Large volumes of freshwater and suspended material debouch from the Fly River in southwestern Papua New Guinea into the Gulf of Papua, greatly influencing the hydrography and sedimentary processes within the river delta and adjacent shelf region. Sedimentary facies within the subtidal regions of the Fly Delta are composed mainly of compacted and eroded very fine black sand, and highly laminated, muddy sand and sandy mud, progressing to prodelta mud with intermixed primary and biogenic structures in the inner Gulf of Papua. These prodelta muds grade further to mixed terrigenous-carbonate deposits southwards into the northern Great Barrier Reef and Torres Strait, and to well-bioturbated, fluid mud northwards into the Gulf of Papua. The transition from physically-dominated, estuarine conditions within the delta to more quiescent, marine conditions on the shelf leads to concomitant changes in sediment chemistry, microbial activity and infaunal and epifaunal communities. Particulate (C, N, P) and dissolved inorganic and organic nutrient concentrations were a function of sediment type (higher in finer deposits) rather than location (delta vs gulf). C: N: P ratios of solid-phase nutrients varied greatly, but were usually less than those predicted by the Redfield ratio. Mean interstitial concentrations of dissolved inorganic nutrients were low (μM range), but dissolved organic carbon, nitrogen and phosphorus levels were equivalent to those found in higher latitude systems. Fluxes of dissolved inorganic nutrients were generally low (μmol m −2 day −1). Flux rates were mostly negative (into the sediment) in the delta suggesting that these deposits are a sink for nutrients. In the offshore deposits, dissolved inorganic fluxes were higher and mostly positive indicating that they are a source for dissolved nutrients. Standing crops of bacteria (range: below detection limits— 2.5 × 10 10 cells g −1 dry wt), meiofauna (range: 5–750 individuals 10 cm −2; 9–1006 μg dry wt 10 cm −2) and infauna (range: 86–5555 individuals m −2; 0.10-5.85 g AFDW m −2) were generally lower in the delta than in the gulf. The infauna was dominated by nematodes, copepods, foraminifera and small, tube-building, deposit- and suspension-feeding polychaetes and amphipods. Rates of bacterial productivity were very erratic with sediment depth across stations, ranging from 0–2108 mg C m −2 day −1 (DNA synthesis) and from 0–228 mg C m −2 day −1 (protein synthesis), respectively. Rates of benthic respiration and DOC flux across the sediment-water interface were generally high, ranging from 63–780 mg C m −2 day −1 and from −797 to 514 mg C m −2 day −1, respectively. Epibenthos were more diverse (at the phyletic level) at the mid-shelf than inshore, composed mainly of sponges, crabs, crinoids, echinoids, bivalves, hydroids and asteroids. Demersal nekton abundance was low, dominated by the leatherjacket, Paramonacanthus filicauda, the pony fish, Leiognathus splendens and the grunter, Pomadasys argyreus, suggesting limited transfer of infaunal biomass to higher trophic levels. The response of the benthic regime to the export of freshwater and material from the Fly River generally conforms to the Rhoads et al. [(1985) Continental Shelf Research, 4, 189–213] model of benthic response to effluent derived from the Changjiang River in the East China Sea and is similar to infaunal and sedimentary patterns off the Amazon. Nutrient release from the delta sediments contributes little to water-column production, but in the gulf, nutrient efflux from the benthos contributes, on average, 38 and 61% of the annual N and P requirements of phytoplankton production, reflecting closer benthic-pelagic coupling and enrichment of biological productivity in the Gulf of Papua due to nutrient export from the Fly River.