In the last decade the political awareness of river water quality issues has grown substantially over the world and legislation is accordingly adapting. In the European Union (EU), two different directives regulate separately the characteristics of the discharged water and the chemical status of the receiving freshwater ecosystem. On the one hand, the characteristics of the urban effluents are regulated by the EU Directive 91/271/EEC, which defines limits on different elements set in the form of both static emission limits and minimum percentage load reductions. On the other hand, the characteristics of the receiving freshwater ecosystems are described in the EU Water Framework Directive (2000/60/EEC), which sets minimum 'good' chemical and ecological status in water bodies that should be achieved by 2015, and aims for an ecosystem-based management. With the support of an example, we show that there is a gap in these EU environmental policies leading to non-integrated management, which may result on adverse environmental and economical consequences. We believe that these policies should be updated and tuned to account for an integrated perspective, allowing a more efficient and sustainable management of wastewater treatment plants, maximizing the ecological, economical and social benefits of the system as a whole ; This research was supported by a Marie Curie Career Integration Grant (PCIG9-GA-2011-293535) and by a Marie Curie European Reintegration Grant (PERG07-GA-2010-259219) within the 7th European Community Framework Programme, aswell as by the Spanish Ministry of Economy and Competitiveness for its financial support through the projects ENDERUS (CTM-2009-13018) and SCARCE (Consolider-Ingenio 2010 CSD2009-00065) and the postdoctoral grant “Juan de la Cierva” (jci-2009-05604). The authors would like to thank the “Consorci per la Defensa de la Conca del Riu Besòs” (CDCRB) for providing the data of the Garriga system