The submarine Zambezi Channel is the deep, stable, north-south orientated, lower portion of a channel system draining the continental slope of central Mozambique; transporting material southwards into the Mozambique Channel and Basin, southwest Indian Ocean. Using recently collected Multi Beam Echo Sounder and PARASOUND data we discuss the geomorphology of the Zambezi Channel. This system is enigmatic in that the main channel is stable, with low sinuosity despite being at a low latitude where rivers seasonally deliver fine grained sediment. A further enigma is that system does not now continue upslope to the Zambezi River, the largest river in southern Africa. Instead this river flows into the northern Mozambique basin to the south-west of the small channels. The Zambezi Channel is compared to small-scale physical models in an attempt to better understand the geomorphology of the channel. The geomorphological features of the main channel show a quite remarkable resemblance to an analogue model produced within a purely erosive environment. To explain these enigmas, it is proposed that geomorphology of the main Zambezi Channel was produced by periodic, high-volume pulses of flood water, and associated sediment, from the Zambezi River, the second largest river in Africa. These events are considered to be due to minor tectonic movements along the Chobe Fault in the Kalahari that permitted the draining of several palaeo-lake systems between the Early Pleistocene through to the early Mid-Pleistocene. Such repetitive draining of palaeo-lakes would have produced flooding comparable to glacial dam bursts. Such events would deliver significantly more sediment laden flood water to the region than “normal” flow conditions. We hypothesise that these significant flood events have influenced the geomorphology of the Zambezi River to the extent that it is no longer comparable to other low-latitude systems, and exhibits characteristics akin to high-latitude systems with highly variable sediment input.