Headwater streams typically make a large contribution to regional biodiversity and are important sources of water, nutrients and other resources to their downstream river networks. However, across the world, they are rapidly being degraded or lost due to human activities, particularly urban development. This has direct negative consequences for the structure and function of headwater streams as well as downstream river networks. Despite the long-held recognition of the ecological value of headwater streams and the impacts of their widespread loss, there remains a large gap between high level strategies or policies aimed at their protection and practical guidance for on-ground action. Beginning with a workshop held during the 2023 Symposium on Urbanization and Stream Ecology (SUSE6) in Brisbane, Australia, we established a group of cross-disciplinary researchers and practitioners from multiple organisations and locations to bridge this gap. We have developed a framework to identify opportunities for waterway managers to strengthen their ability to protect headwater streams in their region, as well as capturing a comprehensive set of structural and non-structural management tools. The framework was critically evaluated by applying it to four contrasting case studies with different physiographic, policy and legislative settings. Our evaluation showed that the framework provides a useful generic mechanism that can be used by policy makers, planners, and other stakeholders to diagnose the maturity of headwater stream protection in a variety of urban areas and support structured stakeholder conversations about what’s desirable, practical and achievable for their context.