Climate change is often predicted to cause a significant perturbation to watershed hydrology. It has been generally associated with negative impacts on natural systems, especially in conjunction with conservation and protection of sensitive ecosystems. In the U.S., spawning habitats of threatened and endangered salmonid species are important areas that are potentially vulnerable to climate change through variations in flood timing and magnitude, water temperature, and sediment input. In this work, we used a numerical model to investigate whether changes in flow regime, of the type predicted by some climate change scenarios for mountain streams in the western U.S.A., would affect spawning site stability. We ran a two dimensional hydraulic model that simulated several flow regimes from low to bankfull stage and mapped grain mobility. We defined the model boundary conditions with high-resolution airborne bathymetric lidar surveys of an important spawning stream in central Idaho, USA. Our analyses showed that such unconfined low-gradient streams have not a great danger of extensive bed mobility, even at high flows. Consequently, in this landscape, alterations in flood timing due to climate change are unlikely to decrease the success rate of salmonid egg incubation by the mechanism of increased channel bed scour.