Coastal aquifers are subject to seawater intrusion. Therefore, managing freshwater aquifers in coastal areas remain challenging. At present, determining safe yields from the coastal aquifers to prevent seawater intrusion is primarily based on the use of numerical simulation-optimization models or by the use of analytical models based on the Ghyben-Herzberg principle. This study examines the cause and effects of seawater intrusion into a coastal aquifer, Lincoln Basin in southern Eyre Peninsula, South Australia and shows that application of simple techniques would have prevented seawater intrusion. Three freshwater lenses, Lincoln A, B, and C of the Lincoln Basin, located about 13 km southwest of Port Lincoln township, have been developed as a town water supply source in 1960. The capacity of the basin has been assessed by three long-term pumping tests. Based on pump tests results, three areas were developed to supply 2×10 . Neither recharge to the freshwater lenses nor a water balance had been assessed, and a precautionary approach to groundwater extraction was not followed. The apparent driver for managing the basin was demand for the township. In this study, we assessed the recharge using two methods; water-table fluctuation (WTF) and the conventional chloride mass balance (CMB) method. Total recharge to the freshwater lenses is estimated at 1.