Seagrass is a key stone component for the Indian River Lagoon (IRL) ecosystem, and therefore it is an important topic for many studies in the lagoon. This study focuses on the effects of seagrass beds on the hydrodynamics in the IRL. A hydrodynamic model based on the Delft3D modeling system has been developed for the southern IRL including the St. Lucie estuary, Ft. Pierce and St. Lucie Inlets, and adjacent coastal waters. The model is driven by freshwater inputs from the watershed, tides, meteorological forcing, and oceanic boundary forcing. The model has been systematically calibrated through a series of numerical experiments for key parameters, particularly the bottom roughness, and configuration including heat flux formulation and bottom bathymetry. The model skills were evaluated with quantitative metrics (point-to-point correlation, root-mean-square difference, and mean bias) to gauge the agreements between model and data for key variables including temperature, salinity, and currents. A three-year (2013-2015) simulation has been performed, and the results have been validated with available data including observations at HBOI Land-Ocean Biogeochemistry Observatory (LOBO) stations and in situ measurements from various sources. The validated model is then used to investigate the effects of 1) model vertical resolution (total number of model vertical layers), 2) spatial variability of surface winds, and 3) seagrass beds on the simulated hydrodynamics. The study focuses on the vicinity of Ft. Pierce Inlet, where significant seagrass coverage can be found. A series of numerical experiments were performed with a combination of different configurations. Overall, the experiment with 2-dimensional (2-D) winds, ten vertical layers and incorporating seagrass provided the most satisfactory outcomes. Overall, both vertical resolution and spatial variability of surface winds affect significantly the model results. In particular, increasing vertical resolution improves model prediction of temperature, salinity and currents. Similarly, the model with 2-D winds yields more realistic results than the model forced by 0-D winds. The seagrass beds have significant effects on the model results, particularly the tidal and sub-tidal currents. In general, model results show that both tidal and sub-tidal currents are much weaker due to increase bottom friction from seagrass. For tidal currents, the strongest impacts lie in the main channel (inter-coastal waterway) and western part of the lagoon, where strong tidal currents can be found. Inclusion of seagrass in the model also improves the simulation of sub-tidal currents. Seagrass beds also affect model temperature and salinity including strengthening vertical stratification. In general, seagrass effects vary over time, particularly tidal cycle with stronger effects seen in flood and ebb tides, and seasonal cycle with stronger effects in the summer than in winter. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection