Water resource systems display complex behavior that challenges our ability to identify paths toward improved management. Such behavior can arise from unanticipated feedbacks between social, ecological, and technological components that are conventionally studied and managed in disciplinary silos, often with limited consideration of interactions across scales of space and time. Convergence research driven by deep integration and co-production of knowledge within research teams is needed to better anticipate water resource system behavior and identify new approaches. We developed and applied a new framework—the Collaborative, Adaptive, and Multi-Scale (CAMS) systems thinking framework—to build a convergence research team around the task of characterizing a watershed as a complex system and hypothesize associated water management dynamics. The CAMS framework applies systems thinking methods within a broader integrated approach to engage and synthesize the knowledge and interests of an intellectually diverse research team and model a water resource system across spatial and temporal scales. Our case study of the Santa Fe Watershed in New Mexico reflects challenges and opportunities to manage water in the western United States of America. The specific methods applied within the framework included a six-session workshop on systems thinking, conceptual model development exercises with a longer-term subgroup, a structural analysis of system variables, and classroom-based projects. We discuss the successes, limitations, and potential of each method and how they interacted within the CAMS framework. We found that use of multiple systems thinking methods within the open-ended, iterative design of the framework provided a structure for long-term use that integrates disparate ideas, hypotheses, and findings from water sustainability research. Creating an inclusive environment within the research team was critical to the framework’s successful application and will remain a core consideration for ongoing work aimed at broader participation.