The streams of the southeastern United States are both hotspots for biodiversity and centers of imperilment. The specific spatiotemporal scales at which stressors impact biota are often unknown, partly due to inadequate knowledge about many species' life-histories. I conducted two complementary studies to investigate the habitat associations of an imperiled highland stream fish, the Candy Darter Etheostoma osburni. In Chapter 2, I asked (1) does micro-habitat suitability correlate with the "robustness" (i.e., viability) of four distinct populations? In Chapter 3, I expanded the extent of investigation, and asked (2) which environmental factors, expressed at what spatial scales, best explain in-stream conditions, and (3) do stream segments where Candy Darters persist have cooler temperatures and less fine-sediment than segments where the species is extirpated or historically went undetected? Chapter 2 revealed Candy Darters demonstrate ontogenetic habitat shifts, with age-0 individuals selecting slower water velocities than adults. Despite, clear habitat selection for multiple habitat variables, suitability attributed to fine-sediment avoidance most strongly correlated with population robustness across streams. Chapter 3 indicated Candy Darters are extirpated from most areas in Virginia and southern West Virginia. Land use and natural catchment features, including geology, elevation, and stream geomorphology, predominantly explained instream conditions. Populations persist in segments with cool stream temperatures and low embeddedness year-round. To recover Candy Darters, managers will need to remedy pervasive land-use threats and restore stream habitat, while operating within the impending context of warming air and water temperatures and the existential threat of the introduced Variegate Darter E. variatum.