The Chesapeake Bay is North America's largest and most biologically diverse estuary, as well as an important commercial and recreational resource. However, excessive amounts of nitrogen, phosphorus, and sediment from human activities and land development have disrupted the ecosystem, causing harmful algae blooms, degraded habitats, and diminished populations of many species of fish and shellfish. In 1983, the Chesapeake Bay Program (CBP) was established, based on a cooperative partnership among the U.S. Environmental Protection Agency (EPA), the state of Maryland, and the commonwealths of Pennsylvania and Virginia, and the District of Columbia, to address the extent, complexity, and sources of pollutants entering the Bay. In 2008, the CBP launched a series of initiatives to increase the transparency of the program and heighten its accountability and in 2009 an executive order injected new energy into the restoration. In addition, as part of the effect to improve the pace of progress and increase accountability in the Bay restoration, a two-year milestone strategy was introduced aimed at reducing overall pollution in the Bay by focusing on incremental, short-term commitments from each of the Bay jurisdictions. The National Research Council (NRC) established the Committee on the Evaluation of Chesapeake Bay Program Implementation for Nutrient Reduction in Improve Water Quality in 2009 in response to a request from the EPA. The committee was charged to assess the framework used by the states and the CBP for tracking nutrient and sediment control practices that are implemented in the Chesapeake Bay watershed and to evaluate the two-year milestone strategy. The committee was also to assess existing adaptive management strategies and to recommend improvements that could help CBP to meet its nutrient and sediment reduction goals. The committee did not attempt to identify every possible strategy that could be implemented but instead focused on approaches that are not being implemented to their full potential or that may have substantial, unrealized potential in the Bay watershed. Because many of these strategies have policy or societal implications that could not be fully evaluated by the committee, the strategies are not prioritized but are offered to encourage further consideration and exploration among the CBP partners and stakeholders.

The Corps of Engineers, in partnership with the U.S. Environmental Protection Agency Chesapeake Bay Program Office, recently completed a three- dimensional model study of eutrophication in Chesapeake Bay and tributaries. The model package applied included an intratidal hydrodynamic model, an intertidal water-quality model, and a benthic sediment diagenesis model. This report comprises a workplan to improve model representation of Chesapeake Bay tributaries and to incorporate living resources directly into the model framework. Four tributaries have been selected for emphasis under this tributary refinements program. They are the James, York, and Rappahannock rivers, and Baltimore Harbor. The James, York, and Rappahannock were specified because tributary-specific models are required to address water-quality and living- resource benefits to be derived from nutrient reductions. Baltimore Harbor was specified because it presents unique management problems, coupled with long-term toxic impacts, which cannot be addressed in the current model framework. The time scale for the project is 4 years from initiation to completion. Anticipated commencement is April 1, 1994.

Chesapeake Bay is one of the most productive ecosystems on the US east coast which supports various living resources and habitat, and therefore has significant impacts on human beings and ecosystem health. Developing the capability of accurately simulating the water quality condition in the Chesapeake Bay, such as seasonal hypoxia, phytoplankton production, and nutrient dynamics, helps to better understand the interactions of hydrodynamical and biochemical processes, and more importantly, to predict conditions under changing climate and human intervention. Currently, most Chesapeake Bay models use structured grids that lack the flexibility for local refinements to fit complex geometry over both large and small scales, which hampers the allocation of local TMDLs for shallow water and small tributaries. In addition, few of them extend their simulations beyond the water column state variables, such as dissolved oxygen and nutrients, to include other living resources such as vegetation. These limitations motivate the model developments in this dissertation of: (1) a new comprehensive water quality model using high-resolution unstructured grids, which possesses the cross-scale capability to study interactions among water bodies and processes of different scales; and (2) a tightly coupled tidal marsh model, which is linked to the water quality model for water column to study the interactions between the marshes and surrounding aquatic system. The new modeling tool can be effectively utilized as a powerful tool for adaptive management in the Chesapeake Bay and can also be exported to other estuaries in the world.In this dissertation, Chapter 2 focuses on the development of a high-resolution water quality model in the water column and sediment flux part of the water quality model. This part of this study also demonstrates the importance of the correct representation of geometry, and the detrimental effects of artificial bathymetry smoothing on model simulations. Chapter 3 of this dissertation studies the impacts of sea-level rise (SLR) on seasonal hypoxia and phytoplankton production in the Chesapeake Bay with the newly developed water quality model. SLR is predicted to increase the hypoxic volume in the Chesapeake Bay by altering the physical processes and enhancing the estuarine respirations. Phytoplankton production in the shallow shoals is also predicted to increase under SLR, as a result of increased light utilization. Chapter 4 of this dissertation focuses on developing a new marsh model in the hydrodynamic-water quality model framework. This new model extends the model coverage to the tidal wetlands which are periodically inundated. The tidal marshes are suggested to affect the estuarine oxygen, carbon, and nutrient dynamics through tidal exchange, e.g., contributing the diel DO cycle. Chapter 5 studies the impacts of SLR on the biochemical processes in the York River Estuary, a tributary of the Bay that has extensive tidal marshes, with the fully-coupled hydrodynamic-water quality-marsh model. The SLR is predicted to enhance the exchanges between the marshes and the adjacent channel, which in turn further impacts the estuarine biochemical processes.

Since the 1970s, conservation in the Chesapeake Bay watershed has been a major focus of local environmental groups as well as the federal government. The health of the estuary has been evaluated by the Chesapeake Bay Foundation, among other organizations, for years and still needs a lot of help. Readers will delve into the important task of saving the Chesapeake Bay through statistics about the bay’s health and engaging sidebars full of even more information. Vivid photographs reveal the dangers of pollution and urban sprawl as the main content introduces readers to endangered animals and plants, troubled habitats, and the problem of population growth. The struggles of the beautiful Chesapeake Bay will engage seafood lovers and conservationists alike to take action, even if only in their daily lives.