Submarine canyons are a key element of the growth of continental margin depocentres such as the Niger Delta, the progradation of which is commonly influenced by syn-sedimentary processes of gravity-driven tectonism. In such setting, canyons commonly constitute combined stratigraphic-structural traps because of: (i) their clayey infilling and, (ii) the incision of marine reservoirs. Nevertheless, most of the time, their drainage network and/or the external factors leading to their formation are poorly characterized, which is also the case in other settings when the resolution of geophysical dataset is less accurate. Here we use 3D seismic reflection data from the onshore eastern Niger Delta to study the morphology of a buried canyon system in relation to extensional tectonic structures, which are E-W trending growth-faults and roll-over anticlines. We map the Afam Incision Surface (AIS), which cuts up to 1000 m into subjacent Eocene-Miocene deltaic and continental series. In planform, the AIS is organized in 6 stream orders. The Afam Canyon which has the highest stream order is globally NNW-SSE oriented and is locally controlled by E-W oriented grabens, which give it right-angle changes of direction. It perpendicularly captures 5th and 4th order tributaries, each of which has an asymmetric cross-sectional profile controlled by one major growth-fault. In the southern area, the western tributaries all include an upstream part that drains in the opposite direction to the regional slope, leading to bayonet-shaped paths in planform. Whatever the stream order of the tributary considered; its increase is controlled by growth-faults. Therefore, the AIS planform network has the characteristics of a rectangular pattern. Erosion of the AIS as a submarine canyon system is consistent with its more than one-kilometer depth, preserved knickpoints within the thalweg of the main canyon; and the many erosional terraces boarded by arcuate scarps located along the main canyon and its tributaries. The formation of the AIS is correlated to the 50 m Tor2 sea-level fall at 9.5–9.2 my, and may have been initiated by by-pass currents that acted in tandem with retrogressive erosion. The latter greatly contributed to deepening and widening of the canyon and its tributaries whatever the orientation of the local slope. Erosion of the AIS was favored by the high-density of growth-faults. During the final excavation phases, the channelization of longshore drift currents by the canyon and its tributaries probably contributed to the destabilization of their upper margins.