Abstract Brackish water or seawater desalination can be used to supply potable water in areas with scarce water resources. Brackish water of 1,000–10,000 ppm TDS can be desalinated at a significantly lower cost, i.e., about one-third of that of seawater, and requires lower energy input, an important consideration for areas with limited energy supply. However, further pumping from groundwater aquifers may worsen significantly the existing situation in coastal regions that already face salinity problems. A decision aid tool has been developed for the investigation of the feasibility and applicability of an alternative water supply strategy involving the use of desalinated brackish groundwater, coupled with an effective strategy for controlling seawater intrusion and the enhancement of the hydrologic budget through reuse of treated wastewater. This strategy may lead to a sustainable water management scheme particularly suited for seasonally demand-stressed Mediterranean coastal regions. This paper outlines a methodology that allows the integration of the different elements of the problem into an optimization shell package that can be used for the economic evaluation of the overall scheme and presents some aspects of two of the system elements, brackish water desalination and recharge with treated wastewater.