Abstract: The main source of water supply for coastal cities in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) mainly comes from river channels. During the dry season, the runoff at the Pearl River Estuary decreases, and the upstream intrusion of saltwater causes difficulties in river water abstraction, leading to water supply issues for coastal cities in the GBA. Since 2004, the Pearl River Water Resources Commission of Ministry of Water Resources(PRWRC) has implemented emergency water regulations for saltwater suppressing and freshwater replenishment for 20 consecutive years, effectively mitigating the upward impact of saltwater intrusion and comprehensively ensuring the water supply safety of cities such as Macao and Zhuhai and other cities. With the high-quality economic and social development and the increasing demand for refined emergency water replenishment dispatch, issues such as inadequate drilling capabilities and low efficiency in scheme formulation exist in the current basin dispatch process. To enhance the refinement level of basinal regulation in the context of the construction of the Ministry of Water Resources' digital twin basin, the PRWRC has constructed digital twin scenarios through the development of data base, water sector professional models, and application systems. The FEDE technologies (forecasting, early warning, drilling, and emergency plan) were successfully applied to the emergency water regulation for suppressing saltwater and replenishing freashwater in 2021-2022, significantly improving the refinement level of regulation and the efficiency of water abstraction. This provides scientific and technological support for further enhancing the water supply security of urban agglomerations in the GBA.