Habitat modifications to benefit aquatic species in riverine systems are widely implemented, but poorly studied, which leaves researchers concerned about their effectiveness. There has been limited documentation of positive fish responses to wood additions in headwaters streams, which has led some researchers to believe wood additions cannot benefit fish in high-gradient and boulder dominated streams (Gowan & Fausch 1996; Sweka & Hartman 2006; Nagayama & Nakamura 2010; Warren et al. 2013; Kratzer 2018). In the headwaters of the Beebe River watershed (Campton/Sandwich, NH), we monitored changing habitat conditions, benthic macroinvertebrate communities, and Brook trout (Salvelinus fontinalis) populations following wood additions and culvert removal. We used a before-after-control-impact (BACI) design and modelling efforts to understand how our systems and Brook trout populations respond to habitat and environmental variation. After habitat modifications, we observed a significant 3-fold increase in benthic invertebrate density in our treated streams, which coincided with a significant increase in Age 1 Brook trout length. Additionally, our modified streams held 3-times more organic material density than our control stream and organic material retention was primarily associated with wood additions. Using Boosted Regression Tree analysis, we discovered that Brook trout growth and movement were best explained by similar variables representing habitat heterogeneity (bankfull width), environmental variation (temperature and relative water level), and Brook trout size/age. Our results indicate that Brook trout growth in coldheadwater streams may be related more to habitat heterogeneity than environmental variation, but these effects are size/age dependent. We observed that effects associated with climate change, such as average water temperatures above 16 °C and lower water levels significantly reduced growth, but increasing macroinvertebrate density and habitatunit bankfull widths significantly increased growth. Overall, our BACI monitoring and modelling results would support the use of habitat modifications in cold-headwater streams to benefit Brook trout populations where they positively shape stream habitat and increase benthic invertebrate production.