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Een onderdeel van het verdrag is de gezamenlijke monitoring van de fysieke en ecologische toestand en evaluatie van de effecten van projecten.Om dit mogelijk te maken heeft de Vlaams Nederlandse Schelde Commissie een monitoringplan laten opstellen. De methoden, die gebruikt worden voor de monitoring van de verschillende onderdelen zijn om allerlei redenen vaak niet gelijk in Nederland en Vlaanderen. Hierdoor kunnen voor die onderdelen verschillen ontstaan en wordt de interpretatie bemoeilijkt. 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