In this study, we used remotely piloted aircraft system (RPAS)-based thermal infrared (TIR) imaging to study fine-scale thermal heterogeneity in a temperature-sensitive salmon stream in the Southern Interior region of British Columbia. We were able to identify cool-water zones at the site level that may provide important thermal refugia for salmonids during periods of high summer stream temperatures. Repeat imaging of our study reach following a major flood event in 2017 found that the abundance of cold alcoves, a type of thermal refuge habitat, increased significantly. Our results highlight the importance of maintaining the fluvial processes that create new habitat, in-keeping with the concept of Shifting Habitat Mosaics. As part of this work, we also provide some best practices for rapid, RPAS-based TIR surveys of stream thermal refugia – expecting that this type of survey will become an increasingly common addition to fish habitat inventories.