Urban watersheds are often degraded by human activities, reducing their ability to provide ecosystem benefits. While governmental agencies have put forward plans for improving watershed health, resources are limited, and choices must be made as to which watersheds to prioritize and what actions to take. Prioritization tools often lack sufficient specificity, resolution, and automation to be useful in guiding decisions regarding restoration and management actions across regional or statewide scales. To address this, we developed a set of assessment and prioritization tools to support the protection of rivers and associated riparian habitats across California. The tool estimates stream condition at the NHD reach scale based on bioassessment data, uses EPA’s StreamCat dataset to identify stressors, includes reach-specific models to help prioritize actions, and accounts for environmental justice using census tract data. Using the prioritization tool, we identified 38% of the stream reaches across California that should be considered the highest priorities for restoration and management actions. At the watershed scale, we were able to identify 7 -40% of reaches that should be prioritized for protection and 10-34% of reaches that should be prioritized for restoration, and management, depending on the watershed. The results of this project can help regional stakeholders and agencies prioritize hundreds of millions of dollars being spent to protect, acquire, and restore coastal stream and riparian habitats. The methods are directly transferable to any regional condition and stress data that can be readily obtained.