Estuaries and coastal bays are among the most dynamic regions that support diverse marine wildlife, provide economic benefits and serve as buffers for shoreline protections from coastal hazards. However, coastal and estuarine processes are extreme complex because of sharp gradient along the terrestrial-marine continuum that is strongly influenced by multiple factors, such as stream flow, tide, wave, storm surge, atmospheric forcing, and sea level rise. To better understand and predict the physical and biogeochemical processes from catchments to coastal seas, we need to develop the capabilities that can capture the key processes and their interactions at desired spatial and temporal scales, especially in consideration of future climate change. An integrated modeling framework is being developed for a coastal watershed-estuary system – Delaware River and Bay as part of the U.S. Department of Energy’s Integrated Coastal Modeling Project (ICoM) and Waterborne Prediction, Assessment, Collection Technologies (WaterPACT) to simulate the estuarine hydrodynamics and transport processes. Model coupling strategy, configurations, resolutions, and influences of floodplain, atmospheric forcing and open boundary conditions are discussed in Delaware River and Bay. Applications of this modeling framework for simulating the complex physical and transport processes such as storm surge, saltwater intrusion, microplastic fate and transport are presented.