Wastewater treatment plants (WWTPs) are at high risk of coastal flooding due to the proximity of water bodies. Furthermore, power outages caused by extreme weather make their recovery process more challenging. In this paper a multi criterion decision-making (MCDM) method is utilized to involve different aspects of WWTPs' flood resilience into the framework developed for distributing financial resources among them. The flood resilience improvement of plants is investigated for a wide range of interventions and related costs. On this basis, utility of the allocations is developed for each plant and a fixed budget is distributed among them in different ways. Due to the stochastic nature of floods, the uncertain resilience attributes of systems and the subjective views of experts and decision-makers, uncertainties are incorporated into this process. Accordingly, the uncertainty of each plant is targeted. The results show that: water-energy interdependence plays a significant role in assessing the flood resilience of WWTPs; using different ways of allocation leads to varying degrees of uncertainty in investment in each plant; and evidence theory is an effective way of integrating experts' beliefs in the process of allocating resources. The proposed methodology can be implemented on similar cases in different geographic settings.