Sediment cover in bedrock rivers can protect or expose bedrock to incision, yet little is known about sediment storage dynamics in deep canyons since it is difficult to observe the bed. We use repeat bed surveys to identify changes in storage, observing vertical changes up to 15 m. Local flow and channel shape determine where storage occurs, yet storage can vary plenty over a single footprint. The location and timing of sediment inputs to the river influence whether storage is gained or lost.