The duration, magnitude, and frequency of heatwaves are predicted to increase in the coming decades, a combination that can reduce the survival of many fish species. Across the world, there is broad interest in identifying thermal refuge for heat-intolerant fish species and exploring opportunities to enhance or protect these areas. Because deeper groundwater maintains a relatively constant temperature, groundwater-influenced areas along streams can provide cool-water refuge for fish during periods of extreme heat. A targeted approach was developed for identifying existing cold-water zones and areas of substantial groundwater discharge in four high priority Lake Ontario tributaries. Our approach included: (1) predicting where groundwater discharge is most likely with a simple geospatial model and (2) using model predictions to select field sites for intensive high-resolution study, including ground-based mapping of groundwater features (springs, seeps, tributaries) as well as drone-based optical and thermal infrared surveys. Results from field sites were used to both verify model performance and map different types and aerial extents of thermal anomalies. Geospatial modelling successfully predicted regions of widespread groundwater upwelling, later verified and mapped by field and drone surveys. Comparison of model and field survey results further highlighted specific geospatial layers, such as soil/bedrock types and topographic wetness index, as being particularly useful for predicting groundwater influence on streams in the study area. In addition, a comparison of geospatial model results with a model of fish abundances along the studied streams showed significant positive correlations for many heat-intolerant fish species over a wide geographic area. The approach developed in this study can be applied to other watersheds to highlight areas of probable groundwater discharge and could be used by fishery and water resource managers to support cold-water fish habitat management decision-making and resource conservation.