The lower St Johns River is a low-gradient coastal river with tidal hydrodynamics that remain active from the Atlantic Ocean through to the upstream end of Lake George (river km 200). Salinity in the lower St Johns River is spatially and temporally variable, whereby the salinity distribution is driven primarily by the combination of ocean processes of tides and storm surges and hydrological processes of watershed runoff. This study examines the probability distributions and modes of behavior of salinity for present-day conditions using data, numerical modeling and eigen-analysis. The hypothesis is that long-term changes (decadal scale) in the ocean processes will cause the probability distributions of salinity to adjust, and therefore there is a quantifiable non-stationarity of salinity in the lower St Johns River (shifts in the probability distribution of salinity, as representative of salinity increase) due to sea-level rise. The numerical modeling is validated against data, then the model is applied to generate synthetic salinity records for the main river stem and tributaries of the lower St. Johns based on present-day conditions. The synthetic salinity records are transformed into probability distribution functions (PDFs) and eigen-functions. The same analysis is performed on synthetic salinity records generated by the model when applied in forecast mode (i.e., sea-level rise). Comparisons of the forecasted PDFs and eigen-functions with those for present-day conditions quantify the non-stationarity (shifts in probability distributions and changes in eigen-structure) of the salinity in the lower St Johns River. The underlying physics of the cause (sea-level rise)-effect (non-stationarity of salinity) relationship are assessed in terms of coastal/river hydrodynamics.

Improved knowledge of sediment dynamics within a lake system is important for understanding lake water quality. This research was focused on an assessment of the vertical sediment flux in Lake Jesup, a shallow (1.3 m average depth) hypereutrophic lake of central Florida. Sediment dynamics were assessed at varying time scales (daily to weekly) to understand the transport of sediments from external forces; wind, waves, precipitation and/or runoff. Four stations were selected within the lake on the basis of water depth and the thicknesses of unconsolidated (floc) and consolidated sediments. At each of these stations, a 10:1 (length to diameter) high aspect ratio trap (STHA) was deployed to collect particulate matter for a one to two week period. The water and sediment samples were collected and analyzed for total carbon (TC), total phosphorus (TP) and total nitrogen (TN). Mass accumulation rates (MAR) collected by the traps varied from 77 to 418 g m-2 d-1 over seven deployments. TN, TP and TC sediment concentrations collected by the traps were consistently higher than the sediments collected by coring the lake bottom and is most likely associated with water column biomass. A yearly nutrient budget was determined from August 2009 to August 2010 with flux calculated as 2,033,882 mt yr-1.

This dissertation presents the development of a two-dimensional St. Johns River model and the coupling of hydrodynamic and wave models for the simulation of storm tides. The hydrodynamic model employed for calculating tides and surges is ADCIRC-2DDI (ADvanced CIRCulation Model for Shelves, Coasts and Estuaries, Two-Dimensional Depth Integrated) developed by Luettich et al. (1992). The finite element based model solves the fully nonlinear shallow water equations in the generalized wave continuity form. Hydrodynamic applications are operated with the following forcings: 1) astronomical tides, 2) inflows from tributaries, 3) meteorological effects (winds and pressure), and 4) waves (wind-induced waves). The wave model applied for wind-induced wave simulation is the third-generation SWAN (Simulating WAves Nearshore), applicable to the estimation of wave parameters in coastal areas and estuaries. The SWAN model is governed by the wave action balance equation driven by wind, sea surface elevations and current conditions (Holthuijsen et al. 2004). The overall work is comprised of three major phases: 1) To develop a model domain that incorporates the entire East Coast of the United States, Gulf of Mexico and Caribbean Sea, while honing in on the St. Johns River area; 2) To employ output from the SWAN model with the ADCIRC model and produce a uni-directional coupling of the two models in order to investigate the effects of the wave radiation stresses; 3) To couple the ADCIRC model with the SWAN model to describe the complete interactions of the two physical processes. Model calibration and comparisons are accomplished in three steps. First, astronomical tide simulation results are calibrated with historical NOS (National Ocean Service) tide data. Second, overland and riverine flows and meteorological effects are included, and computed river levels are compared with the historical NOS water level data. Finally, the storm tides generated by Hurricane Floyd are simulated and compared with historical data. This research results in a prototype for real-time simulation of tides and waves for flash flood and river-stage forecasting efforts of the NWS Forecasting Centers that border coastal areas. The following two main conclusions are reported: 1) regardless of whether one uses uni-coupling or coupling, wind-induced waves result in an approximately 10 – 15 % higher peak storm tide level than without any coupling; and 2) the wave-current interaction described by the coupling model results in decreasing peaks and increasing troughs in the storm tide hydrograph. Two main corollary conclusions are also drawn from a 122-day hindcast for the period spanning June 1 – October 1, 2005. First, wind forcing for the St. Johns River is equal to or greater than that of astronomic tides and generally supersedes the impact of inflows, while pressure variations have a minimal impact. Secondly, water levels inside the St. Johns River depend on the wind forcings in the deep ocean; however, if one applies an elevation hydrograph boundary condition from a large-scale domain model to a local-scale domain model the results are highly accurate.

The focus of this thesis is the forcing mechanisms incorporated with salinity transport for the Lower St. Johns River. There are two primary analyses performed: a historical data analysis of primary forcing mechanisms to determine the importance of each individual influence, and a tidal hydrodynamics analysis for the Lower St. Johns River to determine the required tidal constituents for an accurate resynthesis. This thesis is a preliminary effort in understanding salinity transport for the Lower St. Johns River for engineering projects such as the dredging of navigation canals and freshwater withdrawal from the river. The analysis of the physical forcing mechanisms is performed by examining the impact of precipitation, tides, and wind advection on historical salinity measurements. Three 30-day periods were selected for the analysis, to correspond with representative peak, most-variable, and low-salinity periods for 1999. The analysis displays that wind advection is the dominant forcing mechanism for the movement of salinity over a 30 day duration; however all mechanisms have an impact at some level. The dominant forcing mechanism is also dependent on the period of record examined where tidal influence is vital for durations of hours to a day, while freshwater inflow has more significance over a longer period due to climatological variation. A two-dimensional finite difference numerical model is utilized to generate a one month tidal elevations and velocities simulations that incorporates geometry, nonlinear advection and quadratic bottom friction. Several combinations of tidal constituents are extracted from this modeled tidal signal to investigate which combination of tidal constituents produces an accurate tidal resynthesis for the Lower St. Johns River. The analysis displays the need for 39 total tidal harmonic constituents to accurately resynthesize the original tidal signal. Additionally, due to the nonlinear nature of shallow water, the influence of the overtides for upstream or downstream locations in the Lower St. Johns River is shown to be spatially variable for different frequencies depending on the geometry. The combination of the constituent analysis and the historical analysis provides the basis information needed for the development of an accurate salinity transport model for the Lower St. Johns River.

The goal of this study was to examine the potential health effects of organochlorine (OC) and polycyclic aromatic hydrocarbon (PAH) exposure on Atlantic stingray populations in Florida’s St. Johns River (SJR). Special emphasis was placed on identifying OC- and/or PAH-related effects in stingrays from areas of the lower (LSJR) and middle (MSJR) basins shown to possess elevated levels of these compounds, as well as characterizing baseline levels of pollutant exposure in the SJR shipping channel, which may be subjected to dredging in the near future, potentially resuspending and redistributing contaminated sediments and increasing pollutant-associated effects. To accomplish this, we measured OC and PAH biomarker levels in stingrays collected from contaminated and reference sites. We specifically examined the phase I detoxification enzyme, cytochrome P4501a1 (CYP1a1); the phase II detoxification enzymes, glutathione-S-transferase (GST) and uridine 5’-diphosphate glucuronosyltransferase (UGT); fluorescent aromatic compounds, PAH bile metabolites; and lipid peroxidation (LPO), cell membrane damage. Biomarker values collected between 2014 and 2016 were compared by site. Detoxification enzyme activity and LPO values from individuals collected from the three MSJR lakes between 2002 and 2005 were compared to those collected between 2014 and 2016. The data suggested that biomarker values from the SJR were variable, with elevated levels from Lake Jesup. Compared to reference estuaries, the LSJR has low biomarker values. This indicates that residing in certain portions of the MSJR is detrimental to stingray health, while residing in the LSJR is not. Lake Monroe and Lake George biomarker levels indicated reduced contaminant input over time, whereas Lake Jesup biomarker levels suggested the opposite. This study has developed a baseline for biomarker levels in the LSJR, allowing for the identification of dredging-induced changes to the system, and has identified temporal changes in biomarker levels from three MSJR lakes.

This thesis presents a method, Ensemble Kalman Filter (EnKF), applied to a highresolution, shallow water equations model (DG ADCIRC-2DDI) of the Lower St. Johns River with observation data at four gauging stations. EnKF, a sequential data assimilation method for non-linear problems, is developed for tidal flow simulation for estimation of state variables, i.e., water levels and depth-integrated currents for overland unstructured finite element meshes. The shallow water equations model is combined with observation data, which provides the basis of the EnKF applications. In this thesis, EnKF is incorporated into DG ADCIRC-2DDI code to estimate the state variables. Upon its development, DG ADCIRC-2DDI with EnKF is first validated by implementing to a low-resolution, shallow water equations model of a quarter annular harbor with synthetic observation data at six gauging stations. Second, DG ADCIRC-2DDI with EnKF is implemented to a high-resolution, shallow water equations model of the Lower St. Johns River with real observation data at four gauging stations. Third, four different experiments are performed by applying DG ADCIRC-2DDI with EnKF to the Lower St. Johns River.

Climate change and increasing sea level elevation are predicted to increase salinity in estuarine tidal wetlands in the Southeastern United States. Since much of the ecosystem function in these areas is predicated upon salinity regimes, many fundamental changes are likely to occur as a result. The influence of salinity and SO4 2- reduction on PO4 3- release from tidal wetland soils was evaluated along a salinity gradient at three sites in The St. John’s River, Florida using both field and laboratorybased methods. Porewater was sampled over the course of 10 months to determine ambient levels of SO4 2- and PO4 3-. Lab-based experiments, soils samples were subjected to seawater and SO4 2- treatments in an attempt to induce PO4 3- release. Salinity was lowest at Sixmile Creek (0.45 ± 0.1 g kg-1) and Goodby’s Creek (2.05 ± 2.3 g kg-1) and much higher at Sister’s Creek (27.81 ± 3.1 g kg-1). The organic content of soils was highest (82.35% ± 5.11) at Sixmile Creek, intermediate at Goodby’s Creek (64.45% ± 7.02) and lowest at Sister’s Creek (32.11% ± 9.61). Total soil P was highest at the freshwater Sixmile Creek (1101.64 ± 220.2 μg g-1), intermediate at the brackish Goodby’s Creek (719.61 ± 114.3 μg g-1) and lowest at the Sister’s Creek saltmarsh (475.85 ± 110.9 μg g-1). Porewater PO4 3- was higher at Sixmile and Goodby’s Creek sites (9.44 ± 15.6, 8.99 ± 14.7 !g L-1, respectively) compared to Sister’s Creek (0.6 ± 3.1 !g L-1). Porewater SO4 2- was lower at Sixmile (70.73± 57.58 !g L-1) and Goodby’s Creeks (124.35 ± 152.5 !g L-1) compared to Sister’s Creek (1931.41 ± 557.82 !g L-1). Temporal and spatial trends indicated that SO4 2- and PO4 3- in porewater was likely due to floodwater content and that direct reaction between analytes in soils was unlikely. The addition of aerated seawater failed to cause PO4 3- release from any sites. The incubation of soils under anaerobic conditions, in the presence of Na2SO4 induced SO4 2- reduction, but inhibited PO4 3- flux from both Sixmile and Goodby’s Creek, which is attributed here to likely S- toxicity (Roychoudhury et al., 1999). PO4 3- flux from Sister’s Creek increased in association with Na2SO4 concentration, likely due to more Fe availability to mitigate Stoxicity. Ambient seawater additions to soils under anaerobic conditions followed a similar trend, but the results were not statistically conclusive. Overall, both field and labbased data indicated that Tidal wetland porewater PO4 3- likely originates from floodwaters and that increased salinity and SO4 2- reduction did not directly enhance soil PO4 3- fluxes.