Date of Award

May 2020

Degree Type


Degree Name

Doctor of Philosophy



First Advisor

Hector R Bravo

Committee Members

Jeffery Val Klump, Qian Liao, Eric J Anderson, Changshan Wu, Yin Wang


ecosystem restoration, fate and transport models, FVCOM, Green Bay, hydrodynamic modeling, sediment


Sediment dynamics are strongly linked with biogeochemical and physical changes in estuarine systems. Understanding the links between sediment processes and ecosystem responses is necessary for the restoration of degraded systems. Located in Northern US, and one of the largest freshwater estuaries on earth, Green Bay is a distinct example of these degraded systems. Rapid development and anthropogenic activities increased nutrient loading rates into the bay and led to a major disruption of the pre-existing biogeochemical regimes in the ecosystem. Contaminated and nutrient-rich sediments were discharged to the bay by the Fox River for almost half a century. Green Bay’s seasonal-, morphological-, and physically-restricted mixing is unable to export a significant portion of the supplied materials to Lake Michigan, i.e., Green Bay behaves as an efficient retention basin for the lake. Therefore, several environmental and human-health related issues such as hypoxia, eutrophication, degraded water quality, and harmful algal blooms developed in Green Bay, turning the southern bay into a USEPA area of concern since the 1980s. Restoration programs were consequently developed, including the development of monitoring programs and intensive collection of field data, research projects, and remedial action plans. Several of these efforts have highlighted the importance and usefulness of nutrient and toxic management practices as they relate to sediment processes. Robust models that simulate sediment transport and system biogeochemistry can be instrumental in the improvement of our understanding of these linked processes and the pace of restoration efforts. Previous research has studied the circulation, thermal regime and water quality in Green Bay, using models based on the Princeton Ocean Model and the Environmental Fluid Dynamics Code. Obstacles in those studies included shortage of field measurements and model limitations. Modeling challenges included the creation of boundary conditions for nested models, use of structured grids, modeling stratified flows in shallow areas, and limited model documentation. In this study, a state-of-the-art modeling platform, Finite-Volume Community Ocean Model (FVCOM), is adopted to investigate circulation patterns, surface waves, and 3D sediment dynamics in Lake Michigan, and Green Bay in particular. The FVCOM model runs in parallel mode, with notable advantages in computational efficiency. A well-calibrated and verified physically based hydrodynamic and sediment transport model has several practical applications for the management of the system, including but not limited to, explaining patterns and rates of sediment dynamics, predicting the short- and long-term effects of the restoration plans, providing simulations and early warning forecasts of the potential fate and transport of pollutants, and modeling the hypoxic dead zones within the bay.

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