To investigate organic matter source and reactivity in the Zhujiang River (Pearl River) Estuary and its adjacent areas, particulate organic carbon (POC), particulate hydrolysable amino acids (PHAA), and Chl a during two cruises in July 1999 and July 2000 were measured. The highest POC and PHAA concentration was observed in the waters with maximum Chl a. The spectra distribution, relative content (dry weight in milligram per gram), PHAA-C% POC and other indicators such as the ratios of amino acids vs. amino sugars (AA/As) and glucosamine vs. galactosamine (Glum/Gal) suggested that particulate amino acids in the water column and sediments in the Zhujiang River Estuary were mainly derived from biogenic procures rather than transported from terrestrial erosion. In inner estuary where high turbidity was often observable, organic matter was mainly contributed by re-suspension of bottom sediments with revealed zooplankton, microbial reworked characteristics, which suggest that these organic matters were relatively old. In the estuarine brackish region, organic matter in water column is mainly contributed by relatively fresh, easily degradable phytoplankton derived organic matter. During physical - biological processes within the eastuary, organic matter derived from phytoplankton was subjected to alteration by zooplankton grazing and bacterial reworking.