Watershed-scale stream temperature models are often one-dimensional because they require fewer data and are more computationally efficient than two- or three-dimensional models. However, one-dimensional models assume completely mixed reaches and ignore small-scale spatial temperature variability, which may create temperature barriers or refugia for cold-water aquatic species. Fine spatial and temporal resolution stream temperature monitoring provides information to identify river features with increased thermal variability. We used distributed temperature sensing (DTS) to observe small-scale stream temperature variability, measured as a temperature range through space and time, within two 400 meter reaches in summer 2015 in Nevada’s East Walker and mainstem Walker Rivers. Thermal infrared (TIR) aerial imagery collected in summer 2012 quantified the spatial temperature variability throughout the Walker Basin. We coupled both types of high resolution measured data with simulated stream temperatures to corroborate model results and estimate the spatial distribution of thermal refugia for Lahontan cutthroat trout and other cold-water species. Temperature model estimates were within the DTS measured temperature ranges 21% and 70% of the time for the East Walker River and mainstem Walker River, respectively, and within TIR measured temperatures 17%, 5%, and 5% of the time for the East Walker, West Walker, and mainstem Walker Rivers, respectively. DTS, TIR, and modeled stream temperatures in the mainstem Walker River nearly always exceeded the 21°C optimal temperature threshold for adult trout, usually exceeded the 24 °C stress threshold, and could exceed the 28 °C lethal threshold for Lahontan cutthroat trout. Measured stream temperature ranges bracketed ambient river temperatures by -10.1 to +2.3 °C in agricultural return flows, -1.2 to +4 °C at diversions, -5.1 to +2 °C in beaver dams, -4.2 to 0 °C at seeps. To better understand the role of these river features on thermal refugia during warm time periods, the respective temperature ranges were added to simulated stream temperatures at each of the identified river features. Based on this analysis, the average distance between thermal refugia in this system was 2.8 km. While simulated stream temperatures are often too warm to support Lahontan cutthroat trout and other cold-water species, thermal refugia may exist to improve habitat connectivity and facilitate trout movement between spawning and summer habitats. Overall, high resolution DTS and TIR measurements quantify temperature ranges of refugia and augment process-based modeling.