Wastewater treatment plants (WWTPs) in the City of New York, United States, are particularly vulnerable to frequent extreme weather events, including storm surges, high-intensity rainfall, and sea level rise, and are also affected by the cascade of these events. The complex structural configuration of WWTPs requires very fine-scale flood risk assessment, which current research has not pursued. We propose a robust technique to quantify the risk of inundations for the fourteen WWPTs through an automated sub-basin creation tool; 889 sub-basins were generated and merged with high-resolution building footprint data to create a comprehensive database for flood inundation analysis. The inundation depths and extents for the WWTPs and flood-prone regions were identified from hydrodynamic modeling of storm surge and sea level rise. The economic damage due to flooding for the WWTPs was also quantified using the HAZUS-MH model. Results indicated that the storm surges from various categories of hurricanes have the dominant impacts on flood depths around WWTPs, followed by high-intensity rainfall. Sea level rise was shown to have a relatively minor impact on flood depths. Results from economic damage analysis showed that the WWTPs are subjected to damage ranging from USD 60,000 to 720,000, depending on the size of the WWTP and the extremity of storm surge. The method of analyzing the inundation status of the research object through the sub-basin enables more accurate data to be obtained when calculating the runoff. It allows for a clearer view of the inundation status of the WWTPs when combined with the actual buildings. Using this database, predicting flood conditions of any extreme event or a cascade of extreme events can be conducted quickly and accurately.