A stochastic flood generator and calibrated sediment transport formulae were used to assess the decadal impact of major river rehabilitation strategies on two fraction bed material sediment flux and net storage, first‐order indicators of aquatic riverine habitat, in a large river system. Model boundary conditions were modified to reflect the implementation of three major river rehabilitation strategies being considered in the Sacramento River Valley: gravel augmentation, setting back of levees, and flow alteration. Fifty 30‐year model simulations were used to compute probabilities of the response in sediment flux and net storage to these strategies. Total annual average bed material sediment flux estimates were made at six gauged river cross sections, and ∼60 km reach‐scale sediment budgets were evaluated between them. Gravel augmentation to improve spawning habitat induced gravel accumulation locally and/or downstream, depending on the added mixture. Levee setbacks to recreate the river corridor reduced flow stages for most flows and hence lowered sediment flux. Flow alteration to mimic natural flow regimes systematically decreased total annual average flux, suggesting that high‐magnitude low‐frequency transport events do not affect long‐term trends in bed material flux. The results indicate that each rehabilitation strategy reduces sediment transport in its target reaches and modulates imbalances in total annual bed material sediment budgets at the reach scale. Additional risk analysis is necessary to identify extreme conditions associated with variable hydrology that could affect rehabilitation over decades. Sensitivity analysis suggests that sorting of bed material sediment is the most important determinant of modeled transport and storage patterns.