Hydrocarbon compounds viz. aliphatic hydrocarbons, polycyclic aromatic hydrocarbons (PAHs), sterols, long chain fatty acids, alkanones and alkanals in surface sediment of Setiu Wetland were analysed and characterized using GCMS. The concentration of total identified resolved n-alkanes (TIRNA) in sediment ranged from 2.99–11.6 μ g g− 1 dry weight. The distribution of the aliphatic fraction showed the presence of n-alkanes ranging from C12 to C36 with high predominance for long chain homologues (C25-C31) and a carbon maximum at C29 and C31 with CPI > 3; these observations provide evidence for the presence of biogenic terrigenous input corresponding to epicuticular plant waxes into the lagoon sediments. Positive and strong correlation between n-alkanes associated with terrigenous input (ALK TER) and TIRNA suggest terrestrial input is the main sources of TIRNA in this study area. The absence of unresolved complex mixture (UCM) in the chromatogram and the absence of hopanes, steranes and PAHs compounds are indicative of uncontaminated sediment by petrogenic and pyrogenic hydrocarbons. The concentration of total identified sterols (TIS) ranged from 1.41 μ g g− 1 dry weight to 3.11 μ g g− 1 dry weight with cholesterol, β -Sitosterol and stigmasterol were generally the most dominant and abundant components detected at almost all stations. A positive and strong correlation was observed between B-Sitosterol and TIS and the distribution of long chain n-alkan-2-ones in the range of C21 to C27 with odd to even predominance and n-alkanals (C20 to C28), n-alkanols (C22–C30) and n-alkanoic acids (C22–C30) with even to odd predominance provide further evidence for biogenic sources of hydrocarbons with terrestrial plant input as the predominant source. It was noted that a minor contribution associated with marine phytoplankton (algae) as well as bacteria were also observed in some of the sediment samples superimposing with the terrigenous plant wax input. In general results from this study clearly showed the lagoon sediment of Setiu Wetland is still in uncontaminated condition where terrestrial plants input are the dominant contributor of organic compounds in the sediments with a minor input from marine organisms.

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