Green Bay is a large freshwater estuarine system that drains one-third of the Lake Michigan basin. The International Joint Commission designated southern Green Bay as an area of concern (AOC) in the 1980s due to ecosystem degradation including eutrophication, harmful algal blooms (HABs), hypoxia, lost or altered habitat, and reduced water quality. Restoration studies have found excessive nutrient loading and release of toxic materials, primarily produced in farmlands and industrial units, to be major drivers of Green Bay environmental/ecological issues. The Green Bay geomorphology and restricted mixing is a barrier to the efficient transport of sediments (as well as the accompanying nutrients and contaminants), acting as a retention basin for Lake Michigan. The purposes of this research were to: a) use the existing database of hydrodynamic, wave, and sediment field data to develop a three-dimensional (3D) predictive model of sediment transport in Lake Michigan, with an emphasis in Green Bay; b) use the sediment transport model to contribute to understanding ecological and environmental problems in the bay, and to recommend long-term solutions to those problems; and c) analyze summer patterns of circulation, wave action, current and wave-induced bottom shear stress, thermal structure, and sediment transport in Lake Michigan, with special attention to Green Bay.