The European Water Framework Directive provides a challenge in the development of new and accurate methodologies. It addresses assessment of Ecological Quality Status within European rivers, lakes, groundwaters, estuaries and coasts. Although this directive is simple and flexible in its concept, it is necessary to develop an approach based upon scientific knowledge; however, at the same time it should be as simple as possible, in order to achieve both requirements and comparability of results throughout European waters. This contribution presents the first methodological approach to the problem, as used for estuaries and coasts of the Basque Country (northern Spain), in: selecting typologies and reference conditions; determining biological quality and ecological status; and identifying some problems in implementing the WFD. As such, the present paper could serve as the basis for a discussion document for other regions and countries, throughout Europe.