This paper demonstrates a comprehensive methodology to assess the viability of an environmental management plan which has long-run economic and ecological impacts. The case study under consideration is the implementation of a water resource management plan in a water scarce region of the world, namely Cyprus. Specifically this plan proposes to replenish a depleting aquifer with treated wastewater. The methodology proposed first identifies the key stakeholder groups, namely farmers and the general public, who are hypothesized to derive economic values (benefits) from the implementation of this plan, and then implements stated preference methods to capture the total economic value of these benefits. Benefits are aggregated over the relevant populations of these stakeholder groups and weighed against the total costs of implementing this plan in a long-run cost-benefit analysis (CBA). An econometrically estimated time declining trajectory of discount rates is used for the CBA in order to assess the long run sustainability of the plan. The results reveal that the net benefit trajectory estimated with the time declining discount rate takes thrice as long to come to a plateau, revealing the importance of using declining discount rates, as well as capturing the entirety of benefits generated by such plans. This methodology is recommended especially for the implementation of the EU Water Framework Directive which advocates the use of the CBA and consideration of the notion of sustainability for the achievement of the good water status for all European waters.