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Abstract: This study for the first time examined dissolved metals (Cu, Cd, and Mn) together with dissolved oxygen and carbonate system in the whole Pearl River Estuary system, from the upper rivers to the groundwater discharges until the estuarine zone, and explored their potential impacts in the adjacent northern South China Sea (SCS) during May–August 2009. This river-groundwater-estuary system was generally characterized by low dissolved metal levels as a whole, whilst subject to severe perturbations locally. In particular, higher dissolved Cu and Cd occurred in the North River (as high as 60nmol/L of Cu and 0.99nmol/L of Cd), as a result of an anthropogenic source from mining activities there. Dissolved Cu levels were elevated in the upper estuary near the city of Guangzhou (Cu: ∼40nmol/L), which could be attributable to sewage and industrial effluent discharges there. Elevated dissolved metal levels (Cu: ∼20–40nmol/L; Cd: ∼0.2–0.8nmol/L) also occurred in the groundwaters and parts of the middle and lower estuaries, which could be attributable to a series of geochemical reactions, e.g., chloride-induced desorption from the suspended sediments, oxidation of metal sulfides, and the partial dissolution of minerals. The high river discharge during our sampling period (May–August 2009) significantly diluted anthropogenic signals in the estuarine mixing zone. Of particular note was the high river discharge (which may reach 18.5 times as high as in the dry season) that transported anthropogenic signals (as indicated by dissolved Cu and Cd) into the adjacent shelf waters of the northern SCS, and might have led to the usually high phytoplankton productivity there (chlorophyll-a value >10μg/L). [Copyright &y& Elsevier]