Green Bay is the largest freshwater estuarine system on earth, drains one-third of Lake Michigan basin and delivers one-third of the lake's total phosphorus load . The International Joint Commission designated southern Green Bay as an area of concern (AOC) in the 1980s due to several instances of ecosystem degradation including (but not limited to) eutrophication, harmful algal blooms (HABs), hypoxia, lost or altered habitat, and reduced water quality.Green Bay has stimulated a significant amount of widely relevant research on the fate and behavior of toxics, biogeochemistry, habitat, biodiversity, and ecological processes. In particular, previous research relevant to hydrodynamics and sediment transport in Green Bay includes studies carried out on Green Bay, studies done on Lake Michigan and the Laurentian Great Lakes watershed, and studies done on marine estuaries. We will first concisely list those previous studies, then briefly explain how the present study differs Abstract 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 due to ecosystem degradation that includes eutrophication, harmful algal blooms, 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 wholelake 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.Plain Language Summary Green Bay is a unique ecosystem located in the largest freshwater system on earth, the Laurentian Great Lakes. Almost one-third of tributary waters to Lake Michigan flow through Green Bay. Human activities in the watershed produce excessive amounts of contaminated and/ or nutrient-rich sediments that are discharged to the bay. Sediments are not efficiently transported to Lake Michigan due to physical conditions in Green Bay, leading to ecosystem degradation, environmental and public health risks. We studied the movement, transport, and fate of sediments in Lake Michigan, with a special attention to Green Bay, by developing a physi...