We combine two- and three-dimensional seismic stratigraphic interpretation with paleobathymetric analysis from benthic foraminifera to understand the genetic significance of prominent seismic discontinuity surfaces typically mapped as sequence boundaries and flooding surfaces in the late Paleogene-early Neogene northern Carnarvon Basin.The progradational succession, dominated by heterozoan carbonate sediments, is divided into 5 northwest-prograding clinoformal sequences and 19 subsequences. Clinoform fronts progress from smooth to highly dissected, with intense gullying apparent only after the middle Miocene optimum. Once initiated, gullies become the focus for sediment distribution across the front. Bottomsets remain relatively sediment starved without the development of aprons on the lower slope and basin. Small-scale variability suggests heterogeneous sediment dispersal through the slope conduits. Alongstrike sediment transport superimposed on progradation changes from southwest directed in the late Oligocene to northeast directed in the late middle Miocene, suggesting a major reorganization of circulation in the southeastern Indian Ocean.Prominent seismic discontinuity surfaces represent both intervals of shallow paleowater depth and flooding of the shelf. Partial exposure of the shelf indicated by karst morphology is coeval, with middle to outer neritic paleowater depths on the outer shelf. Instead of building to sea level, progradation occurs with shelf paleowater depths at the clinoform rollover greater than 100 m. Therefore, in the northern Carnarvon Basin, onlap onto the clinoform front is not coastal, and the sensitivity of the clinoforms to sea level changes is muted.