Organic matter in surface sediments from the upper reach of the Pearl River Estuary and Lingdingyang Bay, as well as the adjacent northern South China Sea shelf was characterized using a variety of techniques, including elemental (C and N) ratio, bulk stable organic carbon isotopic composition (?13C), and carbohydrate composition analyses. Total organic carbon (TOC) content was 1.21±0.45% in the upper reach, down to 1.00±0.22% in Lingdingyang Bay and to 0.80±0.10% on the inner shelf and 0.58±0.06% on the outer shelf. ?13C values ranged from ?25.1‰ to ?21.3‰ in Lingdingyang Bay and the South China Sea shelf, with a trend of enrichment seawards. The spatial trend in C/N ratios mirrored that of ?13C, with a substantial decrease in C/N ratio offshore. Total carbohydrate yields ranged from 22.1 to 26.7 mg (100 mg OC)?1, and typically followed TOC concentrations in the estuarine and shelf sediments. Total neutral sugars, as detected by the nine major monosaccharides (lyxose, rhamnose, ribose, arabinose, fucose, xylose, galactose, mannose, and glucose), were between 4.0 and 18.6 mg (100 mg OC)?1 in the same sediments, suggesting that significant amounts of carbohydrates were not neutral aldoses. Using a two end-member mixing model based on ?13C values and C/N ratios, we estimated that the terrestrial organic carbon contribution to the surface sediment TOC was ca. 78±11% for Lingdingyang Bay, 34±4% for the inner shelf, and 5.5±1% for the outer shelf. The molecular composition of the carbohydrate in the surface sediments also suggested that the inner estuary was rich in terrestrially derived carbohydrates but that their contribution decreased offshore. A relatively high abundance of deoxyhexoses in the estuary and shelf indicated a considerable bacterial source of these carbohydrates, implying that sediment organic matter had undergone extensive degradation and/or transformation during transport. Sediment budget based on calculated regional accumulation rates showed that only ~50% of the influxes of terrestrial organic carbon were accumulated in the estuary. This relatively low accumulation efficiency of terrestrial organic matter as compared to the total suspended solids (accumulation efficiency ~73%) suggested significant degradation of the terrestrial organic carbon within the estuarine system after its discharge from the river. This study demonstrated that the combination of the bulk organic matter properties together with the isotopic composition and molecular-level carbohydrate compositions can be an efficient way to track down the source and fate of organic matter in highly dynamic estuarine and coastal systems. The predominance of terrestrially originated organic matter in the sediment and its generally low accumulation efficiency within the estuary is not surprising, and yet it may have important implications in light of the heavy anthropogenic discharges into the Pearl River Estuary during the past thirty years.