The purpose of this work is to characterize several potential sources of organic matter (OM) in the Marquesas Islands, French Polynesia, and to understand how these sources contribute to OM pools. Stable isotope (δ13C and δ15N) and fatty acid (FA) compositions of OM potential sources (algal turf, benthic macroalgae, detrital terrestrial plants (DTP), phytoplankton) and OM pools (sediment (SOM) and particulate organic matter (POM)) were studied in coastal areas in Nuku Hiva Island. Isotope compositions of marine POM (δ13C = − 22.5 ± 0.8 ‰; δ15N = 12.1 ± 1.1 ‰) and SOM (δ13C = − 19.1 ± 0.9 ‰; δ15N = 14.4 ± 0.5 ‰) highlighted that OM sources at the base of the local food web had unusually high δ15N values. Potential FA markers of diatoms and/or cyanobacteria (20:5ω3 and 16:1ω7) were found in these two OM pools. In addition, coastal SOM also displayed FA markers of bacteria, macroalgae and terrestrial plants. For marine POM, potential macroalgae FA markers were recorded (18:2ω6 and 16:2ω4). The stable isotope mixing model highlighted the major contribution of phytoplankton to the coastal SOM (62%), followed by benthic macroalgae (32%), whereas marine POM was mainly composed of a mixture of algal turf and phytoplankton in similar averaged proportions (38%) but presenting wide variations. Our results as a whole strongly suggest that pelagic-benthic coupled processes drive the characteristics and properties of OM sources.