Although an inordinate fraction of the global sediment flux to the ocean occurs in tropical mountainous river margins, little is known regarding the sources and fate of organic matter in these systems. To address these knowledge gaps, the distribution and composition of organic matter in sediments from the Fly River delta-clinoform were examined in the context of the source-to-sink study of the Papuan Continuum. The significant contrasts in the texture of seabed sediments measured across the study area coincided with stark contrasts in concentration and composition of the sedimentary organic matter. Coarser sediments displayed significantly lower organic carbon and nitrogen contents, more enriched stable carbon and nitrogen compositions, lower lignin product yields, and distinctly different lignin and nonlignin product compositions than their fine-textured counterparts. Compositional differences were also measured between high- and low-density fractions of selected sediment samples. Subsurface sediments showed marked compositional variations that were predominantly associated with changes in the texture of the deposits. Most sediments were characterized by moderate carbon loadings (0.5–1.0 mg C m−2), although several samples from the outer topset region, an area of sediment bypass, were characterized by lower carbon loadings indicative of enhanced carbon losses. Overall, the organic matter in both surface and subsurface sediments appeared to have predominantly a terrigenous origin, with no evidence for dilution and/or replacement by marine carbon. The measured compositions were consistent with contributions from modern vascular plant detritus, aged soil organic matter, and very old or fossil organic matter devoid of recognizable biochemicals.