Temperate mountain systems capture and store winter precipitation as snow and ice and slowly release it to downstream ecosystems and human communities during the warm season. Climate warming in these regions is shifting precipitation from snow to rain and shortening the duration and increasing the variability and magnitudes of spring runoff. These changes impact the chemical and physical properties of stream water in these systems, although knowledge of spatial and temporal patterns at the watershed and basin scales is limited. Our study seeks to address this knowledge gap by focusing on headwater streams of the Snake and Green Rivers in the Greater Yellowstone Area (GYA), a snow-dominated temperate mountain landscape where more than half of annual precipitation falls as snow. On average, temperatures in the GYA for the last two decades are higher than during any other period over the last 20,000 years. In the Upper Green River Basin in Wyoming, temperatures observed between 1950 and 2018 have increased by 1.7 °C, contributing to a 44% reduction in snowfall while total precipitation remained largely the same (Hostetler et al. 2021). We combine multi-decadal water quality observations (including pH, conductivity, dissolved oxygen, and turbidity) with measured and modeled stream temperature and discharge to assess how climate driven changes in stream flow have altered the physical and chemical characteristics of water exported from the mountain headwaters of the Upper Green and Snake River Basins of Western Wyoming. By quantifying long-term changes in the lessening meltwater-driven streamflow and water quality, this work advances understanding of how cryospheric change is reshaping freshwater ecosystems in temperate mountain environments. These insights have broad relevance for aquatic habitat, downstream water quality, and water resource management, and contribute to a growing, cross-regional effort to understand the cascading effects of a changing cryosphere on freshwater ecosystems.