Abstract: Airborne thermal remote sensing from four flights on a single day from a single-engine airplane was used to collect thermal infrared data of a 10.47-km reach of the upper East Branch Pecatonica River in southwest Wisconsin. The study uses a one-dimensional stream temperature model calibrated with the longitudinal profiles of stream temperature created from the four thermal imaging flights and validated with three days of continuous stream temperature data from instream data loggers on the days surrounding the thermal remote-sensing campaign. Model simulations were used to quantify the sensitivity of stream thermal habitat to increases in air and groundwater temperature and changes in base flow. The simulations indicate that stream temperatures may reach critical maximum thresholds for brook trout (Salvelinus fontinalis) and brown trout (Salmo trutta) mortality, particularly if both air temperature increases and base flow declines. The approach demonstrates that thermal infrared data can greatly assist stream temperature model validation due to its high spatial resolution, and that this spatially continuous stream temperature data can be used to pinpoint spatial heterogeneity in groundwater inflow to streams. With this spatially distributed data on thermal heterogeneity and base-flow accretion, stream temperature models considering various climate change scenarios are able to identify thermal refugia that will be critical for fisheries management under a changing climate.