Sediment traps were deployed in the Gulf of Papua in June-July 1997, to determine fluxes of organic matter and inorganic elements from the photic zone to deeper waters at the base of the continental slope and in the northern Coral Sea. Three stations, ranging from 900 to 1500 m depth, had "shallow" traps at 300 m below the water surface and "deep" traps set similar to100m above the bottom. Infiltrex II water samplers collected particulate and dissolved organic matter from the Fly, Purari and Kikori rivers, and near-surface water from the shelf of the Gulf of Papua. Samples were analysed for molecular organic biomarkers to estimate the sources of organic carbon and its cycling processes.Dry weight fluxes from the shallow traps ranged from 115 to 181 mg m(-2) day(-1) and particulate organic carbon (POC) fluxes ranged from 1.2 to 1.9mM OCm-2 d(-1) with molar organic carbon to particulate nitrogen ratios (C/N) ranging from 6.0 to 6.5. Fluxes in deep traps were likely influenced by both early diagenesis and entrapment of resuspended shelf sediments. Dry weight fluxes in deep traps ranged from 106 to 574 mg m(-2) day(-1) and POC fluxes ranged from 0.6 to 1.5mM OC m(-2) d(-1), with C/N ratios ranging from 8.5 to 10.8. C-13/C-12 ratios were -20.2parts per thousand to -21.7parts per thousand in all trap samples, indicating that most of the settling POC was "marine-derived". Shallow traps had delta(15)N values of 6.3parts per thousand to 7.2%. while the values in deep traps were 4.9-5.0parts per thousand, indicating the N-rich near-surface OC was less degraded than that in the deep traps. The biogenic lipids consisted of hydrocarbon, sterol and fatty acid biomarkers indicative of marine zooplankton, phytoplankton and bacteria. Sterol markets for diatoms and dinoflagellates were abundant in the water samples. Highly branched isoprenoid alkenes, usually attributable to diatoms, were also detected in both water and shallow traps. Traces Of C-26-C-34 n-alcohols indicative of land-plant biomarkers, were found in river water samples and in the shallow sediment traps. A large unresolved complex mixture (UCM) of hydrocarbons, and a uniform distribution of n-alkanes, indicative of petroleum hydrocarbons, were also detected in the traps. Hopane and sterane biomarkers detected in the trap oil were characteristic of a marine carbonate source, and the aromatic hydrocarbon composition distinguished at least two different oil signatures.We concluded that mass and POC fluxes were similar to those reported for other continental shelves and marginal oceans in tropical and subtropical regions. There was a dramatic decrease in POC as particles sank, due to zooplankton repackaging and photochemical and bacterial decomposition. Carbon isotopic and biomarker patterns showed most of the POC in the sediment traps was marine-sourced with only traces of terrestrial input. There was a significant flux of petroleum, which may signal the existence of natural petroleum seeps in this region. Crown Copyright (C) 2004 Published by Elsevier Ltd. All rights reserved.