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Groundwater depletion threatens global freshwater resources, necessitating urgent water management and policies to meet current and future needs. However, existing data-intensive approaches to assessments do not fully account for the complex human, climate, and water interactions within transboundary groundwater systems. Here, we present the design of and findings from a pilot participatory modeling workshop aiming to advance understanding of the hydrologic–human–climate feedback loops underpinning groundwater systems. Using participatory modeling tools and methods from the system dynamics tradition, we captured the mental models of researchers from water, social, data, and systems sciences. A total of 54 feedback loops were identified, demonstrating the potential of this methodology to adequately capture the complexity of groundwater systems. Based on the workshop outcomes, as an illustrative example, we discuss the value of participatory system modeling as a conceptualization tool, bridging perspectives across disciplinary silos. We further discuss how outcomes may inform future research on existing knowledge gaps around groundwater issues, and in doing so, advance interdisciplinary, use-inspired research for water decision-making more broadly.