The Waiapu River drains a small mountainous basin, characterized by steep terrain, heavy rainfall, and unconsolidated soft Tertiary mudstone and siltstone. These factors, combined with heavy deforestation over the past 100 years have created one of the world's highest sediment yields. Water discharge of the Waiapu River is very episodic over both inter- and intra-annual timescales, and almost all of the discharge is associated with floods brought by cyclonic storms. The Waiapu River drains an active margin that has a narrow shelf and steep slope. Marine conditions on the Waiapu continental shelf are very energetic, with strong waves as well as shelf currents. This special river-ocean system makes the Waiapu area an ideal site to study gravity-driven flows. Instrumented tripods deployed at water depths of 40 m and 60 m on the Waiapu shelf directly offshore of the river mouth recorded data on waves, currents, and sediment fluxes from May through August, 2004. The tripod data showed direct field evidence of current-supported gravity flows on the Waiapu shelf. Data analysis indicated that the Waiapu River floods were characterized by two distinct phases: a flood phase and a resuspension phase. The flood phase was characterized by large sediment input, coupled with moderate to strong waves but weak currents. Strong near-bed sediment signals, however, were not recorded by the tripods until the post-flood resuspension phases, during which seaward near-bed currents started to intensify. A one-dimensional boundary layer model provided the inference that those strong seaward near-bottom turbid flows during the resuspension phase were dynamically similar to wave-supported gravity flows observed on Eel and Po Shelves, except that both waves and currents were important for sediment resuspension. In contrast to thin and dense wave-supported gravity flows, current-supported gravity flows on the Waiapu shelf were significantly thicker and more dilute. Another two-dimensional model for wave- and current-supported sediment gravity flows was used to estimate sediment deposition on the Waiapu shelf from September 2003 to August 2004. The time period for the model calculations was divided into two segments: a low-energy (September to May) and high-energy portion (May to August). Model results showed that sediment delivered by the Waiapu River were trapped between the 20- and 80-m isobaths during the low-energy period, but then redistributed obliquely across the shelf between the 60- and 120-m isobaths during the high-energy period. Depositional locations estimated for the low- and high-energy portions, respectively, matched well with short- and long-term observed accumulation patterns based on 7 Be and 210Pb activity as reported by Kniskern (2007; Kniskern et al. 2008). Sensitivity analysis indicated that the gravity-driven flows on the Waiapu shelf were mainly wave-supported landward of the 40-m isobath, but became increasingly current-supported as wave orbital decayed in deeper water. This dissertation provided the first documentation of current-supported gravity flows, and hence contributed greatly to the study of sediment transport on continental shelves.

The inner continental shelf is a complex environmental system marked by sharp variations in bed roughness. Such heterogeneous systems account for 80% of the non-rocky inner shelves worldwide. Interactions among forces (waves, tides, turbulence, and bioturbation) and roughness elements (bed forms, rocks, and anthropogenic objects) exert major controls on sedimentary processes. This study attempts to advance the knowledge and understanding of the morphodynamics of the inner shelf. This study investigates scour and morphodynamic processes at Tairua, New Zealand; Cedar Island, Virginia; Indian Rocks Beach, Florida; and Beaufort Inlet, North Carolina. Using data from the field, the study develops new conceptual models to characterize and quantify the hydrodynamics and morphology of the seabed. The overall dataset includes side-scan sonograms, sub-bottom profiles, grain-size analyses, suspended sediment concentrations and hydrodynamic measurements. Analysis of the morphological data yielded a six-type classification of bottom features previously termed Rippled Scour Depressions (RSDs). The observed stratigraphic signature of RSDs does not agree with the previous interpretation of their formation. Striking spatial and temporal variations in seabed roughness produce significant enhancements of hydraulic roughness and turbulence over different substrates resulting in a self-organized, feed-back system of erosion (scour), deposition, and modified bed forms. The study demonstrates that widely used ripple models inadequately predict bed form geometry and behavior, especially during storms. Improved understanding of scour processes developed in this study leads to a new model of scour and burial of sea-bed objects such as naval mines and archaeological artifacts. When using the model to predict scour and burial, the greatest errors result from the uncertainties in the available forecasts of wave conditions. The model includes vertical variations in sediment characteristics as field observations indicate abrupt changes in substrate substantially alter the scour process. The overall study makes substantial contributions to the general understanding of RSD behavior by tying together detailed field studies with applicable insights from the area of complexity research. A new conceptual model of complex phase-transition is developed, involving critical process factors (hydrodynamics, underlying geology, and depth), which contribute to the observed spatial complexity and temporal variability of different RSD types.

Shallow coastal bays and lagoons (mean depths <2-3 meters) are important buffer zones and links between terrestrial and deep marine ecosystems. They are inherently vulnerable to eutrophication, and are normally dominated by benthic primary producers such as seagrass, benthic micro- and macroalgae. There is an urgent need for quantitative models that are specifically designed for studying eutrophication dynamics in shallow coastal ecosystems. In this study, a hydrodynamic and water quality modeling system consisting of the hydrodynamic model UnTRIM and the water quality model CE-QUAL-ICM was applied to a representative shallow coastal bay ecosystem, the Maryland and Virginia Coastal Bays (MVCBs). A high-resolution unstructured model grid was generated to resolve the complex geometry. to address the important role played by benthic macroalgae, a benthic macroalgal module, which assimilated macroalgal kinetics from literature and recent laboratory studies, was incorporated into the water quality model framework. The module includes two representative macroalgal species, Ulva lactuca and Gracilaria vermiculophylla , common in the MVCBs, and employs the internal nutrient-limited growth kinetics proposed by Droop. The numerical modeling system has been calibrated against a comprehensive field monitoring data collected by the Maryland Department of Natural Resources in the MVCBs. The data include water level, current velocity, salinity, and major water quality variables, such as chlorophyll a, dissolved oxygen, and nutrients. The calibrated hydrodynamic model was used to calculate the physical transport time scales. The model estimated flushing time for the entire system is on the order of 2-3 months, which are much longer than typical time scales required by most biological processes. In addition, the local residence time is found to be extremely variable throughout the system. Depending on locations, the local residence time can vary from 0 to more than 200 days. The calculated transport time scales were further compared with spatial water quality distributions in the system. The comparisons demonstrate that physical circulations could substantially modulate biological processes in the system. By using the Droop equation, the benthic macroalgae's unique property, the so-called luxury uptake, was satisfactorily captured. Furthermore, the characteristic boom-and-bust life cycle of benthic macroalgae was qualitatively simulated using a box model. The expanded water quality model that includes the benthic macroalgal module reproduced both temporal and spatial distributions of observed benthic macroalgae and major water quality variables reasonably well in the MVCBs. The model results indicate that benthic macroalgae are highly important in regulating ecosystem metabolism in areas where they are abundant. Moreover, spring phytoplankton bloom was substantially suppressed when benthic macroalgae were present. The incorporation of a benthic macroalgal module also improved the model's predictive capability in simulating dissolved oxygen in shallow ecosystems affected by benthic macroalgae. In terms of nutrient budget, the model estimated that benthic macroalgae retain approximately 10% of annual nonpoint source nitrogen inputs from the watershed based on the simulation of year 2004. This is lower than that contributed by benthic microalgae reported in other shallow coastal bays such as the Lynnhaven Bay. It is suspected that the restricted distribution of benthic macroalgae in the MVCBs limited their role from the whole bay perspective. With the incorporation of a benthic macroalgae module, the overall water quality model prediction capability is improved.

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