Extensive physical and biological measurements were made of the surface sediments within the shallow, semi-urbanised Coombabah Lake in southern Moreton Bay, Australia. Sediment bulk parameters (C/N ratios, d13C and d15N) and fatty acid biomarkers were used to determine distributions and sources of organic matter in the intertidal sediments. The determination of organic matter sources within coastal and estuarine settings is important in understanding the roles of organic matter as energy and nutrient sources. Spatial variability of biomarker values within the sediments were interpreted by thematic maps employing the Krigging algorithm. Grain size analysis indicated the lake was dominated by mud (<63 孩 in the southern (landward) and sand (>63 孩 in the northern (seaward) lake regions, respectively. Surface sediment organic C and N values ranged from 0.12% to 1.76% and 0.01% to 0.12% dry weight, respectively, and C/N ratios averaged 16.3ᳮ19%. Sedimentary d13C values ranged from -26.1頴o -20.9鬠with an average value of -23.9ᱮ0鮠Sedimentary d15N values ranged from +1.7頴o +4.8鬠with an average value of +2.8ᰮ8鮠Bulk sediment parameters suggested that sedimentary organic matter is provided predominantly by allochthonous sources in the form of fringing mangroves. Thirty-nine individual fatty acids were identified using gas chromatography-mass spectrometry. The mean contributions of long chain fatty acids (LCFAs), polyunsaturated fatty acids (PUFAs), saturated fatty acids (SAFAs) and bacterial fatty acids (BAFAs) were, respectively, 13.9ᱱ.4%, 7.6ᴮ1%, 53.6Ḯ6% and 18.2ᴮ6% of the identified fatty acid methyl esters (FAMEs), with BAFAs occurring in all sampled sediments. Fatty acid compositions varied throughout lake sediments, which indicated spatial differences in autochthonous and allochthonous organic matter sources, including terrestrial and planktonic (i.e. zooplankton, diatoms and other algal species) sources. The contribution of organic matter from shoreline mangroves was confirmed by the presence of LCFAs and 18:2?6 and 18:3?3, which are markers for mangroves in this ecosystem. BAFAs were identified in increased proportions in sediments adjacent to urban developments and dominated by mud. Grain size was identified as a dominant factor in the fatty acid compositions and contributing values to FAME pool. Spatial patterns of C/N ratios, d13C and d15N values, and fatty acid biomarker contributions illustrated that there is a greater contribution of autochthonous and labile organic matter to the sedimentary organic matter pool in the northern (marine entrance) sediments compared to the more allochthonous sourced organic matter of the southern region of the lake. This study details the distribution and sources of organic matter within Coombabah Lake and illustrates the usefulness of a multiple biomarker approach in discriminating organic matter sources within estuarine environments.