Abstract When forest disturbance impacts adjacent headwater streams, the recovery of habitat conditions and populations can take over several decades. Thus, considering long‐term, historical legacies of forest disturbances is key for understanding and managing forest–stream linkages. We focused on small‐scale forest disturbances such as small‐block harvesting and landslides. We compared the long‐term (past 100 years) cumulative effects between the anthropogenic and natural forest disturbances on stream conditions and the abundance of a headwater specialist, Scopura montana (Plecoptera: Scopuridae). Sampling was conducted in 10 m reaches of 39 first‐order streams with a catchment area up to 5.9 ha during late summer in central Japan. We quantified past clearcut logging areas using plantation records of each harvest block and past landslide areas from contour maps within each catchment. Piecewise structural equation models using the cumulative area of each forest disturbance as an independent variable, revealed different indirect effects of clearcut logging (average area: 1.74 ha) and landslides (0.21 ha) on S. montana abundance through modified stream conditions. Canopy openness and wetted channel width were higher with a larger logged area, and S. montana abundance was lower with higher water temperature (daily maximum). When the magnitude of clearcut logging was similar to the landslide area (<0.77 ha), the negative relationship between water temperature and S. montana abundance was also significant in the model. Streambed roughness and wetted channel width were greater with larger landslide area but there were no significant links between stream conditions and S. montana abundance. Our results suggest that clearcut logging can cause long‐term impacts by exposing the stream surface to solar radiation owing to delayed canopy closure. The preference of S. montana is for cold water conditions in summer. Controlling forest harvesting along streams could benefit forest–stream management, as could including consideration of disturbance‐driven cycles for sustaining headwater populations.