Urban flooding poses environmental and health risks, potentially leading to casualties and social unrest. The Internet of Things (IoT) technology enhances flood management by collecting real-time data on rainfall, water levels, and flow rates, to support early warning systems. However, IoT faces cybersecurity challenges such as data leakage and device vulnerabilities. To address these issues, this paper proposes the establishment of a multi-layered security architecture that includes the perception layer, network layer, data layer, and platform management layer. A protection system is constructed that includes physical security, data encryption, access control, monitoring, and emergency response. In addition, strategies such as updates, patch management, and staff training are of paramount importance. The integration of IoT with an advanced cybersecurity architecture ensures efficient disaster response and the sustainability of the city.