One of the factors for the success of simulation studies is close collaboration with stakeholders in developing a conceptual model. Conceptual models are a useful tool for communicating and understanding how real systems work. However, models or frameworks that are not aligned with the perceptions and understanding of local stakeholders can induce uncertainties in the model outcomes. We focus on two sources of epistemic uncertainty in building conceptual models of food-energy-water systems (FEWS): (1) context and framing; and (2) model structure uncertainty. To address these uncertainties, we co-produced a FEWS conceptual model with key stakeholders using the Actor-Resources-Dynamics-Interaction (ARDI) method. The method was adopted to specifically integrate public (and local) knowledge of stakeholders in the Magic Valley region of Southern Idaho into a FEWS model. We first used the ARDI method with scientists and modellers (from various disciplines) conducting research in the system, and then repeated the process with local stakeholders. We compared results from the two cohorts and refined the conceptual model to align with local stakeholders’ understanding of the FEWS. This co-development of a conceptual model with local stakeholders ensured the incorporation of different perspectives and types of knowledge of key actors within the socio-ecological systems models.