Precise indices based on n-alkane signatures were developed in order to determine the sources and composition of sedimentary organic matter (SOM) in coastal systems. The Arcachon Bay (France), a well-studied temperate lagoon, was used as an example of a complex coastal system sheltering a wide diversity of OM sources. Three main groups of sources were well discriminated from their n-alkane signatures: seagrass (Zostera sp.) produced mainly n-C17, n-C19, n-C21, n-C23 and n-C25 alkanes, algae (Rhodophyta, Chlorophyta) produced n-C15 and n-C17 and the terrigenous input [Quercus sp., Spartina sp. and river suspended particulate OM (SPOM)] was characterized by n-C25, n-C27, n-C29, n-C31 and n-C33. From the above and literature n-alkane fingerprints, we developed a set of indices (n-alkane ratios) to quantify the contribution of these three major sources of the SOM. At the Arcachon Bay scale, they indicated that SOM was composed mainly of seagrass (ca. 53±19%) and terrestrial (ca. 41±17%) material, followed by algae (ca. 6±9%). Moreover, the new n-alkane indices exhibited more relevant spatial patterns than classical ones – the TAR (C27+C29+C31/C15+C17+C19; terrestrial to aquatic ratio) and the Paq (C23+C25/C23+C25+C29+C31; aquatic plant %) – with a greater contribution from marine sources in the central part of the lagoon where a high density of Zostera seagrass was observed. Therefore, the development of precise indices adapted to the local diversity of OM sources is needed when using n-alkanes for quantifying the source composition of SOM in complex coastal systems.