Over the past decade, water professionals have begun to focus on a new paradigm for urban water systems, which entails the recovery of resources from wastewater, the integration of engineered and natural systems, and coordination among agencies managing different facets of water systems. In the San Francisco Bay Area, planning for nutrient management serves as an exemplary model of this transition. We employed a variety of methodological approaches including stakeholder analysis, multi-criteria decision-making weight elicitation, and document analysis to understand and support decision-making in this context. Based on interviews with 32 stakeholders, we delineate goals that are considered to be important for achieving the new paradigm and we highlight management strategies that can help reach these goals. We identify and analyze the social, institutional, and technical impediments to planning and implementing multi-benefit wastewater infrastructure projects and identify strategies to overcome some of these challenges. Transitioning to a new paradigm for urban water infrastructure will require stakeholders to proactively forge collaborative relationships, jointly define a shared vision and objectives, and build new rules to overcome limitations of current institutional policies.