Estimates of decadal bed material sediment flux and net storage are derived by driving sediment transport calculations with a stochastic hydrology model. The resulting estimates represent the whole distribution of sediment flux based on natural variability in channel characteristics (gradient, width, and bed grain size) and the magnitude, duration, and interarrival time of flood events. A procedure for calibrating a fractional sediment transport equation of a commonly used form to bed material grain size distributions (BMGSDs) at cross sections is presented. The procedure was applied to the Sacramento River channel network to compute estimates of annual total and annual peak bed material discharges into and through the main stem over a 30-year period. Main stem bed material budgets were evaluated to identify reaches in states of net accumulation or scour. Simulations highlight large imbalances in sand and gravel storage throughout the Sacramento River, which can be explained by a combination of local hydraulics and BMGSDs and for which there is at least some empirical support.