Ashmore Trough in the western Gulf of Papua (GoP) represents an outstanding modern example of a tropical mixed siliciclastic-carbonate depositional system where significant masses of both river-borne silicates and bank-derived neritic carbonates accumulate. In this study, we examine how benthic foraminiferal populations within Ashmore Trough vary in response to sea level–driven paleoenvironmental changes, particularly organic matter and sediment supply. Two 11.3-m-long piston cores and a trigger core were collected from the slope of Ashmore Trough and dated using radiocarbon and oxygen isotope measurements of planktic foraminifera. Relative abundances, principal component analyses, and cluster analyses of benthic foraminiferal assemblages in sediment samples identify three distinct assemblages whose proportions changed over time. Assemblage 1, with high abundances of Uvigerina peregrina and Bolivina robusta, dominated between ∼83 and 70 ka (early regression); assemblage 2, with high abundances of Globocassidulina subglobosa, dominated between ∼70 and 11 ka (late regression through lowstand and early transgression); and assemblage 3, with high abundances of neritic benthic species such as Planorbulina mediterranensis, dominated from ∼11 ka to the present (late transgression through early highstand). Assemblage 1 represents heightened organic carbon flux or lowered bottom water oxygen concentration, and corresponds to a time of maximum siliciclastic fluxes to the slope with falling sea level. Assemblage 2 reflects lowered organic carbon flux or elevated bottom water oxygen concentration, and corresponds to an interval of lowered siliciclastic fluxes to the slope due to sediment bypass during sea level lowstand. Assemblage 3 signals increased off-shelf delivery of neritic carbonates, likely when carbonate productivity on the outer shelf (Great Barrier Reef) increased significantly when it was reflooded. Benthic foraminiferal assemblages in the sediment sink (slopes of Ashmore Trough) likely respond to the amount and type of sediment supplied from the proximal source (outer GoP shelf).