Submerged aquatic vegetation (SAV) plays a significant role in many aquatic systems, and impacts both physical and ecological quantities. It can baffle currents, attenuate waves, recycle nitrogen and phosphorus from the sediment bed, perform ecosystem function as a primary producer, and provide critical habitat for many aquatic species. Conversely, the invasive SAV, Egeria densa (Brazilian waterweed), in the San Francisco Bay & Delta has been a nuisance since its introduction into the system in the 1960s. It has displaced most of the native submersed aquatic plant species in the Delta and restructured the ecosystem, thus threatening the survival of several endangered native fishes such as Delta Smelt. Its impacts on the ecological system remain largely unknown and the need for assessment is growing. This multi-interdisciplinary study, incorporating biogeochemistry, hydrodynamics, and numerical computing and field survey data, accomplishes two main goals. The first goal is to develop a new SAV model imbedded into the unstructured-grid SCHISM-ICM framework. in addition to the advantages of directly simulating the SAV impact on hydrodynamics using high-resolution unstructured grids, this new SAV model can also simulate the competition between SAV and phytoplankton for light and nutrient supplies. The second goal is to apply the new model to Cache Slough Complex, Sacramento-San Joaquin Delta, to estimate the impact on the water quality from intervening SAV removal. Removal of SAV is already being studied in Little Hastings Tract and this study can serve to develop hypotheses for monitoring and ultimately guidance for managing SAV removal in the Bay-Delta region. We benchmark the new SAV model with the tests on the SAV biomass, growth and impacts on light supply and nutrient budget in the water column and sediment bed, respectively. Starting from a uniform biomass distribution, we simulate the evolution of biomass over seasonal scales and validate the calculated distribution with the observed distribution. The model is able to successfully simulate the SAV die-off process in areas where it is known to be unable to colonize. By applying the fully coupled SCHISM-ICM-SAV model in the Cache Slough Complex area, the changes of the water quality state variables due to SAV are estimated over spatial and seasonal scales. Generally, SAV increases the accumulation of phytoplankton by locally reducing flushing and thus increasing the residence time, but in the meantime, reduces its local growth rate due to light shading and nutrient competition. A combination of direct impact from SAV and indirect impact through changed phytoplankton results in changes in other water quality variables: dissolved oxygen and nutrients. SAV tends to increase oxygen and organic nutrients while decreasing inorganic nutrients. For this system, the feedback loop from SAV to the hydrodynamics plays the most important role in the water quality variables among all feedback loops.

Storm surge and inundation induced by hurricanes and nor'easters pose a profound threat to coastal communities and ecosystems. These storm events with powerful winds, heavy precipitation, and strong wind waves can lead to major flooding for cities along U.S. Coasts. Recent examples of Hurricane Irene (2011) in North Carolina and Virginia and Hurricane Sandy (2012) in New York City not only demonstrated the immense destructive power by the storms, but also revealed the obvious, crucial need for improved forecasting of storm tide and inundation. in part I, a large-scale unstructured-grid 3-D barotropic storm tide model SCHISM (Semi-implicit Cross-scale Hydroscience Integrated System Model) is developed with open ocean boundary aligning along the 60-degree West longitude to catch most Atlantic hurricanes that may make landfall along U.S. East and Gulf Coasts. The model, driven by high-resolution NAM (North America Mesoscale) and ECMWF (European Centre for Medium-Range Weather Forecasts) atmospheric fields, was coupled with Wind Wave Model (WWMIII) to account for wave effects, and used to simulate storm surge in 3-D barotropic mode rather than the traditional 2-D vertical average mode. For Hurricane Sandy, the fully coupled wave-current interaction 3-D model using ECMWF atmospheric forcing performs the best. The storm tide results match well with observation at all nine NOAA tidal gauges along the East Coast. The maximum total water level in New York City, is accurately simulated with absolute error of amplitude less than 8 cm, and timing difference within 10 minutes. The scenarios of "2-D" versus "3-D" and "with" versus "without" wind wave model were compared and discussed in details. Overall, the wave contribution amounts to 5-10% of surge elevation during the event. Also, the large-scale model with similar setup is applied to hindcasting storm tide during Hurricane Irene and the results are excellent when compared with observed water level along Southeast Coast and inside Chesapeake Bay. in part II, a high-resolution sub-grid inundation model ELCIRC-sub (Eulerian-Lagrangian CIRCulation) was developed from the original finite-volume-based ELCIRC model. It utilized the sub-grid method for imbedding high-resolution topography/bathymetry data into the traditional model grid and delivering the inundation simulation on the street level scale. The ELCIRC-sub contains an efficient non-linear solver to increase the accuracy and was executed in the MPI (Message Passing Interface) parallel computing platform to vastly enlarge the water shed coverage, and to expand the numbers of sub-grids allowed. The ELCIRC-sub is first validated with a wetting/drying analytic solution and then applied in New York City for Hurricane Sandy (2012). Temporal comparisons with NOAA and USGS water level gauges showed excellent performance with an average error on the order of 10 cm. It accurately captured the highest surge (during Hurricane Sandy) at Kings Point on both maximum surge height and the explosive surge profile. Spatial comparisons of the modeled peak water level at 80 locations around New York City showed an average error less than 13 cm. The modeled maximum modeled inundation extent also matched well with 80% of the FEMA flooding map. in terms of robustness and efficiency for practical application, ELCIRC-sub surpasses the prototype model UnTRIM2.

The spatial and temporal variability of phytoplankton biomass in estuaries is determined by both local processes and transport processes. Local processes include biological processes (e.g., photosynthesis, respiration/excretion, and grazing) and settling, whereas transport processes include advective and diffusive transports. Transport processes have been demonstrated to regulate phytoplankton dynamics significantly by distributing both phytoplankton and other dissolved and particulate substances (e.g., nutrients, salts, sediments, and chromophoric dissolved organic matter). Yet, these transport properties lack a framework that unifies the pieced description of their various effects, and quantification of their importance under various environmental conditions. This dissertation highlights the role of horizontal transport processes on phytoplankton dynamics in estuaries, including the initiation of harmful algal blooms (HABs). in Chapter 2, the flushing effect of transport processes and its interaction with local processes are exclusively examined, and its relative importance on the variability of phytoplankton biomass is quantified and compared to that of the local processes over timescales from hours to years, using an introduced concept of transport rate that can be numerically computed. in Chapter 3, a simple yet inclusive mathematical model is developed to examine the temporal and spatial variabilities in phytoplankton biomass in response to the various effects of physical transport, under nutrient and light limiting conditions. For estuaries whose dominant nutrient loading is from river input, three basic patterns are revealed for the relationships between phytoplankton biomass and flushing time under various environmental conditions. in Chapters 4 and 5, the flushing effect of transport processes on the initiation of harmful algal blooms (HABs) in estuaries is investigated, which is then applied to examine the location and timing of the initiation of an annual Cochlodinium (recently renamed Margalefidinium) polykrikoides bloom in the lower James River. Theoretical analysis shows that the flushing is the key factor that affects HAB initiation in multiple interconnected systems, and a relatively long period of time (weeks) is required for a successful bloom. A HAB tends to be observed first in locations with relatively long residence time, such as tributaries or areas with large eddies. Multiple unconnected originating locations can co-exist within an estuary that highly depends on hydrodynamics and salinity. A numerical module for C. polykrikoides bloom is developed and built into a 3D numerical model - EFDC, which considers the competitive advantages of C. polykrikoides such as mixotrophic growth, swimming, grazing suppression, and resting cyst germination. Numerical model results show that the flushing effect determines the origins of C. polykrikoides blooms in the lower James River, and the sub-tributary of Lafayette River, which is characterized by relatively long residence time, is favorable for the first bloom to occur, regardless of the cyst distribution. A further investigation of various environmental conditions for the C. polykrikoides bloom reveals that temperature and physical transport control the interannual variability in the timing of its initiation, and individual perturbations by southerly wind, heavy rainfall, and spring tide can cause strong flushing capable of interrupting, or even terminating, initiation of a HAB event in the lower James River.

Understanding the nature of suspended particles is crucial to explaining water clarity issues in many estuaries, including the Chesapeake Bay and its tidal tributaries. Typical near surface estuarine particles are not individual sediment grains, but rather are clusters of inorganic and organic components known as flocs. Because of their fragile nature, flocs are challenging to observe in-situ, so their influence on the optical properties of the system are not well-known. This dissertation used a combination of state-of-the-art optical instrumentation, including laser scattering and transmissometry, a high-definition particle imaging camera system (PICS), and irradiance meters, along with supporting laboratory analysis techniques to investigate the surface waters of the York River estuary. This work characterized estuarine floc properties while simultaneously identifying relationships between estuarine light attenuation, absorption, and scattering due to flocs as well as other water column constituents. The relative organic fraction of suspended solids was found to be an important control on the fractal nature of estuarine flocs, including primary particle size and density, as well as bulk floc properties. A new approach is presented here that simultaneously solves for multiple floc fractal characteristics (e.g., fractal dimension, primary particle size, and primary particle density) and identifies whether simple fractal models are appropriate to describe individual suspensions. Results indicate that suspensions in the York River estuary with lower organic fraction and higher total suspended solids (TSS) are dominated by larger flocs composed of smaller, denser primary particles. In contrast, suspensions with higher organic fraction and lower TSS are composed of smaller flocs with larger, less dense primary particles. Paradoxically, the organic-rich flocs containing larger, lower density primary particles are, in terms of solids content, actually denser overall. This is because the larger, organic-rich primary particles take up more space within the flocs, leaving less room for water. Diffuse light attenuation, scattering, and absorption were related to the nature of the flocs in the York estuary, as well as to other water column constituents. It was found that as TSS increases, larger, lower density flocs containing less organic matter and more water increasingly dominate. This causes scattering to increase more quickly than TSS. In contrast, absorption increased more slowly than TSS. This is because the organics more prevalent at low TSS absorb more light per mass than the inorganic solids that dominate suspensions with higher TSS. Under most conditions, total scattering was dominated by inorganic particles. However, the combined effects of other components (the water itself, colored dissolved organic matter, phytoplankton, plus non-algal organic solids) typically dominated both absorption and attenuation. The importance of phytoplankton and organic solids relative to inorganic solids from land runoff have important ramifications for water clarity management, specifically suggesting revaluation of strategies solely focused on reducing inorganic sediment input. Even with an advanced video-settling column (e.g. PICS), there are issues resolving smaller flocs and sampling very low TSS. A major challenge in processing particle images is correctly identifying and sizing particles of varying composition and size, while correctly separating in-focus particles from out-of-focus particles. A new automated analysis approach was created that efficiently resolves particles, while rejecting out-of-focus objects, and was implemented into the automated processing algorithm for the PICS. Field- and laboratory-based experiments were conducted to evaluate video-based size, settling velocity, and density estimates, and it was found that all three parameters were adequately measured with the PICS.

Fine-grained material such as silts and clays are the predominant sediment type in low energy systems such as micro-tidal embayments and estuaries. Due to its cohesive nature, fine sediment typically moves through marine systems as aggregated particles, or flocs, rather than as individual mineral grains. The particle's components, local hydrodynamics, and concentration influence floc size, density, and fall velocity. These, in turn, impact suspended sediment transport, which complicates predictions of the fate of sediment for water quality, contaminant distribution, and dredging purposes in these systems. This dissertation used a state-of-the-art modeling system and observations to examine the variability in sediment distribution due to cohesive processes along a partially mixed estuary and to determine the role of flocculation on sediment transport for a muddy site within the York River estuary, Virginia. The Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) modeling system was used to simulate the hydrodynamics and suspended sediment transport in a muddy estuarine system. The model accounted for flocculation dynamics with a population balance model, FLOCMOD, changes in the erosion of sediment from the bed due to compaction or bed consolidation, and sediment-induced density gradients. The sensitivity of the sediment distribution was performed using an idealized two-dimensional (vertical and longitudinal) model that produced key estuarine features such as salinity-driven circulation and an estuarine turbidity maximum (ETM). The reference model included the effects of flocculation, bed consolidation, and sediment-induced density gradients. Results from the reference model were compared to test cases, each of which removed one of these processes. This showed that the effects of flocculation on suspended sediment concentrations (SSC) were most significant in the surface waters and in the ETM; whereas bed consolidation decreased SSC along the full length of the estuary. Another test case demonstrated that calculations of SSC and median floc diameter (D50) were sensitive to the number of sediment classes used to represent the floc population. The capabilities of the idealized two-dimensional estuary were extended and used to examine the contribution of flocculation compared to other sediment transport mechanisms such as advection, diffusion, settling, and erosion. The dominant processes that impacted the sediment mass balance in the idealized estuary were flocculation, vertical diffusion, and erosion. Next, the D50 produced by FLOCMOD in the idealized estuary was compared to a theoretical equilibrium floc size (Deq) estimated based on the ratio of SSC to the square root of the shear rate (G). This analysis also produced an estimate for a timescale for flocculation. In general, D50 reached Deq in the bottom boundary of the estuary when the flocculation timescales were on the order of minutes. However, immediately above the sediment bed, Deq was very similar to D50 when erosion was minimal or when finer flocs were eroded from the bed. However, the computed D50 most often differed widely from Deq, indicating that equilibrium theory was not appropriate for much of the idealized estuary. To facilitate the direct application of the flocculation model to the York River estuary, a one-dimensional (vertical) model was designed using observations of hydrodynamics and floc properties from the Claybank site for the vertical water column structure. The sensitivity of SSC and floc distribution to the parameterization of FLOCMOD was assessed using a model representing a spring-neap tidal cycle. The SSC was more sensitive to parameterization in the bottom boundary layer, D50 was less sensitive than SSC, and the grain size distribution width (spread) was more sensitive to the fractal dimension. Model results were then compared to observations to choose parameters to represent the floc population in the York River estuary. Parameterization was challenging, but the preferred representation for the York floc population had a low relative error for SSC and acceptable error for the distribution mode and spread. For the spring-neap tidal cycle in general, vertical diffusion, settling, and erosion accounted for more sediment mass transport than flocculation, but flocculation played an important role in the vertical distribution of sediment via changes in floc size.

The Southern Ocean plays a major role in global climate system. An understanding of Southern Ocean dynamics allows for a better understanding of the carbon cycle and possible future climate conditions. Earth System Models are used to study Southern Ocean dynamics and are currently producing reliable global annual carbon uptake but have limiting seasonal abilities. These models produce dependable results on a global scale, with more conflicting results on a basin scale. Here we study the impact of mesoscale variability on the Mixed Layer Depth in the Sub-Tropical and Sub-Antarctic Zone of the South Atlantic. The region is hugely impacted by the mesoscale variability as a result of the South African boundary currents. We use two regional simulations both at 1/4o resolution, with one model containing online nested child domain over the South African boundary currents (1/12o resolution). The inter-annual simulations both use the same forcing which allow for a comparison study between the two models. Both the nested and standalone model are able to capture the large scale oceanographic features in the domain. The biggest difference is seen in the Agulhas Current region, where the nested model simulates better mesoscale features, resulting in a fairly accurate position of the Agulhas retroflection and return current. The standalone model contains a high temperature and salinity bias which influences the vertical structure of the water column. Both models are able to simulate the seasonality of the MLD in the Sub-Tropical and Sub-Antarctic Zone in the Atlantic sector. The models overestimate MLD in regions closer to the boundary currents. In the nested model the presence of increased mesoscale features promotes stratification of the water column. The differences seen in the MLD of the two models are linked to the temperature and salinity bias in the standalone model as well as the increased mesoscale variability in the nested model.

Iron (and silicate) (co-)limitation of phytoplankton is considered a primary cause of the Southern Ocean's inefficient biological pump. However, the role of phytoplankton community structure and response to nutrient cycling remains poorly understood. In a mass balance sense, phytoplankton consumption of new nitrogen (N; e.g., allochthonous nitrate) is proportional to net carbon (C) export, while growth fueled by recycled N (e.g., ammonium) yields no net C flux. The N isotope ratio (δ15N) of surface biomass has long been used as an integrative tracer of new versus regenerated uptake. This approach is rendered more accurate by coupling either fluorescence-activated cell sorting (FACS; of nano- and picophytoplankton; 0.4-20 μm) or microscopy (for microphytoplankton; >20 um) with groupspecific δ15N measurements. Samples were collected for the analysis of nutrients and nitrate-, FACS-, and microscopy-δ15N on a mid-summer transect of the Subantarctic Indian basin during the 2016/17 Antarctic Circumnavigation Expedition (ACE) cruise. The data show that all phytoplankton populations preferentially utilize nitrate (≥55%) across the Indian Sector of the Subantarctic, potentially driving higher C export potential than previously estimated. Indeed, near the Subantarctic islands, 72% of microand >80% of nano- and picophytoplankton growth is supported by nitrate. This is likely due to the partial alleviation of phytoplankton iron and silicate stress, largely as a result of bathymetric upwelling, which constitutes a manifestation of the island mass effect. C export potential is lower in the open ocean region away from the islands where iron stress has been shown to be higher; here, nitrate supports >55% of micro- and picophytoplankton and 7 to 79% of nanophytoplankton growth. In terms of relative abundance (RA), the open Subantarctic is dominated by picoeukaryotes (64%), although there exists a large disconnect between relative abundance and potential contribution to C export. The three largest surface-ocean phytoplankton populations included in this study – microphytoplankton, cryptophytes, and nanoeukaryotes – each contribute ~30% to the total C export potential across the Subantarctic Indian sector while picophytoplankton contribute ~5%. Thus, as has been concluded previously, the larger phytoplankton size classes are disproportionately important drivers of the Subantarctic biological pump. Other interesting ecological findings include diatom-dominated microphytoplankton populations apparently fueled by a significant fraction of regenerated N, even in areas of iron supply, and Synechococcus relying near-exclusively on new N, in contrast to subtropical observations. Additionally, the abundance of Synechococcus appears to be controlled by the availability of iron across the Subantarctic, with silicate and temperature playing a supporting role.

Human impacts on the Chesapeake Bay through increased nutrient run-off as a result of land-use change, urbanization, and industrialization, have resulted in a degradation of water quality over the last half-century. These direct impacts, compounded with human-induced climate changes such as warming, rising sea-level, and changes in precipitation, have elevated the conversation surrounding the future of water quality in the Bay. The overall goal of this dissertation project is to use a combination of models and data to better understand and quantify the impact of changes in nutrient loads and climate on water quality in the Chesapeake Bay. This research achieves that goal in three parts. First, a set of eight water quality models is used to establish a model mean and assess model skill. All models were found to exhibit similar skill in resolving dissolved oxygen concentrations as well as a number of dissolved oxygen-influencing variables (temperature, salinity, stratification, chlorophyll and nitrate) and the model mean exhibited the highest individual skill. The location of stratification within the water column was found to be a limiting factor in the models’ ability to adequately simulate habitat compression resulting from low-oxygen conditions. Second, two of the previous models underwent the regulatory Chesapeake Bay pollution diet mandated by the Environmental Protection Agency. Both models exhibited a similar relative improvement in dissolved oxygen concentrations as a result of the reduction of nutrients stipulated in the pollution diet. A Confidence Index was developed to identify the locations of the Bay where the models are in agreement and disagreement regarding the impacts of the pollution diet. The models were least certain in the deep part of the upper main stem of the Bay and the uncertainty primarily stemmed from the post-processing methodology. Finally, by projecting the impacts of climate change in 2050 on the Bay, the potential success of the pollution diet in light of future projections for air temperature, sea level, and precipitation was examined. While a changing climate will reduce the ability of the nutrient reduction to improve oxygen concentrations, that effect is trumped by the improvements in dissolved oxygen stemming from the pollution diet itself. However, climate change still has the potential to cause the current level of nutrient reduction to be inadequate. This is primarily due to the fact that low-oxygen conditions are predicted to start one week earlier, on average, in the future, with the primary changes resulting from the increase in temperature. Overall, this research lends an increased degree of confidence in the water quality modeling of the potential impact of the Chesapeake Bay pollution diet. This research also establishes the efficacy of utilizing a multiple model approach to examining projected changes in water quality while establishing that the pollution diet trumps the impact from climate change. This work will lead directly to advances in scientific understanding of the response of water quality, ecosystem health, and ecological resilience to the impacts of nutrient reduction and climate change.

The efficiencies of water exchanges in both vertical and horizontal directions reflect the overall impact of various physical processes and serve as important indicators of physical control over a variety of ecological and biogeochemical processes. The vertical exchange between surface layers and bottom layers of a waterbody has proved to exert great control over the hypoxic condition, while the horizontal exchange between an estuary and coastal ocean determines the flushing capacity of the estuary and the retention rate of riverine materials. Various processes, such as tidal flushing, tidal mixing, gravitational circulation, and lateral circulation, can affect water exchange. Therefore, water exchange processes are complex and varying in time and space in estuaries. Besides the impact of numerous forcing variables, large-scale climate oscillation, sea-level rise, and human activities can result in a change of estuarine dynamics. Two biologically relevant timescales, residence time (RT) and vertical exchange time (VET), are used in this study to quantify the overall horizontal and vertical exchange, aiming to understand the physical transport control over the ecosystem functioning in a simpler way. A long-term simulation of VET in the Chesapeake Bay over the period of 1980-2012 revealed a high spatial and seasonal similarity between VET and the dissolved oxygen (DO) level in the mainstem of the Chesapeake Bay, suggesting a major control over the DO condition from the physical transport. Over the past three decades, a VET of about 20 days in the summer usually indicates a hypoxic condition in the mainstem. Strong correlation among southerly wind strength, North Atlantic Oscillation index, and VET demonstrates that the physical condition in the Chesapeake Bay is highly controlled by the large-scale climate variation. The relationship is most significant during the summer, during which time the southerly wind dominates throughout the Chesapeake Bay. By combining the observed DO data with modeled VET, decoupling the physical and biological effect on the DO condition becomes possible. Bottom DO consumption rate was estimated through a conceptual model that links DO with VET. Using observed DO data and modeled VET, the overall biological effect on the DO condition can be quantified. The estimated bottom DO consumption rate shows strong seasonal variation and its interannual variation is highly correlated with the nutrient loading. The response of an estuary ecosystem to a change of nutrient loading depends on the flushing capacity of the estuary, which is related to the horizontal water exchange. The overall flushing capacity can be quantified by resident time, which determines the retention and export rates of materials discharged in the estuary. The horizontal exchange in Chesapeake Bay was investigated over the period of 1980-2012. Quantified by the residence time (RT), the horizontal exchange in Chesapeake Bay exhibits high interannual and spatial variability. The 33-year simulation results show that the mean RT of the entire Chesapeake Bay system ranges from 110 to 264 days, with an average value of 180 days, which is smaller than 7.6 months (approximately 230 days) reported in previous studies. There is significant lateral asymmetry of RT in the mainstem, with a larger RT along the eastern bank than that along the western bank in the lower Bay, which is mainly attributed to the horizontal shearing of estuarine circulation and large freshwater input along the western bank. Because of the persistent stratification and estuarine circulation, the vertical difference between the surface RT and bottom RT is dramatic, with a difference as large as 100 days. Relations among RT, river discharge, and strength of estuarine circulation reveal that the variation of horizontal exchange is mainly controlled by the river discharge and modulated by the estuarine circulation. A strengthened estuarine circulation will enhance the water exchange and reduce the RT. By affecting the estuarine circulation, wind forcing has a great impact on the horizontal exchange. The horizontal and vertical exchanges, together, contribute to the unique pattern of riverine material redistribution in Chesapeake Bay. By conducting long-term numerical simulations using multiple passive tracers that are independently released in the headwater of five main rivers (i.e., Susquehanna, Potomac, Rappahannock, York, and James Rivers), the relative contribution of discharge from each river to the total material in the mainstem can be calculated. The results show that the discharge from Susquehanna River has the dominant control on the riverine material throughout the entire mainstem. Despite the smaller contribution from the lower-middle Bay tributaries to the total materials in the mainstem, materials released from these rivers have a high potential to be transported to the middle-upper Bay through the bottom inflow by the persistent estuarine circulation. Depending on the magnitude of river discharge and the location of the tributary, material released at the headwaters of the main five rivers contributes differently to the riverine material in the mainstem. Material released in the upper estuary tends to have a longer residence time and a larger contribution, while materials released near the mouth are subject to a rapid flushing process, a small retention time, and a strong shelf-current induced dilution. The results reveal three distinct spatial patterns for materials released from the main river, tributary, and coastal oceans. One of the potential factors to change the exchange processes is the degree of human activities, such as construction of large infrastructures. With projected intensified hurricane and an accelerated sea-level rise in the 21st century, building storm surge barriers to mitigate the flooding risk has been considered as feasible climate change adaptation strategies in many coastal areas, which will surely affect the ecosystem functioning by affecting the water exchange. Two types of partially embanked storm surge barriers across the mouth of Chesapeake Bay were examined. Under modeled scenarios, surge barriers exert a significant influence on the tide, salinity, residual current, and transport processes. The vertical exchange is weakened, mainly due to the reduction of tidal range and tidal mixing. Even though the stratification is enhanced, the estuarine circulation is weakened due to accumulation of freshwater in the downstream and a decreased horizontal salinity gradient. The overall horizontal exchange is weakened due to a barrier, but the impact varies spatially.

To understand the morphodynamics of the inner shelf, a benthic boundary layer tripod supporting 6 point-measuring current meters, an acoustic Doppler current profiler, and three near-bed profiling acoustic backscatter sensors documented storm and swell conditions during October, 1996, at a depth 13 in on the inner shelf off Duck, North Carolina. The relationship between eddy viscosity and eddy diffusivity during storm and swell conditions was examined using data collected in October 1996 on the inner shelf off Duck, NC. Sediment suspension models, including Rouse-type diffusion models, combined advection and diffusion models, and a Rouse model with a thickened wave boundary layer, were compared to determine which model best reproduces observed sediment concentration profiles. A physics-based morphodynamics model was then developed to determine which components of hydrodynamic forcing and resulting sediment transport are predicted to be most significant to morphological change outside the surf zone on the inner shelf of the Middle Atlantic Bight. The simplest possible analytical solutions were sought for depth-dependent currents driven by the along- and across-shelf components of the wind and by waves via Stokes return flow and boundary layer streaming. Predicted currents and sediment concentrations were compared with observations collected at 13 m depth off Duck, NC, during October, 1996. Sediment transport and morphologic change were modeled and the morphologic change model was applied to 24 significant storms, which were documented by before-and-after shoreface profiles collected by the Field Research Facility of the US Army Corps of Engineers at Duck, NC, between 1987 and 1993. Significant correlations were found between observed shoreface volume change between 600--800 in offshore and predicted depth change on the inner shelf due to across-shelf sediment flux. Overall, correlations between observed and predicted change were higher for wave-driven components of sediment flux than for wind-driven components.