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.