The rapid economic development in The Pearl River delta region (PRDR) has exerted serious potential pollution threats to areas in the vicinity, which have complicated the task of environmental protection in Hong Kong and Macau. In this paper, a three-dimensional numerical pollutant transport model coupled with a synchronised numerical hydrodynamic model, is developed and employed to simulate the unsteady transport of a representative water quality variable chemical oxygen demand in The Pearl River Estuary. It is demonstrated that there exists a transboundary pollutant transport action between Guangdong Province and Hong Kong for the pollutants in the wastewater discharged from PRDR.