Quaternary depositional sequences of the Mahakam delta were analyzed combining shallow portions of 3D seismic data sets together with high resolution 2D seismic profiles. Stratigraphic pattern and depositional geometries of incised valleys and low stand deltas prograding over the shelf contemporaneously with turbidite channels were studied in relation with Quaternary sea level changes and tectonic movements. During period of sea level fall, 3D images demonstrate that distributary channels are converted into incised valleys with adjacent characteristic dendritic tributary channels. These features previously interpreted as shelfal tidal channels and hard to map with 2DHR seismic grid clearly indicate that the northern part of the shelf was exposed during a prolonged period of time and flooded during the Holocene rapid sea level rise. Main incised valleys reached the shelf break bringing sediments beyond the shelf break. During sea level rise, the incised valleys are flooded and remains largely underfilled with a thin drape of transgressive sediments while the interfluves are colonized by mounded Halimeda calcareous bioherms. Growth of Halimeda bioherms continue until the modern high stand delta progradation. The distribution of the bioherms is strongly influenced by the presence of tilted faulted panels on top of which Halimeda bioherms developed. The effect of tectonics is marked with pronounced incision of the valleys while crossing upthrown block and with more sinuous unconfined profile in the downthrown compartments. The southern depocenter is showing a thicker prograding perched low stand deltaic wedge capped with a network of channels showing limited incision and less abundant Halimeda build-up. This demonstrate the effect of larger scale shelf physiography on the coeval development of a southern thick deltaic low stand delta while to the north incised valleys appear as tectonically induced features.