This study focuses on the engineering design of a Soil-Aquifer Treatment (SAT) system for the artificial recharge of the coastal aquifer system of River Nestos eastern delta area, as a method to countermeasure seawater intrusion and groundwater/soil salinization. The design of such a groundwater engineering project recharging effluent from the nearby Xanthi City Wastewater Treatment Plant (WWTP) can be also proved a valuable method for water re-use with multi-fold positive impacts for the management of the water resources of the area. The design of the SAT groundwater recharge system in question is proposed after studying the geological and hydrogeological regime of the coastal aquifer system at the eastern Nestos River delta. The most important and objective requirements for the design and implementation of a SAT system is the presence of a suitable unsaturated zone underneath the SAT installation in order to ensure all necessary aerobic processes and the removal of certain virus and bacteria, as well as the minimum vertical distance between the bottom of the recharge basin and the water table being at least 3 m. Based on these two main criteria, three (3) SAT system sites are indicatively proposed at a plain part extending approximately 15 km from the nearby Xanthi City WWTP. The proposed pilot SAT system should include the following: (a) the assessment and dimensioning of the effluent tank in order to effectively receive the treated effluent from the wastewater treatment plant, (b) the excavation and formation of 2 systems of shallow recharge basins each system containing 4 recharge basins of individual dimensions: surface area 20x60 m, depth 0.80-1.00 m, in order to be filled with water not more than 20-30 cm in height so that the clogging of the basin bottom (and hence the effectiveness of the SAT system itself) will be minimized, (c) coating of the bottom of the recharge basins with the use of gravels or medium grained sand (0.10-0.20 cm), (d) installation of proper water pipes for the transfer of water from the effluent tank to the recharge basins as well as proper water pipes which will be connecting the adjacent recharge basins of the SAT system, (e) the installation of a monitoring network of groundwater wells and piezometers in order to monitor on sufficient time intervals the qualitative and quantitative effectiveness of the SAT system.