Temperature profoundly affects ecology, a fact ever more evident as the ability to measure thermal environments increases and global changes alter these environments. The spatial structure of thermalscapes is especially relevant to the distribution and abundance of ectothermic organisms but the ability to describe biothermal relationships at extents and grains relevant to conservation planning has been limited by small or sparse datasets. Here, we combine a large occurrence database of >23,000 aquatic species surveys with stream microclimate scenarios supported by an equally large temperature database for a 149,000-km mountain stream network to describe thermal relationships for 14 fish and amphibian species. Species occurrence probabilities peaked across a wide range of temperatures (7.0–18.8 °C) but distinct warm- or cold-edge distribution boundaries were apparent for all species and represented environments where populations may be most sensitive to thermal changes. Warm-edge boundary temperatures for a native species of conservation concern were used with geospatial datasets and a habitat occupancy model to highlight subsets of the network where conservation measures could benefit local populations by maintaining cool temperatures. Linking that strategic approach to local estimates of habitat impairment remains a key challenge but is also an opportunity to build relationships and develop synergies between the research, management, and regulatory communities. As with any data mining or species distribution modeling exercise, care is required in analysis and interpretation of results, but the use of large biological datasets with accurate microclimate scenarios can provide valuable information about the thermal ecology of many ectotherms and a spatially-explicit way of guiding conservation investments.