Understanding the chemical and C, N isotopic alteration of organic matter (OM) during early diagenesis is crucial to the studies of biogeochemical processes in marine and lacustrine environments. In this study, isotopic composition ( δ 13C and δ 15N), total organic carbon and total nitrogen content of sediment cores, plankton and particulate organic matter (POM) from the coastal area off-shore the Pearl River estuary were determined. In addition, the fractional carbon content of total hydrolysable amino acids, total carbohydrates, total lipids and acid-insoluble organic compounds and their respective δ 13C were analyzed. The δ 13C org of sediment cores from geographically distinct sites (C5 and E4) is fairly constant and just slightly lower than that of the plankton, suggesting that δ 13C can be used as a reliable geochemical proxy indicating OM origin in the studied coastal area. Considerable diagenetic alteration of OC/N was observed, and the diagenetic alteration of δ 15N was significant. A rapid degradation of OM was associated with a rapid bacteria growth in the water column, which governed the diagenesis of the OM. In addition to the kinetic isotopic fractionation associated with the biodegradation of OM, formation and degradation of bacterial biomass contributed significantly to the observed change of δ 13C and δ 15N during diagenesis. Although the bacteria biomass was believed to be rich in 13C relative to the substrate, bacteria biosynthesis also produced 13C-rich and 13C-poor fractions, and the subsequent biodegradation preferentially decomposes the 13C-rich compound classes and the 13C-rich compounds in a specific class as well, which made the δ 13C of remaining organic matter similar to the substrate in the sediment. On the other hand, the low δ 15N of the POM and sedimentary OM relative to the fresh plankton was resulted from the addition of 15N-depleted biomass that was possibly generated by the preferential uptake of 15N-depleted ammonium during bacterial growth.