This study analyzed the cognitive maps of senior level scientists and planners involved in natural resource management to characterize their mental models of water management and salmon health. The complexity of protecting ecosystem health while managing resource use requires the integration of traditionally disciplinary specific knowledge. In particular, recent policies effecting government agencies in the Puget Sound demand that science be incorporated into planning strategies. Although policy literature has discussed the cultural obstacles that can prevent effective cross-disciplinary communication, this study examines mental models specifically as a potential cultural difference. Research in cognitive science suggests that the structure and classification of prior knowledge influences the acquisition of new knowledge. This study used the Conceptual Cognitive Content Map (3CM) method (Kaplan and Kearney, 1997) along with a diagramming task to solicit cognitive maps from participants. The study incorporated three analysis methods to characterize the participants' mental models: commonality among elements, patterns within natural resource management themes, and framework characterization. The findings indicate that although participants identified a diverse set of significant issues, disciplinary differences influence the way participants structure, classify and frame the issues related to water management and salmon health.