Floods pose serious threats worldwide. During this disaster, civil engineering structures, such as buildings, bridges, dams, water supply, coastal structures, infrastructure facilities are severely affected, causing immense inconvenience to people and disrupting routine life. In the context of water-food security, floods have been a major source of natural disturbance to rice productivity in Malaysia. The consequences of floods will bring losses to the rice production and cause instability. The damage of paddy production due to floods needs to be handled seriously as the negative impact could lead to insufficient food supplies in the country. The purpose of this paper is to estimate flood risk in paddy production considering different flood inundation durations and plant’s ages. The calculation of risk considers the probability of extreme flood levels and fine cell resolution of paddy field in the total loss estimation. The location used for this study is in Kedah, where rice production is among the most prominent in Malaysia. Flood risk is expected mounting to nearly half a million ringgits for the 330 ha plots considering the current condition. This emphasize on an effective long-term flood risk management in order to reduce flood risk to paddy production.