Flood damage in West Africa has increased appreciably during the last two decades. Poor communities are more at risk due to the vulnerability of their livelihoods, especially in rural areas where access to services and infrastructures is limited. The aim of this paper is to identify the main factors that contribute to flood risk of rural communities in the Oti River Basin, Togo. A community-based disaster risk index model is applied. The analyses use primary data collected through questionnaires during fieldwork, the analytic hierarchy process (AHP) method, population and housing census data and flood hazard mapping of the study area. The results showed a moderate level of flood risk despite a high level of hazard and vulnerability for all investigated communities. In addition, the results suggest that decreasing vulnerability through creation of new income-generating opportunities and increasing capacity of communities to manage their own flood risk should be paramount in order to reduce flood risk in the study area. The results of this work contribute to the understanding of flood risk and can be used to identify, assess, and compare flood-prone areas, as well as simulating the impacts of flood management measures in the Oti River Basin.