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 salinity structure of the bay plays a key role in the bay’s ecosystem. Florida Bay receives 45% of its freshwater directly from rainfall, the largest source of freshwater, while the Taylor River is the second largest source. A hydrodynamic model was applied to determine if doubling the Taylor River flow, as currently planned, is adequate to meet salinity performance measures and protect the bay’s ecosystem health. Model-predicted salinity indicated that rainfall caused the largest reduction (10–15 ppt) followed by Taylor River discharges, and none of the predicted salinity scenario means exceeded 38 ppt. The salinity restoration target was achieved more than 70% of the time, by doubling the Taylor River freshwater discharges, only for the existing bay conditions. To protect Florida Bay’s ecosystem health and counterbalance saltwater intrusion in the Everglades wetlands, caused by future sea-level rise, additional freshwater sources needs to be identified. Yet, the question becomes, do we have enough available freshwater sources to achieve the restoration target and protect the bay’s ecosystem health now and for future sea-level rise?