The effects of contemporary logging practices on headwater stream amphibians have received considerable study but with conflicting or ambiguous results. We posit that focusing inference on demographic rates of aquatic life stages may help refine understanding, as aquatic and terrestrial impacts may differ considerably. We investigated in-stream survival and movement of two stream-breeding amphibian species within a before-after timber harvest experiment in the Oregon Coast Range. We used recaptures of marked individuals and a joint probability model of survival, movement, and capture probability, to measure variation in these rates attributed to stream reach, stream gradient, pre- and post-harvest periods, and the timber harvest intensity. Downstream biased movement occurred in both species but was greater for Coastal Tailed Frog (Ascaphus truei) larvae than aquatic Coastal Giant Salamanders (Dicamptodon tenebrosus). For D. tenebrosus, downstream biased movement occurred early in life, soon after an individual's first summer. Increasing timber harvest intensity reduced downstream movement bias and reduced survival of D. tenebrosus, but neither of these effects were detected for larvae of A. truei. Our findings provide insight into the demographic mechanisms underlying previous nuanced studies of amphibian responses to timber harvest based on biomass or counts of larvae.