Floods are a climatic risk that can result in significant yield losses for smallholder farmers. In this study, the impacts of the 2012 floods on rice productivity in Benin were investigated. A socioeconomic and productivity survey of 150 rice farmers was conducted in 17 villages across 2 districts that are highly vulnerable to climate change. The generalised propensity score method was employed to account for the continuous nature of the treatment variable, with the results indicating a decrease in rice yield accompanied by an increase in flooded farm proportion. The expected rice yield for a 10% flooded rice land was 7.20 tons/ha throughout the year. Additionally, an increase in the proportion of flooded rice land from 10% to 20% resulted in a decrease of 1.19 tons/ha of rice yield. During the wet season, floods negatively impacted rice yield, irrespective of their severity. Conversely, flooding benefited rice production in the dry season following flooding. These findings offer policymakers insight into appropriate protection plans and adaptation strategies.