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Fish populations have declined in many estuarine and freshwater ecosystems in part due to the loss of habitat in recent decades. Reconstructing lost habitat for larvae fish is a potential method for recovering larvae fish populations. Three-dimensional artificial floating wetlands (AFWs) on which Phragmites australis was planted were experimentally deployed to recover the lost habitat in the Changjiang (Yangtze) River estuary from May to July 2018. The AFW area was characterized by slow velocity, high transparency, low dissolved oxygen, and relatively constant water temperature. The total individuals of larvae fish in the AFW area (12 122 in total) was higher than that in the non-AFW area (1 250 in total), and the densities of most larvae fish species were higher in the AFW habitat than in the non-AFW area. The distributions of larvae fish species were positively influenced by habitat type because they were strongly related to the negative part of the first axis of the redundancy analysis, and Cyprinus carpio and Cyprinus auratus were inclined to habitat in the slow velocity and high transparency AFW habitat area. These results indicate that larvae fish species are inclined to inhabit the AFW habitat. The use of three-dimensional P . australis AFWs would be a potential method for enhancing the habitat of larvae fish in the degraded habitats along the estuary.