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Semi-arid coastal zones often suffer water-stress, as water demand is high and markedly seasonal, due to agriculture and tourism. Driven by scarcity of surface water, the communities in semi-arid coastal regions turn to aquifers as prime water source; but intensive exploitation of coastal aquifers causes seawater intrusion, which degrades the quality of groundwater. The cost-efficient and sustainable development of coastal aquifers can be achieved through a holistic management scheme which combines two non-traditional water sources: (a) saltwater, to be treated to the desired quality, and (b) wastewater, to be re-claimed to augment aquifer recharge for control of seawater intrusion, and also to meet certain demands. This management scheme is based on the idea that it is cost-advantageous to: (i) desalt brackish groundwater, instead of seawater, as the former requires far less energy, and (ii) to re-use wastewater at only the differential cost to any treatment already practiced. In this paper, we present the general framework of the proposed management scheme, and a decision aid tool (DAT) which has been developed to assist decision makers to explore the scheme’s decision space. The DAT uses cost as optimization criterion to screen various management scenarios, via modelling of the dynamic natural-engineered system behaviour, and identifies those cost-efficient ones that meet the water demand and achieve aquifer protection.