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Summary: The rapid economic development has caused heavy pollution in the Pearl River Delta Region (PRDR) and neighboring regions. In order to investigate the polluted characteristics, a coupled modelling approach has been deployed and the study area in the Pear River Delta is divided into two modelling systems: a river network that is simulated by a 1D hydrodynamic and water quality model, and an estuary that is modelled by a 3D model. The 1D river network model is coupled with the 3D estuary model based on the mass conservation criteria. The hydrodynamic (HD) model is based on 1D hydrostatic shallow water equations, and is solved by the Alternating Direction Implicit Approach. The water quality (WQ) model component is based on advection–diffusion equations. Some physical and bio-chemical processes are included in the WQ model to address the water pollution problems by different pollution substances, in particular, to the chemical oxygen demand (COD). The water quality data of the main rivers from 2004 to 2007 were collected, processed and evaluated. Because no detailed water quality data in the river is available, the COD source pollution intensity in the water quality model is taking the pollutant load from the confluence of the main five outlets of the Pearl River Estuary (PRE) for 1996–2007 as surrogate. The results show that the pollutants from the PRDR have a large impact on the quality of the Hong Kong seawater and much more serious in the wet season with high river discharge. An insight of the flow and transportation mechanism in the river and estuary system has been obtained through the paper, and a reliable basis to control water pollution of the Pearl River Delta is provided in this paper. [Copyright &y& Elsevier]