The government of Colombia has taken a leadership role in facilitating research in high mountain ecosystems to provide a scientific base for understanding climate change and land use impacts on water and carbon cycles. With support from the World Bank and GEF, the Colombian Institute of Hydrology, Meteorology, and Environmental Studies (IDEAM) has undertaken a national pilot project on integrated adaptation to climate change (INAP). A key component of this project has been the development of a protocol for the characterization of carbon and water cycles in high mountain ecosystems. The protocol is designed for use by government, university, and NGO partners interested in climate change impacts, with IDEAM leading the project and consolidating data and results. The present article provides an overview of the protocol design.