Bedrock river bathymetry is dynamic, with incision rates dependent on sediment cover, supply, and mobility in the channel. However, the scale and fluctuation of this dynamic sediment storage is not well understood, particularly in large bedrock rivers where the bed is not visible at low flows. We used repeat, high resolution, multibeam bathymetric surveys from 2021–2023 to characterize bed and bank topography in nine bedrock canyons that are representative of a wide range of width, depth, slope, and velocity observed through the 375 km long Fraser Canyon in British Columbia. Change in elevation as high as 15 m is identified between surveys. We characterize patches of contiguous change to measure changes in sediment storage volume. Our observations reveal that channel morphology determines where storage occurs. We find that sediment is 'staged' through canyons, initially being deposited in a canyon near a sediment supply site, then moving downstream as the initial deposit declines. Substantial changes in storage volume occur without substantial changes in patch footprint. These findings provide key context for interpreting the reach-scale structure of bedrock erosion, the long-term evolution of mountain river networks, and the moderation of sediment delivery to lowland environments.