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Estuaries, in particular freshwater estuaries, provide valuable economic, social, and ecological services, but their ecosystems are often heavily stressed. Located in the Laurentian Great Lakes basin, Green Bay is a large freshwater estuary and a prominent example of a degraded ecosystem due to intensive human interventions and rapid development. Excessive amounts of contaminants and nutrients were discharged to the bay by inflowing tributaries for almost half a century, while in contrast Green Bay's seasonal‐, morphological‐, and physically‐restricted mixing is unable to export a significant portion of those materials out of the bay, that is, Green Bay behaves as an efficient retention basin for the Lake Michigan. Consequently, several environmental and public health‐related issues have risen in Green Bay and turned the lower bay into an area of environmental concern since the 1980s. To address these challenges, restoration programs were developed, including the development of monitoring programs, scientific research, and remedial action plans. There is a consensus that accelerated loading rates of contaminated and nutrient‐rich sediments are a major driver of the environmental crisis in the bay, yet the fate and transport patterns of Green Bay sediments are not clearly understood. While field observations in Green Bay are season‐limited and costly, advanced computing techniques provided opportunities to refine our understanding of sediment dynamics in this estuarine system. This review of existing knowledge on Green Bay sediment processes can help to better understand the interplay between sediments, and physical/biogeochemical activities in estuarine systems and contributes conceptually to the restoration of degraded aquatic ecosystems. This article is categorized under:Science of Water > Hydrological ProcessesScience of Water > Water QualityWater and Life > Stresses and Pressures on Ecosystems [ABSTRACT FROM AUTHOR]

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 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. 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 physically based, 3D sediment transport model. This model development effort helps to predict circulation of contaminants and nutrients that are attached to the sediments, their settlement and burial, and the detachment from the bottom during storm events. The knowledge gained in this study will enhance our understanding of water quality conditions and nutrient recycling in freshwater estuaries, and will improve future restoration efforts and management plans. Key Points: Understanding the simultaneous effects of tributary flows and lake intrusions is crucial to comprehend the dynamics of freshwater estuariesCirculation, thermal regime, wave action, and sediment transport depend on meteorological forcing, tributary flows, and lake intrusionsThe stage is set to apply this approach to study biogeochemical processes in lakes and estuaries [ABSTRACT FROM AUTHOR]