Abstract: A new methodology to classify European North-East Atlantic transitional waters into ecological types has been developed based on the most important hydrological and morphological features that are likely to determine the ecology of aquatic systems in transitional waters. Hydrological indicators help identifying if a transitional water area is dominated by fresh or sea water and/or by intertidal or subtidal areas, while morphological indicators allow an estimation of the complexity of the transitional water and the diversity of the habitats involved. Twelve transitional waters of the southern Bay of Biscay were classified using this methodology and the five hydro-morphological types obtained were validated with benthic macro-invertebrate data. Transitional waters with a complex morphology showed the highest values of species diversity, while those with a smaller tidal influence showed lower species diversity. The ?Scrobicularia? and ?Abra? assemblages, previously identified in the study area, were found to be related to different types of transitional waters. The ?Abra? assemblage only appeared in estuaries with a complex morphology and dominated by tidal influences, while the ?Scrobicularia? assemblage was detected in all the transitional waters except for a single coastal lagoon. This classification of transitional waters may therefore be useful to establish the biological reference conditions needed for European Directives.

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