A numerical model was developed for the Mobile Bay system to investigate the impacts associated with certain system alterations. The Adaptive Hydraulics (AdH) Code was used to validate the numerical model for hydrodynamics and transport. Due to the physics based nature of the AdH numerical model, the validated model could be altered to represent the plan conditions (removal of the Mobile Bay Causeway). Comparisons of the base and plan model results indicate the impacts of removing the causeway are not widespread and are primarily limited to Chocolatta Bay and the areas adjacent to the causeway. The model results suggest an increased exchange of water between Chocolatta Bay (north of the causeway) and Mobile Bay for the removed causeway configuration. Chocolatta Bay also experiences an increased inflow from the river systems which result in increased suspended sediment concentrations and sediment deposition.

Estuaries are vital environmental and economic resources, providing habitat for thousands of species, absorbing runoff, and supporting recreation and commerce. Yet, despite their importance, estuaries are threatened by human activities. Empirical Orthogonal Function (EOF) analysis and Cross Spectral techniques were used in the analysis and prediction of estuarine morphology. The estuaries selected for study were Suisun Bay, CA and Mobile Bay, AL. It was found that EOF is an effective and efficient technique to analyze morphology, a coupling with cross spectral methods such as Fourier Transformation (FFT) resulted in determination of forcing functions responsible for imparting variance to the bathymetry. In both the estuaries it was found that the first two eigenvalues represented almost 80% of the morphological/bathymetric dataset. The second eigenfunction was found to be closely dependent on the freshwater inflows to the estuaries. EOF analysis on Suisun Bay revealed that the bay is depositional particularly in the shallow bays of Honker and Grizzly, whereas the main channels as well as Carquinez Straits maintained their depths throughout the period studied. Utilizing a Cross spectral technique, Amplitude Response Function (ARF), temporal eigenfunctions for the bay were determined for year 2100. The temporal eigenfunctions were predicted for cases where river inflows to the bay were varied by 1 standard deviation unit. These predicted eigenfunction values combined with the eigenvalues resulted in the recovery of predicted depths for year 2100. It was found that Suisun Bay remains depositional through the year 2100 and maintains depths in the main channels as well as Carquinez Straits. This depositional behavior results in the decrease of bay volume to almost 40% of the volume in 1989. EOF analysis on Mobile Bay revealed that the bay is predominantly depositional except in the navigation channel and the shoreline of the Bay. The navigation channel maintaining it depth is attributed to the regular dredging carried to facilitate shipping. The second temporal eigenfunction showed a close correlation with river inflows as in the case of Suisun Bay. However, a cross correlation performed on the second temporal eigenfunction and inflows revealed that the response of the eigenfunction is perturbed by almost 9 years, as opposed to 6 to 9 years for Suisun Bay. An ARF on the temporal eigenfunctions combined with a reverse EOF resulted in the formation of bathymetric datasets for the year 2100 for inflows variation of 1 standard deviation. It was revealed that increasing the flows results in an increase of bay volume by approximately 30% and a decrease in flows results in a loss of volume by approximately 20%.

Nearly half of the population of the United States lives in coastal regions, and millions of visitors from across the nation and world enjoy the coasts every year. Coastal and marine areas provide for recreation, economic activities essential for the financial health of the nation, and vital ecological services. As they provide so many benefits to the U.S., it is vital to protect and preserve the coastal and ocean areas from the increasing, competing demands they are facing. In order to protect and preserve these complex systems, a comprehensive approach incorporating science, engineering, humanities, and social sciences should be taken; this approach is commonly referred to as Ecosystem-Based Management. This dissertation focuses on developing a framework that can be used to identify appropriate sub-regions in Northern Gulf of Mexico coastal and marine environments for the purposes of Ecosystem-Based Management. Through this work, the roles of three management protocols used for managing coastal areas – coastal and marine spatial planning, ecosystem-based management, and integrated ecosystem assessment – were examined individually as well as their integrations with each other. Biological, ecological, physical, human, and economic indicators for partitioning an ecosystem were developed and weighted for each management protocol using the analytic hierarchy process and expert elicitation. Using the weighted indicators, a framework for identifying sub-regions and estuarine classification system was developed. The framework and classification system were applied to five estuaries within the Northern Gulf of Mexico: Barataria, Galveston, Mobile, and Perdido Bays and Mississippi Sound. Initial results from this work show that: 1. Sub-regions can be identified as associated to each other based upon indicator data values and not upon physical location. 2. Even though the weights calculated for the management protocols vary significantly, for systems that were not highly homogeneous in indicator data values, the different weights did not produce the vastly different cluster maps expected. 3. The scale work indicates that to identify appropriate sub-regions using the developed framework, a larger grid size produces more consistent results for larger systems whereas a smaller grid size produces more consistent results for smaller systems. Recommendations for further research are also presented.