction.