Stream temperature data and streamflow data from headwater streams in the upper Snake River basin, Wyoming and upper Yellowstone River basin and Flathead River basin in Montana. These datasets were assembled to assess how stream temperature and streamflow in headwater streams deviates from downstream gages in order to better understand tools to estimate streamflow at a variety of temporal scales. The datasets range from 2011 through 2023 and were collected using standard stage-discharge relationships and commonly used sensors. Data were collected by the U.S. Geological Survey and/or affiliated field crews with support from the U.S. Geological Survey.