Decision-making processes for integrated wastewater management plans require the support of cost accounting and management techniques. This is particularly challenging in the Kidron – Wadi an-Nar basin, whose river is currently an open sewer and plans need to account for water stress, complex topography and socio-political differences. For these reasons, plans suggesting large centralised treatment facilities are difficult to implement. A potential solution, that can partially alleviate the problem, is the use of a number of smaller decentralised treatment facilities. The question that arises is, how to optimally configure combinations of centralised and decentralised wastewater treatment plants to achieve proper sanitation coverage in the basin and a sound water reuse? This study suggests a step forward towards solving the problem using a multi-objective optimisation framework. The objective functions considered are based on a Cost-Benefit analysis and the assessment of different wastewater treatment configurations. Sets of Pareto-optimal combinations of centralised and decentralised wastewater treatment solutions have been generated and evaluated in terms of the objective functions. The evaluation and comparison of wastewater treatment configurations include the potential reuses of the treated water. This analysis is especially essential in arid regions where limited water resources require an integrated and efficient water allocation.