Integrated Water Resource Management (IWRM) aims at finding practical and sustainable solutions to water resource issues. Research and practice have shown that innovative methods and tools are not sufficient to implement IWRM – the concept needs to also be integrated in prevailing management paradigms and institutions. Water governance science addresses this human dimension by focusing on the analysis of regulatory processes that influence the behavior of actors in water management systems. This paper proposes a new methodology for the integrated analysis of water resources management and governance systems in order to elicit and analyze case-specific management paradigms. It builds on the Management and Transition Framework (MTF) that allows for the examination of structures and processes underlying water management and governance. The new methodology presented in this paper combines participatory modeling and analysis of the governance system by using the MTF to investigate case-specific management paradigms. The linking of participatory modeling and research on complex management and governance systems allows for the transfer of knowledge between scientific, policy, engineering and local communities. In this way, the proposed methodology facilitates assessment and implementation of transformation processes towards IWRM that require also the adoption of adaptive management principles. A case study on flood management in the Tisza River Basin in Hungary is provided to illustrate the application of the proposed methodology.