Alpine aquatic ecosystems are sensitive to climate change due to the central role of snow and ice in shaping community and ecosystem characteristics. Long-term data on abiotic factors and biological communities remains relatively rare, however, making it challenging to understand shifts over time or space. Focusing on the Niwot Ridge Long-term Ecological Research Site in the Southern Colorado Rockies, we review evidence for long-term shifts in climate and cryosphere characteristics in relation to aquatic ecosystems. To understand possible future consequences of changing hydrology, we also document benthic stream communities using morphology and metabarcoding approaches across sites varying in source waters, including ephemeral and permanent streams dominated by glacier meltwater, snowmelt, lake outflows, and mixed source waters. Discharge, water temperature, conductivity, pH, total dissolved nitrogen, and total dissolved phosphorus differed between water source types. Macroinvertebrate composition was more strongly correlated with stream permanence and conductivity than with water temperature or nutrient availability. Lake outlets showed the highest beta diversity, with unique communities dominated by filter feeders. Alpha diversity was similar at the glacial, snowmelt, and lake outlet sites, but increased at the downstream mixed source sites which had proportionally more non-dipteran taxa. Taken together, these results help to understand and predict how ongoing and future changes in climate and hydrology will influence alpine aquatic communities.