Wastewaters are often discharged into coastal waters through long submarine outfalls, optimizing the treatment on shore with the water body assimilative capacity. The Water Framework Directive (WFD) establishes a “combined approach”, based on adopting both Environmental Quality Standards (EQS) and Emission Limit Values (ELV). However, the WFD doesn’t specify where the EQS must be applied and this omission is a limitation for the implementation of this approach. A new Directive (2008/105/EC) was adopted to establish the EQS values for the priority substances and the possibility of designing mixing zones around the discharge points. Inside these zones non compliance of one or more EQS is acceptable for any of these substances, if this doesn’t imply a non compliance of these EQS on the other water bodies. It is necessary to establish methodologies to delimitate Environmental Mixing Zones (EMZ) and EU member states must develop, adopt and implement EMZ definitions in national regulations until 2010. In this research a new methodology to establish EMZ for outfall discharges into coastal waters is proposed, considering simultaneously hydrodynamic mixing processes, the water body ecological value and sensibility and the natural and human uses of the coastal water. This holistic approach is innovative, because the actual proposals are based only on the hydrodynamic mixing processes. An EMZ equation is proposed as well as valuation scales for the used indicators, based on field data analysis. The proposed methodology can be used as regulatory criteria for implement discharge permits and for engineering design, to specify where must be applied the EQS and to design the sampling network. The proposed methodology was validated with the establishment of the Santander outfall EMZ, located on Gulf of Biscay. This shows the suitability of the proposed EMZ and compliance of the discharges with the EQS values on the edge of the proposed EMZ.