Green Bay is the largest freshwater estuarine system on earth, drains one-third of the Lake Michigan basin and delivers one-third of the lake’s phosphorus load. Southern Green Bay is a designated area of concern (AOC) due to ecosystem degradation that includes eutrophication, harmful algal blooms (HABs), hypoxia, lost or altered habitat, and reduced water quality. While marine estuaries are subject to tidal influence and saltwater intrusion, this freshwater estuary is subject to lake intrusion of freshwater with different quality parameters. Understanding the simultaneous effects of tributary flows and lake intrusions is crucial to comprehend the dynamics of freshwater estuaries. A single hydrodynamic, wind-wave, and sediment transport model was developed for the lake and its estuary. This approach provides fine resolution in the estuary and simulates directly the combined effects of tributary flows and lake intrusions. The approach overcomes open-boundary limitations of nested models, and of whole-lake models that lack sufficient resolution or wind-wave and sediment transport simulation. The model confirms findings of previous studies and demonstrates how the circulation, thermal regime, wave action, and sediment transport in the estuary depend on meteorological forcing, tributary flows, and lake intrusions. The stage is set to apply this approach to study biogeochemical processes in lakes and estuaries.