Riparian-management zones protect aquatic species and their habitats in managed forests, yet the effects of riparian-management alternatives warrant further study. We examined effects of alternative riparian-buffer widths on fish and amphibians in small headwater streams with upland forest thinning in western Oregon, USA. Previously, we reported apparent lag-time effects developing 10 years after thinning of upland second-growth forest, and additional effects 1–2 years after a second-thinning harvest. Here, we analyze effects on fish and amphibian abundances, body-size metrics, and habitats 5 years after the second thinning at 58 stream reaches across eight study sites. Riparian-buffer effects were evident for several species and species groups: higher densities of fish and amphibians (e.g., coastal giant salamander [Dicamptodon tenebrosus], torrent salamanders [Rhyacotriton spp.], sculpins [family Cottidae]) were detected in reaches with a no-entry one site-potential tree-height buffer (∼70 m wide) in comparison with lower densities in two narrower no-entry buffers (6-m-wide, and a variable-width buffer with a 15-m minimum width) and a thin-through managed buffer (two site-potential tree-heights wide, ∼140 m). In addition, indicator-species analyses showed that torrent salamander densities were positively associated with stream reaches in unmanaged controls. Some amphibians changed habitat affinities slightly, being found during the most-recent sampling in locations with habitats related to larger stream sizes (i.e., more-perennial stream flows) than they had been in earlier sampling. Analyses of body-size metrics showed associations with buffers across 42% of species × post-treatment years analyzed, yet patterns were inconsistent within species, and more consistent associations of body metrics were found with microhabitat types, finding larger animals in pools. Although the mechanism driving changes is unclear, the positive associations of species’ densities with one-tree buffers suggest that either lag-time or cumulative effects of factors associated with treatments are developing, with benefits of wider streamside protections over longer time periods for headwater-associated fish and amphibians. Our findings of higher densities of headwater-reliant Rhyacotriton species in stream-reach treatments with the one-tree buffers, and affinities with unthinned control reaches, support the benefits of greater headwater-stream protections for that species complex, which includes species of conservation concern. The mix of different buffer widths and unmanaged units across our eight sites may be promoting site-scale persistence of a community of aquatic-vertebrate species—a mix of buffer widths with upslope forest management may be an alternative for larger-scale riparian forest-management objectives.