This paper outlines the evolution of the late Cenozoic mixed carbonate-siliciclastic depositional system in the Gulf of Papua (GoP), using seismic, gravity, multibeam bathymetry, well data sets, and Landsat imagery. The deposition of the mixed sedimentary sequences was influenced by dynamic interplay of tectonics, eustasy, in situ carbonate production, and siliciclastic sediment supply. The roles of these major factors are estimated during different periods of the GoP margin evolution. The Cenozoic mixed system in the GoP formed in distinct phases. The first phase (Late Cretaceous–Paleocene) was mostly driven by tectonics. Rifting created grabens and uplifted structural blocks which served later as pedestals for carbonate edifices. Active neritic carbonate accumulation characterized the second phase (Eocene–middle Miocene). During this phase, mostly eustatic fluctuations controlled the large-scale sedimentary geometries of the carbonate system. The third phase (late Miocene–early Pliocene) was characterized by extensive demise of the carbonate platforms in the central part of the study area, which can be triggered by one or combination of several factors, such as eustatic sea level fluctuations, increased tectonic subsidence, uplift, sudden influx of siliciclastics, or dramatic changes in environmental conditions and climate. The fourth phase (late Pliocene-Holocene) was dominated by siliciclastics, which resulted in the burial of drowned and/or active carbonate platforms, although some platforms still remain alive until present-day.