We investigate the general methodology for an intensive development of coastal aquifers, described in a companion paper, through its application to the management of the Akrotiri aquifer, Cyprus. The Zakaki area of that aquifer, adjacent to Lemessos City, is managed such that it permits a fixed annual agricultural water demand to be met, as well as and a fraction of the water demand of Lemessos, which varies according to available surface water. Effluents of the Lemessos wastewater treatment plant are injected into the aquifer to counteract the seawater intrusion resulting from the increased pumping. The locations of pumping and injection wells are optimized based on least-cost, subject to meeting the demand. This strategy controls sea intrusion so effectively that desalting of only small volumes of slightly brackish groundwater is required over short times, while ∼2.3 m³ of groundwater is produced for each 1 m³ of injected treated wastewater. The cost over the 20-year period 2000-2020 of operation is ∼40 M€ and the unit production cost of potable water is under 0.2 €/m³. The comparison between the deterministic and stochastic analyses of the groundwater dynamics indicates the former as conservative, i.e. yielding higher groundwater salinity at the well. The Akrotiri case study shows that the proposed aquifer management scheme yields solutions that are preferable to the widely promoted seawater desalination, also considering the revenues from using the treated wastewater for irrigation.