Ecological classification of coastal waters has become increasingly important as one of the basic issues in the biology of conservation. Management and protection of coastal areas take place at different spatial scales. Thus, proper classification schemes should integrate equivalent information at various levels of definition in order to show its feasibility as a useful tool for assessment of coastal environments at the required scales. In this work, a global approach applied to the classification of the NE Atlantic coast is analysed in order to discuss pros and cons regarding different conceptual and technical issues for effective implementation of such a management tool. Using the hierarchical system applied at three different geographic scales: Biogeographic (NE Atlantic coast), Regional (Bay of Biscay) and Local (Cantabria region), five different topics were considered for debating strengths and weaknesses of the methodological alternatives at those spatial scales, using for validation the rocky shore macroalgae as a representative biological element of benthic communities. These included: (i) the spatial scales; (ii) the physical variables and indicators; (iii) the classification methodologies; (iv) the biological information; and (v) the validation procedure. Based on that analysis, the hierarchical support system summarized in this paper provides a management framework for classification of coastal systems at the most appropriate resolution, applicable to a wide range of coastal areas. Further applications of the physical classification for management of biodiversity in different environmental scenarios are also analysed.