European Water Directive 91/271/EEC introduced a series of measures aimed at protecting sensitive areas against the emission of nutrients originating from waste water treatment plants. There are, however, environmental costs associated with achieving the required level of water quality, such as greenhouse gas emissions resulting from energy consumption. The goal of this study is to assess these environmental costs in an enhanced biological phosphorus removal (EBPR)- sequencing batch reactor (SBR) system for a population equivalent (p.e.) of 45 people and compare it to a conventional activated sludge (CAS) system. For that purpose, three major environmental indicators have been estimated: the global warming potential (GWP); eutrophication potential (EP) and power consumption (PC). Moreover, two different functional units, one based on volume (m3) and the other on eutrophication reduction (kg PO4 removed3−), were used to further determine sustainability. In this case study, the 45 p.e. EBPR-SBR showed a GWP of 150 kg CO2/kg PO4 removed3−, an EP of 13.6 equivalent g PO43−/m3 and a PC of 175 kWh/kg PO4 removed3−. These values are below those obtained for a CAS system.