In tropical and sub-tropical mixed siliciclastic–carbonate depositional systems, fluvial input and in situ neritic carbonate interact over space and time. Despite being the subject of many studies, controls on partitioning of mixed sediments remains controversial. Mixed sedimentary records, from Ashmore Trough shelf edge and slopes (southern Gulf of Papua), are coupled with global sea-level curves and anchored to Marine Isotope Stage stratigraphy to constrain models of sediment accumulation at two different timescales for the past 130 kyr: (i) 100 kyr scale for last glacial cycle; and (ii) millennial scale for last deglaciation. During the last glacial cycle, carbonate production and accumulation were primarily controlled by sea-level fluctuations. Export of neritic carbonate to the slopes was initiated during re-flooding of previously exposed reefs and continued during Marine Isotope Stage 5e and 1 interglacial sea-level highs. Siliciclastic fluxes to the slope were controlled by interplay of sea level, shelf physiography and oceanic currents. Heterogeneous accumulation of siliciclastic mud on the slope, took place during Marine Isotope Stage 5d to Marine Isotope Stage 3 sea-level fall. Siliciclastics reached adjacent depocentres during Marine Isotope Stage 2. Coralgal reef and oolitic–skeletal sand resumed at the shelf edge during the subsequent stepwise sea-level rise of the last deglaciation. Contemporaneous, abrupt siliciclastic input from increased precipitation and fluvial discharge illustrates that climate controlled deglacial sedimentation. Siliciclastic input persisted until ca 8.5 ka. Carbonate accumulation waned at the shelf edge after ca 14 ka, whereas it increased on the slopes since ca 11.5 ka, when previously exposed reef and bank tops were re-flooded. When comparing the last sea-level cycle sedimentation patterns of the southern Gulf of Papua with other coeval mixed systems, sea level and shelf physiography emerge as primary controls on deposition at the 100 kyr scale. At the millennial scale, siliciclastic input was also controlled by climate change during the unstable atmospheric and oceanic conditions of the last deglaciation.