In alpine regions worldwide, climate change is dramatically altering ecosystems, affecting biodiversity across habitats and taxonomic scales. For streams, the associated recession of mountain glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, and basal resources – often threatening the very existence of some habitats and biota. Globally, alpine streams harbor particularly substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity: however, anthropogenic warming threatens to homogenize habitats through the reduction of the cryosphere, thereby reducing biodiversity from micro- to macroscopic organisms and genes to communities. Still, alpine stream biodiversity, particularly in North America, is poorly understood, making it difficult to predict future changes without baselines for comparison. For my dissertation, I used genetic tools to assess biodiversity in alpine streams of the central Rocky Mountains in North America. Here, I begin by reviewing the current state of alpine stream biology from an organismal perspective. Next, I provide two perspectives on macroinvertebrate diversity. The first, a population genetic comparison of three highly similar species, is followed by a fine-scale genomic study of one species, Lednia tumana. I follow these largely macroinvertebrate-centric chapters with a modern synthesis of the microbial ecology of mountain glacier ecosystems. Finally, I conclude with a study of microbial diversity that addresses how microbial diversity is shaped by geography, habitat, and hydrological source in North America. Collectively, this research refines existing themes in alpine stream biology by revealing unexpected differences in population genetic patterns among closely related species, the influence of recent deglaciation on population genetic structure and demographic history of a threatened stonefly, and clarification of the environmental drivers shaping microbial diversity.