The new ISO 14045 framework is expected to slowly start shifting the definition of eco-efficiency toward a life-cycle perspective, using Life Cycle Assessment (LCA) as the environmental impact assessment method together with a system value assessment method for the economic analysis. In the present study, a set of 22 wastewater treatment plants (WWTPs) in Spain were analyzed on the basis of eco-efficiency criteria, using LCA and Life Cycle Costing (LCC) as a system value assessment method. The study is intended to be useful to decision-makers in the wastewater treatment sector, since the combined method provides an alternative scheme for analyzing the relationship between environmental impacts and costs. Two midpoint impact categories, global warming and eutrophication potential, as well as an endpoint single score indicator were used for the environmental assessment, while LCC was used for value assessment. Results demonstrated that substantial differences can be observed between different WWTPs depending on a wide range of factors such as plant configuration, plant size or even legal discharge limits. Based on these results the benchmarking of wastewater treatment facilities was performed by creating a specific classification and certification scheme. The proposed eco-label for the WWTPs rating is based on the integration of the three environmental indicators and an economic indicator calculated within the study under the eco-efficiency new framework.