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In the Seine estuary, intertidal mudflats have been greatly reduced (< 30 km2) following channel management of the Seine river from Poses, in the upper part, to the sea. There are great differences between the biological compartments, ranging from areas with very high abundance of organisms (benthos on the muddy intertidal zone and, zooplankton in the lower part of the estuary) to areas with very low abundance (macrobenthos in the Seine river). There is also a contrast between the high abundance at the first levels of the trophic chain in a contaminated environment and the low abundance of fish. In the future, global management of the estuary will be required to ensure the biological compartments current level of functioning and to propose measures for rehabilitation of migrating fish.