The Biscayne Aquifer is a primary source of water supply in Southeast Florida. As a coastal aquifer, it is threatened by saltwater intrusion (SWI) when the natural groundwater flow is altered by over-pumping of groundwater. SWI is detrimental to the quality of fresh groundwater sources, making the water unfit for drinking due to mixing and reactions with aquifer minerals. Increasing water demand and complex environmental issues thus force water utilities in South Florida to sustainably manage saltwater intrusion and develop alternative water supplies (e.g., aquifer storage and recovery, ASR). The objectives of this study were to develop and use calibrated geochemical models to estimate water quality changes during saline intrusion and during ASR in south Florida. A batch-reaction model of saltwater intrusion was developed and important geochemical reactions were inferred. Additionally, a reactive transport model was developed to assess fate and transport of major ions and trace metals (Fe, As) at the Kissimmee River ASR. Finally, a cost-effective management of saltwater intrusion that involves using abstraction and recharge wells was implemented and optimized for the case of the Biscayne Aquifer. Major processes in the SWI areas were found to be mixing and dissolution-precipitation reactions with calcite and dolomite. Most of the major ions (Cl, Na, K, Mg, SO4) behaved conservatively during ASR while Ca and alkalinity were affected by carbonate reactions and cation exchange. A complex set of reactions involving thermodynamic equilibrium, kinetics and surface complexation reactions was required in the ASR model to simulate observed concentrations of Fe and As. The saltwater management model aimed at finding optimal locations and flow rates for abstraction and recharge wells. Optimal solutions (i.e., minimum total salt and total cost Pareto front) were produced for the Biscayne Aquifer for scenarios of surface recharge induced by climate change-affected precipitation. In general, abstraction at the maximum rate near the coast and artificial recharge at locations much further inland were found to be optimal. Knowledge developed herein directly supports the understanding of SWI caused by anthropogenic stressors, such as over-pumping and sea level rise, on coastal aquifers.