Located on a divergent margin dominated by gravity tectonics above overpressured marine shales, the Niger Delta slope has been described as having a stepped profile characterized by ‘filled ponded basins’ that are prone to erosion and sediment bypass. Previous studies based on 3D seismic data have described the depositional architecture of the western Niger Delta's upper slope, but calibration of the seismic facies is lacking and the timing of major changes in sedimentary record remains elusive. In this study, seismic sequence-stratigraphy, 3D geomorphological analyses of high-resolution 3D seismic data, and bio/chronostratigraphic analyses from four boreholes, enabled the identification and characterization of the depositional architecture in Neogene ‘filled ponded basins’. Seven major seismic units were dated as Chattian, Burdigalian, Serravallian, Tortonian, Middle Pliocene and Middle Pleistocene to the present day. Major changes in the sedimentary record occurred in the Plio-Pleistocene, with the onset of erosive channel levee systems (CLSs) and mass-transport deposits (MTDs) generally capped by a hemipelagic drape. Amalgamated CLSs characterize the Tortonian-Late Miocene while erosive MTDs and CLSs characterize the Plio-Pleistocene units. Thick, laterally extensive MTDs are associated with regional slope instability, while active mobile shale triggered local spatially confined MTDs. Submarine channels evolved from moderate to highly sinuous. The degree of channel confinement generally decreases downstream where they are characterized by abandoned meander loops and avulsion resulting from levee breaching. Channel fills and levees/overbank deposits topped by hemipelagic drapes provide effective reservoir/seal (traps) for hydrocarbons. The alternation of channel deposits and hemipelagic layers indicate that eustasy controlled depositional patterns at a regional scale, while the spatio-temporal switches in submarine channel courses show that shale tectonics locally controlled deposition in intraslope basins.