Abstract Late Pleistocene to Holocene margin sedimentation on the Great Barrier Reef, a mixed carbonate-siliciclastic margin, has been explained by a transgressive shedding model. This model has challenged widely accepted sequence stratigraphic models in terms of the timing and type of sediment (i.e. carbonate vs. siliciclastic) deposited during sea-level oscillations. However, this model documents only hemipelagic sedimentation and the contribution of coarse-grained turbidite deposition, and the role of submarine canyons in this process, remain elusive on this archetypal margin. Here we present a new model of turbidite deposition for the last 60 ky in the north-eastern Australia margin. Using high-resolution bathymetry, 58 new and existing radiometric ages, and the composition of 81 turbidites from 15 piston cores, we found that the spatial and temporal variation of turbidites is controlled by the relationship between sea-level change and the variable physiography along the margin. Siliciclastic and mixed carbonate-siliciclastic turbidites were linked to canyons indenting the shelf-break and the well-developed shelf-edge reef barriers that stored sediment behind them. Turbidite deposition was sustained while the sea-level position allowed the connection and sediment bypassing through the inter-reef passages and canyons. Carbonate turbidites dominated in regions with more open conditions at the outer-shelf and where slope-confined canyons dominated or where canyons are generally less abundant. The turn-on and maintenance of carbonate production during sea-level fluctuations also influenced the timing of carbonate turbidite deposition. We show that a fundamental understanding of the variable physiography inherent to mixed carbonate-siliciclastic margins is essential to accurately interpret deep-water, coarse-grained deposition within a sequence stratigraphic context.