This study explored the community perception of maternal deaths influenced by natural disaster (flood), and the practice of maternal complications during natural disaster among the rural population in Bangladesh. It also explored the challenges faced by the community for providing healthcare and referring the pregnant women experiencing complications during flood disaster. Three focus group discussions (FGDs) and eight in-depth interviews (IDIs) were conducted in the marginalized rural communities in the flood-prone Khaliajhuri sub-district, Netrakona district, Bangladesh. Flood is one of the major risk factors for influencing maternal death. Pregnant women seriously suffer from maternal complications, lack of antenatal checkup, and lack of doctors during flooding. During the time of delivery, it is difficult to find a skilled attendant, and referring the patient with delivery complications to the healthcare facility. Boats are the only mode of transport. The majority of maternal deaths occur on the boats during transfer from the community to the hospital. Rural people feel that the maternal deaths influenced by natural disaster are natural phenomena. Pre-preparation is needed to support pregnant women during disasters. There is unawareness of maternal health, related care, and complications during disasters among local health service providers and volunteers.