The innovative and evolutionary principles of Water Framework Directive (2000/60/EC) towards the "good" ecological status of the water bodies, comprise a burdensome issue for most of the member states in European Union. In particular, the European Water Supply and Sewerage companies which are in a major extent responsible for the environmental impacts in water bodies, argue for a very costly and rigid goal-setting of the implied for the achievement of the so called "good" water quality status. On the other hand, the environmental, social and economic benefits derived from the adoption of Water Framework Directive principles, are not clearly defined because of the difficulty to define and further on assess the multiple ecological functions occurring in water bodies. This paper attempts to integrally evaluate through an innovative economic-ecological approach, the direct and indirect benefits of the ecological improvement in water receiving bodies as provoked by compliance of the urban wastewater treatment systems with the targets set by the Water Framework Directive.