ABSTRACTIn regulated rivers, relicensing of hydropower projects can provide an opportunity to change flow regimes and reduce negative effects on sensitive aquatic biota. The volume of flow, timing and ramping rate of spring spills, and magnitude of aseasonal pulsed flows have potentially negative effects on the early life stages of amphibians, such as the Foothill yellow‐legged frog (Rana boylii). Two‐dimensional hydrodynamic modeling is one method to evaluate potential effects of flow variation on frog egg masses and tadpoles. We explored the usefulness of this technique by modeling habitat suitability under several pulsed flow scenarios in two river reaches in northern California, USA. We conducted analyses beyond simple weighted usable area calculations, such as quantifying the risk of scour or stranding, in order to quantify potential loss under different flow scenarios. The modeling results provided information on potential susceptibility to flow fluctuations as well as the influence of channel morphology on habitat suitability. Under each flow scenario, low percentages of suitable habitat remained suitable or were ‘buffered’ from the pulse, creating high potential for scour of egg masses or tadpoles. However, due to differences in channel morphologies, the wide, shallow study site provided 2‐3 times the buffering capacity of the entrenched study site.Additional analyses suggested that limited buffering capacity and lack of connectivity between suitable egg mass and tadpole habitats may explain why some hydraulically suitable habitats are unoccupied. This type of model‐based analysis would be useful for managing foothill yellow‐legged frogs or similar aquatic species in regulated river systems. Copyright © 2010 John Wiley & Sons, Ltd.