Water supply and wastewater systems are essential infrastructure affected by floods. Additional risk is posed in developing countries, where access to sanitation is not universal. Few studies assess the flood risk to the sanitation-health nexus. Therefore, this study aims to present a theoretical and general framework for assessing the resilience of flood-sanitation-public health nexus in urban environments, composed by risk estimation and risk management assessment. The framework was developed from a system analysis approach focusing on central supply systems. Regarding risk assessment, the main vulnerability and exposure factors identified were land use, social vulnerability, coverage of sanitation systems, occurrence of waterborne diseases, number of people affected by floods and intersection with the flood map. From the risk management assessment stage three main typologies of trade-offs and synergies were identified: urban territorial planning versus runoff control, water quality versus sanitation infrastructure and flood management policy versus social behavior.