Benthic and pelagic communities in the central Gulf of Papua, a major deltaic clinoform located on the south coast of Papua New Guinea, reflect the spatial and seasonal patterns in physical sedimentation conditions and the availability of food resources across this system. The distribution of terrigenous and marine organic substrates, the transport of riverine-derived sediment, and seafloor dynamics are largely controlled by two seasons and wind patterns: the relatively quiescent NW Monsoon and more energetic SE Trades. The physically disturbed inner-topset deposits (<20 m) are dominated at all times by bacterial biomass and have depressed numbers of macrofauna, with evidence of periodic recolonization recorded in sedimentary structures. The inner-topset region also shows strong seasonality in the production and availability of labile organic matter and in bacterial activity. As measured by the concentrations of photopigments and microbial biomass in the upper 2 cm of surface sediments and in the water column, the comparatively quiescent NW Monsoon period is associated with net delivery of reactive substrates as labile organic matter to the bottom and net growth of the benthic microbial community, whereas the Transition period between the NW Monsoonal-Winds ( NW Monsoon) and SE Trade-Winds ( SE Trades), and the SE Trades, are periods of reactive substrate depletion in bottom deposits and decreased benthic bacterial and macroinfaunal biomass. In contrast to the inner-topset, the less physically disturbed outer-topset and foreset show relatively enhanced, but still low, abundances of large macrobenthos and possible evidence of variation related to food supply. The greatest observed seasonal variation in macrofauna occurs in the Umuda Valley off the Fly River, an apparent mobile sediment conduit.