Research dating back to the 1950 s has documented negative effects from harvesting of primeval forests on stream ecosystems of the Pacific Northwest. By the early 1990 s, state and federal forest practice rules governing timber harvest were modified throughout North America to better protect aquatic habitats and biotic resources, principally salmonids. These rules inspired a generation of studies using a before-after-control-impact (BACI) design to document the capacity of contemporary timber harvest rules to protect salmonids in headwater streams of second-growth forests. One important unanswered question concerns the potential effects of successive clearcuts in second growth forests. Consequently, we used a paired watershed approach to evaluate the effects of two successive clearcut harvests in the Alsea Watershed, site of the seminal Alsea Watershed Study that was conducted from 1958 to 1973, on relative biomass, movement, survival, and distribution of coastal cutthroat trout (Oncorhynchus clarkii clarkii) and three physical habitat characteristics (pool area and depth, and water temperature). Although the total clearcut harvest encompassed 87% of the treatment catchment in six years, no negative effects of logging were detected for either age-1 + coastal cutthroat trout or habitat variables. Comparisons between the harvested and reference catchments suggested the survival of coastal cutthroat trout (>94 mm fork length) and total catchment relative biomass of age-1+ (i.e., > 80 mm) exhibited similar patterns, increasing from the pre-logging period (2006–2009) through the Phase I post-logging period (2009–2014), and decreasing to levels observed in the pre-logging period during the Phase II post-logging period (2014–2017). Additionally, there was no evidence for differences in movement of coastal cutthroat trout related to the harvesting treatment. In terms of habitat variables, there was a relative increase in annual total pool area in the harvested catchment during the Phase II post-logging period, but there was no evidence the 7-day moving mean maximum stream temperature changed after the Phase I and Phase II harvests. Moreover, stream water temperatures never exceeded the criterion designed to protect core coldwater habitat for salmonids (16 °C). As such, it is unlikely that cutthroat trout experienced thermal stress following either harvest. More generally, results from this and other recent studies suggest that forest practice rules developed in conjunction with current best management practices for logging in headwater catchments have substantially improved outcomes for stream biota relative to unregulated forest harvest, at least for short periods of time after logging (i.e., ≤ 8 years).