Four analytical approaches support the hypothesis that altered flow regimes, particularly spring and summer pulsed discharges, contribute to the decline of foothill yellow‐legged frogs (Rana boylii) in regulated rivers. (1) A review of literature and FERC re‐licensing reports indicates that egg masses are negatively affected by pulsed flows via scouring, or desiccation, if spawning occurs during spills that abruptly cease. Tadpole stranding was documented in several studies. Effects on young of the year and older life stages were equivocal.  (2) Long‐term population monitoring in three watersheds shows that frequency and magnitude of pulsed flows that harm embryos and tadpoles are factors in determining adult population status. These effects are offset by 2‐3 years, representing the time to reproductive maturity in central and northern California. (3) Experiments illustrate that tadpoles seek refuge in the substrate as velocity increases, are not adapted for sustained swimming, and are swept downstream. Tadpoles confined to refugia face predation and energetic costs in terms of growth and development. (4) Simulations using River2D, a 2‐dimensional hydrodynamic model, show that velocity and depth conditions exceed tolerances of R. boylii egg masses and tadpoles during a range of pulsed flows.  While meso‐scale suitability of near shore habitat was accurately predicted, error in modeled point velocities at egg locations arose from limitations in fine scale surveying of the large, poorly sorted, rock substrate.  Management that avoids aseasonal flow fluctuations would benefit R. boylii, and other taxa, whose lifecycles are synchronous with the natural timing of runoff in Californiaʹs rivers.