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This thesis provides a mass conservation analysis of the Lower St. Johns River for the purpose of providing basis for future salinity transport modeling. The analysis provides an assessment of the continuous (CG) and discontinuous (DG) Galerkin finite element methods with respect to their mass conservation properties. The following thesis also presents a rigorous literature review pertaining to salinity transport in the Lower St. Johns River, from which this effort generates the data used to initialize and validate numerical simulations. Two research questions are posed and studied in this thesis: can a DG-based modeling approach produce mass conservative numerical solutions; and what are the flow interactions between the river and the marshes within the coastal region of the Lower St. Johns River? Reviewing the available data provides an initial perspective of the ecosystem. For this, salinity data are obtained and assembled for three modeling scenarios. Each scenario, High Extreme, Most Variable, and Low Extreme, is 30 days long (taken from year 1999) and represents a unique salinity regime in the Lower St. Johns River. Time-series of salinity data is collected at four stations in the lower and middle reaches of the Lower St. Johns River, which provides a vantage point for assessing longitudinal variation of salinity. As an aside, precipitation and evaporation data is presented for seven stations along the entire St. Johns River, which provides added insight into salinity transport in the river. A mass conservation analysis is conducted for the Lower St. Johns River. The analysis utilizes a segmentation of the Lower St. Johns River, which divides the domain into sections iv based on physical characteristics. Mass errors are then calculated for the CG and DG finite element methods to determine mass conservative abilities. Also, the flow interactions (i.e., volume exchange) between the river and marshes are evaluated through the use of tidal prisms. The CG- and DG- finite element methods are then tested in tidal simulation performance, which the results are then compared to observed tides and tidal currents at four stations within the lower portion of the Lower St. Johns River. Since the results show that the DG model outperforms the CG model, the DG model is used in the tidally driven salinity transport simulations. Using four stations within the lower and middle part of the Lower St. Johns River, simulated and observed water levels and salinity concentrations are compared.

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.