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Water management within vulnerable ecosystems managed by multiple jurisdictions can be very complex. This study compares regulatory environments and deconstructs the approaches used for watershed governance and environmental management inside two UNESCO’s Biosphere Reserves to identify possible transferability between the two management entities. Three methodological approaches were applied: participatory observation, in-depth interviews of key informants, and document research. We concluded that while there are differences between the regulatory frameworks and localized practices, at a foundational level the goals and desired outcomes relating to environmental protection are not dependent on location, but mainly on the integration and the establishment of common objectives among the diverse social actors involved in the management and from the interaction between different organisms of social control. Additionally, there are elements in the application of regulations and practices in both locales that could be transferred to other jurisdictions interested in addressing watershed protection in vulnerable ecosystems governed by multiple jurisdictions.