To address impacts of climate change and other stressors on stream ecosystems, managers must prioritize resources and locations for conservation actions to facilitate effective cross‐boundary solutions. Through a science management partnership, we co‐produced a spatially explicit landscape assessment framework for cold‐water fish habitat and riparian corridors in three large watersheds of the southwestern United States. Using literature review and stakeholder workshops, we developed indicators of vulnerability and built spatial datasets depicting areas of low to high vulnerability based on exposure, sensitivity, and adaptive capacity for each resource. We found that, in general, vulnerability was greater for cold‐water fish habitat than for riparian corridors. The Little Colorado River and San Juan River watersheds had the highest percentages of subwatersheds with high vulnerability of cold‐water fish habitat. Conversely, the Upper Rio Grande watershed had the highest percentage with high vulnerability of riparian corridors. Assessments like ours facilitate the management of water resources at the scale of watersheds or river basins and incorporate physical characteristics, land‐use history, current management practices, and status of imperiled species into actionable management plans.