Local knowledge and modern science are both valuable inputs to environmental Disaster Risk Reduction (DRR) approaches. Local knowledge for DRR is particularly important in countries where government capabilities are limited and where long-standing customary practices of natural resource management still exist and may be harnessed for governance purposes. Modern science can add value by expanding the knowledge base using methods not available to local people through empirical studies and using theory in data-poor locations to fill empirical gaps and test empirically derived inferences. Timor-Leste is an impoverished post-conflict nation prone to disasters from connected threats of droughts, floods and landslides and human dependence on low yield, shifting agriculture. In this paper, the results of community meetings in the catchments of the Laclo and Caraulun rivers are compared with scientific research to identify explanations of hazard cause and effect. The major difference between the two knowledge spheres is that while local people shared causal connections with scientific explanations they also simultaneously held ‘naturalist’ explanations of disasters. In particular, they attributed environmental disasters to the failure to put to rest the spirits of the many people killed during the previous decades of militarised occupation. The paper considers the implications of these findings for developing effective governance and preparedness policies for DRR in Timor Leste and evaluates recent developments.