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The surface distribution of lipid biomarkers, elemental and isotopic compositions ( δ 13 C and δ 15 N, C/N) were investigated from coastal sediments of Brunei Bay, in order to understand the sources and biogeochemical processes of the organic matter. Fatty acid biomarkers from terrestrial higher plants (e.g., long-chain fatty acids > 20), phytoplankton (e.g., 20:5n-3 and 22:6n-3) and microbial activity (e.g., iso-, anteiso fatty acids, 10Me-16:0) were identified. The ratios of carbon and nitrogen isotopes ( δ 13 C, δ 15 N) and C/N had values ranging from –30.62 to –27.43‰, 1.70 to 3.57‰, and 4.07 to 15.62 respectively, suggesting the prevailed inputs of terrestrially-derived organic matter sources with typical characterization of mangrove estuaries. Principal component analysis separated lipids of autochthonous aquatic production as the major source, followed by allochthonous terrestrial derived input. The presence of bacterial derived lipids and short chain lipids with low and C/N ratios suggest the preferential utilization and decomposition of organic matter by microbial activity. An enrichment of the δ 15 N ratios could be due to marine cage culture activities and surface runoff from cultivated areas via fluvial transport.