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In the past, little attention was paid to the possible ecological impact provoked by engineering, bank protection works and dredging activities. Today, many European ports located on estuaries demand a better maritime access by dredging. Because of the European Bird and Habitat Directives, projects must undergo EIA or SEA studies, which traditionally are executed with numerical modeling tools. Most stakeholders do not know enough about the limitations of numerical modeling of the morphological and ecological effects. Information of the stakeholders about these limitations is necessary. However, uncertainties exist about these effects and because of the precautionary principle, projects might be rejected while these would be needed for curbing negative evolutions in the estuary. A cautious approach is therefore needed, assessing new projects with not only numerical models, rather with in addition scale modeling, desk studies, field surveys and studies and, last but not least expertise. 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