This dataset presents the fatty acid concentrations (range: n-C12 to n-C34) from 9 sediment samples which are given in µg/g sediment. Different fatty acid compounds were found: n-fatty acids, iso-branched, anteiso-branched, monounsaturated, methyl branched, cyclopropyl, di-unsaturated and hydroxyl fatty acids, as well as phytanic acid. Biomarker parameters include the concentrations of short-chain (n-C12 to n-C19) and long-chain (n-C20 to n-C34) n-fatty acids, the higher plant fatty acid index (HPFA) and the ratio of iso- and anteiso-branched fatty acids C15 and C17 versus long-chain n-fatty acids (IA index). The fatty acids were measured using a TRACE 1310 Gas Chromatograph coupled to a TSQ 9000 Mass Spectrometer (Thermo Scientific).