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Natural infrastructure (NI) and nature-based solutions in urban riverscapes can provide a spectrum of environmental, societal, and economic benefits, but widespread implementation of NI strategies remain limited because of their context-dependent nature. Windows of opportunity have opened through legislation and funding to expand NI solutions that address flooding, water quality, air pollution, extreme heat, and environmental equity. System-level approaches may offer these projects a framework that is flexible yet holistic enough to streamline implementation. In fact, a systems approach is essential to realize the potential of NI for equitably achieving these goals, and a critical step includes identification of vulnerabilities (e.g., exposure to environmental harm). The purpose of this study was to support decision makers and managers in prioritizing their urban riverscapes with multiple vulnerabilities: flood risk, water quality, ecosystem function, and environmental inequity. We conducted an urban stream spatial multicriteria decision analysis (MCDA) case study with Charlotte–Mecklenburg Storm Water Services to support equitable and efficient stream reach, floodplain, and watershed planning. Our study assessed the social and ecological characteristics of the system and prioritized vulnerable watersheds and subbasins using a spatial MCDA. We developed an urban stream prioritization framework that could be tailored to complement existing management strategies and also more broadly implemented in other social–ecological systems.