The development of large infrastructure to address the water challenges of cities around the world can be a financial and social burden for many cities because of the hidden costs these works entail and social conflicts they often trigger. When conflicts erupt, science is often expected to play a key role in informing policymakers and social actors to clarify controversies surrounding policy responses to water scarcity. However, managing conflicts is a sociopolitical process, and often quantitative models are used as an attempt to depoliticize such processes, conveying the idea that optimal solutions can be objectively identified despite the many perspectives and interests at play. This raises the question as to whether science depoliticizes water conflicts or whether instead conflicts politicize science-policy processes. We use the Zapotillo dam and water transfer project in Mexico to analyze the role of science-policy processes in water conflicts. The Zapotillo project aims at augmenting urban water supply to Guadalajara and León, two large cities in western Mexico, but a social and legal conflict has stalled the project until today. To analyze the conflict and how stakeholders make sense of it, we interviewed the most relevant actors and studied the negotiations between different interest groups through participant observation. To examine the role of science-policy processes in the conflict, we mobilized concepts of epistemic uncertainty and ambiguity and analyzed the design and use of water resources models produced by key actors aiming to resolve the conflict. While the use of models is a proven method to construct future scenarios and test different strategies, the parameterization of scenarios and their results are influenced by the knowledge and/or interests of actors behind the model. We found that in the Zapotillo case, scenarios reflected the interests and strategies of actors on one side of the conflict, resulting in increased distrust of the opposing actors. We conclude that the dilemma of achieving urban water security through investing in either large infrastructure (supply augmentation) or alternative strategies (demand-side management) cannot be resolved if some key interested parties have not been involved in the scientific processes framing the problem and solution space.