Brook trout (Salvelinus fontinalis) is an iconic native trout species in eastern North America but has declined range-wide, particularly in the southern distribution range where remnant populations persist in small and isolated habitats. Threats are both local (habitat loss, invasive species) and regional (climate change), and may interact with each other across spatial scales. A quantitative assessment of these threats on brook trout populations needs to incorporate information from genetic to landscape levels. In this talk, I highlight the challenges of conserving a native inland trout at the southern distribution margin, and summarize recent research and management activities to inform conservation efforts. Southern populations are typically characterized with low allelic diversity and number of breeders, but many populations retain southern genetic signatures despite a long history of stocking from the northern range. Active management practices are pursued to suppress invasive trout species and translocate native brook trout. I also present an analysis of long-term trout count (30-year time series) to address stream flow impacts on population dynamics and implications for climate change that may differ between native and invasive species, and among life stages. Future research should address how information could be better integrated across scales to identify complex ecological patterns and inform management actions.