Knowledge of the sources, distribution and fate of organic matter (OM) in estuarine and adjacent shelf sediments are important for the understanding of the global biogeochemical cycles. Bulk organic carbon (C-org), total nitrogen (TN), biogenic silica (BSi), stable carbon (δC-org) and nitrogen (δN) isotopes, and sediment grain sizes were measured to study the spatial distributions and sources of sediment OM in the Cross River estuary system (CRES) and adjacent shelf. Surface sediments in the CRES were composed of clayey silt and sandy silt, while the adjacent shelf sediments were mainly silty sand. The range of the studied parameters was -28.79‰ to -22.20‰ for δC-org, -1.32‰-6.31‰ for δN, 6.7-29.2 for C-org/N ratios, 0.08%-0.33% for TN, 0.24‰-0.74‰ for BSi, and 0.47%-5.28% for C-org, and their spatial distributions showed a general decreasing trend in both the terrestrial and estuarine OM from the riverine regions to the adjacent shelf. Based on the three-end-member mixing model using the δC and δN isotopic values, ~58.01 ± 15.32% of sediment OM are derived from terrestrial sources dominated by C vascular plants, while ~26.34 ± 9.71% are attributed to estuarine sources dominated by aquatic macrophytes, and ~15.65 ± 12.37% for marine plankton source. Other sources of OM identified included soils underlain C vascular plants and agricultural farms enriched with N, sewage, and petroleum hydrocarbons. The relationship between C-org vs. BSi, and the atomic BSi/Corg ratios suggested that diatoms also play an important role in OM sequestration in surface sediments of the CRES and adjacent shelf. The correlations of the δC-org and δN isotopic values vs. C-org/N ratios resulted in scatter plots, indicating that the distributions of sediment OM in the CRES and adjacent shelf are influenced by post depositional processes, fixed inorganic N adsorbed on fine-grained sediments, microbial degradation, as well as sediment grain size.