Urban flooding poses compound risks, not only through physical inundation but also through transport of microbial contaminants in floodwaters. This study presents HyEco, an integrated hydrodynamic-ecological modeling framework that captures the dual hazards of flood exposure and waterborne disease risk. Applied to Delhi, a densely populated megacity with frequent monsoonal flooding and inadequate wastewater infrastructure, the framework simulates the 2023 flood event using a fully dynamic, three-way coupled MIKE+ model. Flood simulations revealed that 63.5% of the study area falls within high or very high hazard zones, with vulnerable populations concentrated in many of these areas. These outputs informed ecological modeling of Escherichia coli transport using MIKE ECO Lab, showing concentrations exceeding 790,000 MPN/100 mL in flood-affected zones. To assess health risks, we conducted a Quantitative Microbial Risk Assessment (QMRA) under two behavioral scenarios: (i) pedestrian splash exposure and (ii) children playing in floodwaters. Annual infection probabilities exceeded USEPA safety thresholds, with children facing risks up to 2.60×10⁻³. This study highlights the need to integrate microbial contamination dynamics into urban flood risk assessments. The HyEco framework offers a scalable approach for multi-hazard risk analysis, supporting early warning systems, resilient infrastructure design, and public health protection in climate-exposed urban regions.