Integrating climate-smart principles into riparian and upland forest management can facilitate effective and efficient land use and conservation planning. Emerging values of forested headwater streams can help forge these links, yet climate effects on headwaters are little studied. We assessed associations of headwater discontinuous streams with climate metrics, watershed size, and forest-harvest treatments. We hypothesized that summer streamflow would decrease in warm, dry years, with possible harvest interactions. We field-collected streamflow patterns from 65 discontinuous stream reaches at 13 managed forest sites in Western Oregon, USA over a 16-year period. We analyzed spatial and temporal variability in field-collected stream habitat metrics using non-metric multidimensional scaling ordination. Relationships between streamflow, climate metrics, basin size, and harvest treatments were analyzed with simple linear models and mixed models with repeated measures. Using past effects of climate variation on streamflow, we projected effects to 2085 under three future scenarios, then quantified implications on headwater networks for a case-study landscape. Ordination identified the percent dry length of stream reaches as a top predictor of spatial and temporal variation in discontinuous stream-habitat types. In our final multivariate model, the percent dry length was associated with heat: moisture index, mean minimum summer temperature, and basin area. Across future climate scenarios in years 2055–2085, a 4.5%–11.5% loss in headwater surface streamflow was projected; this resulted in 597–2058 km of additional dry channel lengths of headwater streams in our case study area, the range of the endemic headwater-associated Cascade torrent salamander (Rhyacotriton cascadae Good and Wake) in the Oregon Cascade Range, a species proposed for listing under the US Threatened and Endangered Act. Implications of our study for proactive climate-smart forest-management designs in headwaters include restoration to retain surface flows and managing over-ridge wildlife dispersal habitat from areas with perennial surface water flow, as stream reaches with discontinuous streamflow were projected to have reduced flows in the future with climate change projections.