Purpose The Great War Island (GWI) is a landform of exceptional features and a protected area located in the center of Belgrade at the Sava and Danube River's confluence. The position of GWI causes a large number of possible hydrocarbons inputs that influence the quality of both river waters and sediments. The main objective of this research is to assess the distribution and source of hydrocarbons in sediments deposited at the GWI depending on the river's flow regimes and depositional environment. Material and methods Sediment samples were collected from 16 sites (11 sites along the GWI's coast, 4 sites from the inner of the Island, and 1 specific wetland site). The grain size was determined using a standard wet sieving procedure. The extractable organic matter (OM) was quantified after Soxhlet extraction, and aliphatic and aromatic fractions were isolated by column chromatography. n-Alkanes, diterpanes, terpanes, steranes, and 16 PAHs are analyzed by gas chromatographymass spectrometry. Results and discussion Sand fraction predominates in coastal samples, and clay size fraction in the samples from the inner island environment. The predominance of odd higher n-alkanes indicates the terrestrial origin of OM, while the distribution of lower n-alkanes indicates a certain proportion of algae, bacteria, and/or high maturity of OM. The presence of oil-type pollutants is confirmed by thermodynamically stable biomarker isomers and/or the presence of unresolved complex mixture (UCM). Inner island samples are characterized by the largest amount of C org (up 6%), indicating high bioproductivity and good preservation of OM. Samples from wetland environment are distinguished by the domination of pimaranes and phyllocladanes among saturated hydrocarbons. Conclusions This study revealed that sediments of the GWI mainly contain native OM with a certain anthropogenic input. The native OM predominately comes from higher terrestrial plants (Salix alba, Populus nigra, Fraxinus viridis, Taxodium distichum Rich.), followed by various types of grasses, macrophytes (Salvinia natans, Nymphaea alba), bacteria, algae, and phytoplankton. Anthropogenic OM originates from petroleum, but also combustion products arrived by deposition from the air and runoff.