Using an integrated watershed-coastal modeling framework, we conducted long-term historical simulations (1980-2019) of fluvial and coastal flooding in the Delaware Bay and River, a vulnerable estuarine system in the U.S., at high spatial resolutions. By employing physical and process-based models, we generated physically-consistent and spatially-detailed estimates of estuarine, riverine, and compound flooding compared to previous studies that used field data only. We then evaluated changes in the magnitude of flood events using the 40-year simulations and detrended floodwater depth values with stationary extreme value analysis. Our detailed assessment of spatial-varying extreme values revealed how different flood-generation mechanisms can dominate various zones in the estuary. The datasets produced through this work will be valuable for long-term flood hazard mitigation planning in coastal communities in the Delaware Bay and River region. Additionally, this work will serve as a benchmark for other coastal flood hazard modeling communities worldwide, aiding them in systematically modeling long-term and continuous extreme flood events.