Populations of wild Brook Trout (Salvelinus fontinalis) continue to decline across their historic range, making relatively healthy populations and intact habitats within northern New England increasingly important for conservation. The Beebe River watershed, located in central New Hampshire, is home to intact headwater populations of wild Brook Trout despite movement barriers and riparian manipulation affecting tributaries to the mainstem river. The region has also experienced two centuries of widespread timber harvest and a century of stream acidification, creating further ecological stressors. We focused on three headwater tributaries with 1) impassable road crossing and reduced canopy cover, 2) passable road crossing and reduced canopy cover, and 3) no impediments to movement and unaltered canopy. We documented Brook Trout abundance, density, age structure, condition, biomass, growth, net movement, cumulative movement, home range, and recruitment with the goal of better understanding potential habitat influences on fish across tributaries and among geomorphic threshold regions. Our primary sampling methods included depletion electrofishing, PIT tag mark-recapture techniques, and detailed habitat assessments and temperature monitoring. We hypothesized that undersized crossings and no-low canopy reaches would create physical and thermal barriers for fish. In particular, we predicted that fish in streams with these barriers would exhibit lower density, fewer age classes and lower growth rates while seasonal and annual movement would increase compared to fish in an unimpacted stream. Overall, tributary populations were comprised of young fish that exhibited little movement. We failed to support many of our hypothesis metrics due to underestimating the indirect influences of no-low canopy reaches. Although we documented a crossing barrier inhibiting upstream movement, fish with unrestricted access to the no-low canopy primarily grew more and moved less, while density remained stable interannually. In contrast, fish in the most impacted stream and the unimpacted stream exhibited increased movement and significant declines in interannual density. This project was a unique opportunity to compile a detailed description of the spatial and temporal differences in Brook trout populations for two seasons prior to multiple crossing replacements and habitat enhancement. Our research helps fisheries managers to better understand the benefit of watershed-wide restoration to inform the protection of wild Brook Trout populations.