Submarine channels are the primary conduits for terrestrial sediment, organic carbon, and pollutant transport to the deep sea. Submarine channels are far more difficult to monitor than rivers, and thus less well understood. Here we present 9 years of time-lapse mapping of an active submarine channel along its full length in Bute Inlet, Canada. Past studies suggested that meander-bend migration, levee-deposition, or migration of (supercritical-flow) bedforms controls the evolution of submarine channels. We show for the first time how rapid (100-450 m/year) upstream migration of 5-to-30 m high knickpoints can control submarine channel evolution. Knickpoint migration-related changes include deep (>25 m) erosion, and lateral migration of the channel. Knickpoints in rivers are created by external factors, such as tectonics, or base-level change. However, the knickpoints in Bute Inlet appear internally generated. Similar knickpoints are found in several submarine channels worldwide, and are thus globally important for how channels operate.