Abstract: A method to evaluate the ecological integrity of estuaries at a biogeographical scale is presented. Based on a conceptualisation which systematically establishes how human uses and stressors affect ecosystem functioning, the method allows for regional evaluations of the effect produced by human impacts on the ecological integrity. Comparisons across nine medium size estuaries (Bay of Biscay) showed major alterations in the connectivity (>65% of estuaries) and tidal dynamics (>55% of estuaries) in NE Atlantic estuaries. Likewise, the results obtained highlighted physical barriers such as dykes and land reclamation as the main hydromorphological stressors threatening the ecological integrity. The methodological approach was validated at a restored estuary. The validation primarily confirmed the ability of the conceptual model to identify the main stressors threatening the ecological integrity in estuaries. Secondly, it allowed the identification of the most suitable restoration solutions. Thirdly, it emphasised the importance of the hydrological dynamics to recover the ecosystem's ecological integrity.

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