Wastewater treatment plants (WWTPs) with the process of treatment, discharge under appropriate conditions, and recycling of the wastewater are strategic elements that directly serve the purpose of access to clean water and prevention of water pollution. In addition, the issue of the effective, efficient and sustainable operation of WWTPs has also gained importance. In this study, a three-stage methodology has been proposed to evaluate the effectiveness of WWTPs considering the uncertainties and some hesitations in the data. The case study has been carried out using the data of 88 WWTPs of the Istanbul Metropolitan Municipality. Firstly, expert opinions have been taken to determine the input and output variables for calculating efficiency values. These opinions have been evaluated with the extended-stepwise weight assessment ratio analysis (SWARA). Secondly, the data of the WWTPs have been converted into interval values to allow the evaluation of different year efficiencies at once and to eliminate the hesitations and uncertainties. Efficiency scores have been calculated using output-oriented DEA for the best-case, original, and worst-case scenarios that form the interval values. Finally, it has been examined whether there is a difference in the efficiency values of WWTPs based on age and type of facility. This study is an exemplary study for evaluating and developing the effectiveness of WWTPs in Turkey under uncertain conditions, considering different time intervals and expert opinions.