A combination of long-term daily temperature records and depth to bedrock measurements were used to parameterize one-dimensional models of shallow aquifer vertical heat transport in Shenandoah National Park, VA, USA. Spatially discontinuous roving water surface and bank temperatures surveys were performed with a handheld thermal infrared camera in September and December 2015 along the main channel of a headwater stream supporting coldwater-dependent brook trout (Salvelinus fontinalis). We also installed vertical arrays of thermal data loggers to estimate bulk thermal diffusivity of the saturated alluvium at two stations in the upper trout section. The methods are fully documented in the associated journal article, Briggs, M.A., J.W. Lane, C.D. Snyder, E. White, Z.C. Johnson, D.L. Nelms, and N.P. Hitt, 2017, Shallow mountain bedrock limits seepage-based headwater climate refugia, Limnologica, https://dx.doi.org/10.1016/j.limno.2017.02.005. This Data Release includes temperature measurements collected as part of the study. The directory RAW_DATA contains the measured temperature time series at streambed, stream, and air locations as described in the local read.me file. The OUTPUT directory contains the processed temperature time series and VFLUX2 calculations of thermal diffusivity (Ke) from streambed data, and annual temp signal amplitude/phase lag from stream/air data are listed.