Coastal cities worldwide face increasing flood risks due to climate change, rising sea levels, and changes in hurricane patterns. Since the 1950s, there has been a notable increase in flooding in cities near the U.S. coastline. Based on this trend, the Department of Energy’s (DOE) Integrated Coastal Modeling Project (ICoM) has developed a high-resolution integrated modeling framework with hydrologic (DHSVM) and hydrodynamic (RIFT, FVCOM) models to capture time-evolving flood risks within coastal regions. Using this framework, we first examined the sensitivity of estuarine flooding to different hurricane characteristics. We chose Delaware Bay and River (DBR), a shallow and convergent estuary in the U.S. Mid-Atlantic, historically highly vulnerable to storm-induced flooding. Then, using the earth system model, E3SM, we perturbed Hurricane Irene (2011) to get an ensemble of Irene-like tracks with different characteristics. Our results showed that the hurricane landfall locations and the estuarine wind can severely amplify the extreme surge in a converging system. The results also demonstrated the need for integrated modeling to capture the tide, surge, and river interactions and why such a framework is critical for projecting future coastal hazards. Subsequently, using the same setup in DBR, we conducted a long-term simulation (1980-2019) of historical estuarine flooding. By employing physical and process-based models, we produced a complete estimate of estuarine, riverine, and compound flooding and generated an extreme flood dataset that can be valuable for long-term flood hazard mitigation planning. Overall, this research highlights the importance of representing fine-scale tide-surge-river interactions for modeling estuarine flooding, which directly impacts the flood risk of coastal urban regions.