The assessment of wastewater treatment plant (WWTP) performance has gained the interest of water utilities and water regulators. Eco-efficiency has been identified as a powerful indicator, as it integrates economic and environmental variables into a single index. Most previous studies have employed traditional data envelopment analysis (DEA) for the evaluation of WWTP eco-efficiency. However, DEA allows the selection of input and output weights for individual WWTPs for the calculation of eco-efficiency scores. To overcome this limitation, we employed the double-frontier and common set of weights methods to evaluate the eco-efficiency of a sample of 30 WWTPs in Spain. The WWTPs were ranked based on eco-efficiency scores derived under several scenarios including best- and worst-case scenarios; this approach to performance assessment is reliable and robust. Twenty-six of the 30 WWTPs were not classified as eco-efficient, even under the most favorable scenario, indicating that these facilities have substantial room for the reduction of costs and greenhouse gas emissions. The ranking of WWTPs varied according to the scenario used for evaluation, which has notable consequences when eco-efficiency scores are used for regulatory purposes. The findings of this study are relevant for water regulators and water utilities, as they demonstrate the importance of weight allocation for eco-efficiency score estimation.