The important role that local knowledge and practices can play in reducing risk and improving disaster preparedness is now acknowledged by disaster risk reduction specialists, especially since the 2004 Indian Ocean earthquake and tsunami. However, they have yet to be commonly used by communities, scientists, practitioners and policy-makers. We believe that local and indigenous knowledge needs to be integrated with science before it can be used in policies, education, and actions related to disaster risk reduction and climate change. This paper presents a process for integrating local and indigenous knowledge related to hydro-meteorological hazards and climate change with science, developed through a project implemented among coastal and small island communities in Indonesia, the Philippines and Timor-Leste. The process involves observation, documentation, validation, and categorization of local and indigenous knowledge, which can then be selected for integration with science. This process is unique in that it allows communities to (1) identify knowledge that can be integrated with science, which could then be further disseminated for use by scientists, practitioners and policy-makers, and (2) safeguard and valorize those that cannot be scientifically explained. By introducing a process that can be used in other communities and countries, we hope to promote the use of local and indigenous knowledge to enable communities to increase their resilience against the impacts of climate change and disasters.