The mixed carbonate-siliciclastic depositional system in the Gulf of Papua (GoP) was studied by standard sequence stratigraphic method based on a large industry seismic and well datasets, in addition to gravity, multibeam bathymetry, Landsat imagery, and core data. The Cenozoic geological history of the mixed system is represented by four-phase evolutionary model, which includes (1) tectonic, (2)carbonate, (3) carbonate system demise, and (4) siliciclastic phases, defined based on the intensity of such factors as tectonics, eustasy, climate, carbonate production, and siliciclastic supply.

During the Late Cretaceous - Paleocene tectonic phase, the Coral Sea spreading triggered extensional tectonics, consequent uplift, and erosion which formed a structural configuration controlling the later evolution of the system. During the Eocene and late Oligocene - middle Miocene carbonate phase, basinal scale sedimentary geometries are largely controlled by eustatic seal level fluctuations. Because the geometry pattern identified within the carbonate sequences in the GoP mimics contemporaneous sedimentary geometry pattern observed in other pure carbonate and even siliciclastic depositional systems around the world, eustasy had to be the major factor influencing the GoP mixed system during this second phase.

Although partial carbonate demise was observed during the early Miocene, the demise phase per se occurred during the late middle Miocene exposure of the system and its subsequent drowning in the early late Miocene, and was probably related to a major sea level rise enhanced by fold belt loading.

During the Oligocene Peninsular Orogeny, the siliciclastics did not influence the carbonate system because they were trapped in the Aure Trough, a foreland basin to the northeast of the study area. The siliciclastic phase in the GoP was initiated during the late Miocene Central Range Orogeny. At that time and in the early Pliocene, siliciclastic infill was limited to the deep troughs in northeast corner of the GoP. The major siliciclastic input and progressive burial of the GoP carbonate system only occurred in the late Pliocene, as a response to the contemporaneous renewed uplift and exhumation of Peninsular region. During this fourth phase, the siliciclastics infilled 3-4 km deep troughs and completely buried the most of the carbonate system. The northern end of the Great Barrier Reef along with several large isolated carbonate platforms located far away from the siliciclastic sources are still active today.