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A two-dimensional finite element hydrodynamic and salinity transport BB-MFL-TABS-MDS model was developed to predict flow circulation and salinity distribution in Biscayne Bay under various freshwater discharge scenarios and climate conditions. The numerical results of this study may be used to develop technical criteria for the establishment of minimum water flows for Biscayne Bay in order to prevent significant harm to the natural resources. This manuscript discusses the model grid and implementation of the complex spatial and temporal boundary conditions surrounding the Biscayne Bay and details the modeling results. Comparison of the results was made among an average year (base run) and a drought year (drought run). Overall, the maximum average salinity was 33.23 ppt and 34.42 ppt for the base run and drought year, respectively. Analyses of the results show that the average monthly salinity values for October (end of the wet season) are much lower than for April (end of the dry season).As expected, the numerical results show that salinity values increase with reduction in freshwater flow. Environmental scientists may use the modeling results to determine the minimum flows and levels to the Bay based on a set of given ecological indicators.