Wastewater treatment plants (WWTPs) are regarded as units designed for the efficient removal of organic matter and nutrients from polluted wastewaters, avoiding their discharge into the environment. Despite these benefits, they have also been found to be highly energy intensive, with consequent increased emissions in terms of greenhouse gases and other environmental impacts. Therefore, it has become imperative to monitor thoroughly the overall functioning of WWTPs from an integrated perspective with the aim of understanding how these can improve their eco-efficiency. In this case study, a group of 113 WWTPs located in regions across Spain were analysed using the methodology that combines life cycle assessment (LCA) and data envelopment analysis (DEA). The aim of this work was to determine the operational efficiency of each unit in order to obtain environmental benchmarks for inefficient plants. Thereafter, the environmental gains linked with the inputs reduction proposed for the DEA model for each unit were computed in order to verify eco-efficiency criteria. The operational complexity of WWTPs resulted in several identified factors affecting their efficiency which are discussed in depth, including the size of the facility, the climatic influence, the influent load and the over- or underuse of the plant.