The largest canyons on Earth occur on the seafloor, and seabed sediment flows called turbidity currents play a key role in carving these submarine canyons. However, the processes by which turbidity currents erode submarine canyons are very poorly documented and understood. Here we analyse the first detailed time-lapse bathymetric surveys of a large submarine canyon, and its continuation as a less-deeply incised channel. These are also the most comprehensive time-lapse surveys before and after a major canyon-channel flushing turbidity current. These unique field data come from the Congo Submarine Fan offshore West Africa, where canyon flushing turbidity currents between 2019 and 2020 eroded ~2.65 km3 of seabed sediment, as they travelled for over 1100 km at speeds of 5–8 m/s. This eroded sediment volume is equivalent to ~19–33 % of global sediment flux from all rivers to the oceans. The time-lapse surveys cover 40 % of the 1100 km long submarine canyon-channel. They show that erosion was predominantly (94 %) along the canyon-channel axis, with only 6 % from failures along canyon or channel flanks. However, erosion along the canyon-channel floor was very patchy; some areas were eroded to depths of 10–20 m, whilst intervening areas showed no significant change. Knickpoints with up-slope migrating headscarps account for 22 % of the total eroded volume. One knickpoint in the deep-sea channel migrated by 21 km in one year, making it the fastest moving submarine knickpoint yet documented. Most (62 %) eroded sediment was in zones extending across the canyon or channel floor, without distinct headscarps as is the case for knickpoints. Erosion restricted to outer bends only comprised 10 % of the total, suggesting processes of erosion differ significantly from meandering rivers in which outer bend erosion is more important. Patchy seabed erosion appears to be mainly due to flow-bed processes (e.g. knickpoints), but spatial variations in seabed sediment properties may also play a role. The irregular seabed erosion occurs despite near-uniform flow speeds observed between moorings and submarine cable breaks with spacing of tens to hundreds of kilometers. Patchy and localised erosion has important implications for assessing hazards to seabed telecommunication cables, which are more likely to break in areas of deep erosion, and for creating appropriate numerical models of seabed erosion and turbidity current behaviour, or how to interpretate ancient submarine canyons and channels in rock outcrops.