We quantified all components of a fluvial sediment budget for a discrete flood on an aggrading gravel bed river. Bed load transport rates were measured at the upstream and downstream ends of a 4 km study area on the Provo River, Utah, during a dam-controlled flood. We also collected high-resolution measurements of channel topography before and after the controlled flood for the entire reach. Topographic uncertainty in the digital elevation models (DEM) was characterized using a spatially variable approach. The net sediment flux provided unambiguous indication of storage. Sediment input to the reach (319 m3) exceeded output (32 m3), producing a net accumulation of approximately 290 m3. The difference between the scour and fill was also positive (470 m3), but uncertainty in the topographic differencing was larger than the observed net storage. Thus, the budget would have been indeterminate if based on morphologic data alone. Although topographic differencing was not sufficiently accurate to indicate net storage, it was able to demonstrate that internal erosion was a larger sediment source than the net sediment flux. The magnitude of total erosion (1454 m3) and deposition (1926 m3) was considerably larger than net change in storage, showing that internal sources and sinks were the dominant driver of channel change. The findings provide guidance for the development of sediment budgets in settings in which one must choose between a morphological approach and the direct measurement of sediment flux.