Florida Bay, a large and shallow estuary, serves as a vital habitat for a diverse range of marine species and holds significant environmental, commercial, and recreational value. The Florida Bay ecosystem is under extensive stress due to decades of increased nutrient loads. Based on the Environmental Fluid Dynamics Code (EFDC), a hydrodynamic model was developed in this study. The model was calibrated with a comprehensive dataset, including measurements over 7 years from 34 tidal stations, 42 current stations, and 14 temperature and salinity stations. Key findings include the following: (1) the bay exhibits a shift in the tidal regime, transitioning from macro-tidal in the western region to micro-tidal in the central and eastern/northeast regions; (2) local winds and the subtidal variations from the coastal ocean are the primary drivers for the hydrodynamic processes in the eastern and central regions; (3) salinity changes in the bay are primarily controlled by three processes: the net supply of freshwater, the processes that drive mixing within the estuary (e.g., wind, topography, currents), and the exchange of salinity with the coastal ocean. This hydrodynamic model is essential for providing a comprehensive tool to address environmental challenges and sustain the bay’s ecosystem health.