Forest harvest is one of the primary landscape-scale management actions affecting riparian forests of the Pacific Northwest, U.S, yet the effect of harvest on headwater steam amphibians is largely understudied. Existing information is often limited because of the difficulty separating movement and emigration processes from occupancy and abundance estimates. We designed a before-after control-impact experiment to account for instream movement in the responses of three unique headwater stream amphibians to clearcut logging as part of the Trask River Watershed Experimental Study in the Oregon Coast Range. We captured and marked larval tailed frogs (Ascaphus truei), Coastal giant salamanders (Dicamptodon tenebrosus), and Columbia torrent salamanders (Rhyacotriton kezeri) across 3,915 sampling occasions that spanned 13 study reaches and eight years.