Habitat Stability in Appalachian Headwater Systems and Potential Impacts on Brook Trout Populations Zac Zacavish The impact climate change will have on the habitat for Brook Trout (Salvelinus fontinalis) could directly impact key demographic characteristics. Traditionally, broad-scale studies of climate change effects on the family Salmonidae focus on the thermal shifts predicted over the next century. While some studies shed light onto other variables such as biotic interactions, flow regime, and disturbance, the significance of the climate-trout interaction is not always observed. With the high degree of influence climate cycles can have on habitat and channel morphology, this study aimed to highlight temporal habitat shifts to begin addressing climate-habitat interaction. By studying habitat distribution and trends in 25 headwater systems over 14 years, Chapter 1 documented a significant decreasing trend in critical pool habitat (S=-73.0, p=0.0004) and significant increase in distance between these pools (r=0.86, p=0.003) since 2003. Chapter 2 used presence only data to build a maximum entropy model to assess probability of occurrence of pool habitat throughout the study region. According to the highest scoring AUC models (AUC=0.89), pool habitat decreased by 23 percent across the national forest between the two periods; and only demonstrated "stability" in 13 percent of its model presence probability. Finally, we were able to show the impact pool stability had on spawning age Brook Trout. Particularly, the directional change associated with each pool unit deviation from stable pools (0.31 individuals per 100 meters) accounting for variations of the random effects' year, site and reach. These results highlight the need to further understand the potential impacts of acute disturbances like floods, debris flows, and other formidable events could have on temporal habitat availability and overall persistence of Brook Trout populations due to a changing climate. Many thanks to my advisor, Dr. Kyle Hartman, whom read many confusing writing samples. He helped give foundation for writing organization and overall guidance in Brook Trout research. Additionally, this project would not have been possible without the Hartman Lab who collected the long-term data necessary to put this thesis together. Dr. Ross Andrew was a core member of this lab whom helped not only in structuring my statistical design but also was valuable help to flesh out ideas. Dr. Charlene Kelly for invaluable help in critiques in thesis writing. Many thanks to the West Virginia Watershed Institute, whom provided the funding for me to pursue this project, even though it was not in the scope of the Institute's mission. Dr. James McGraw was an undergraduate mentor that showed me a career path I could be motived within. I am grateful for each piece that helped me along the way and the patience provided in my long absences from campus iv Table of Contents Trends in Brook Trout Habitat in Appalachian Headwater Streams.