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Due to water supply increase and water quality deterioration, water resources are a critical problem in saltwater intrusion areas. In order to balance the relationship between water supply and water environment requirements, the nexus of water supply-water environment capacity should be well understood. Based on the Saint-Venant system of equations and the convection diffusion equation, the water supply-water environment capacity nexus physical equation is determined. Equivalent reliability is employed to estimate the boundary design water flow, which will then lead to a dynamic nexus. The framework for determining the nexus was then applied to a case study for the Pearl River Delta in China. The results indicate that the water supply-water environment capacity nexus is a declining linear relationship, which is different from the non-salt intrusion and tide-impacted areas. Water supply mainly relies on freshwater flow from upstream, while water environmental capacity is affected by both the design freshwater flow and the water levels at the downstream boundary. Our methods provide a useful framework for the quantification of the physical nexus according to the water quantity and water quality mechanisms, which are useful for freshwater allocation and management in a saltwater intrusion area or the tail area of cascade reservoirs.